# Patent

## Title
Compositions and methods for the delivery of oxygen

## Abstract

H-NOX proteins are mutated to exhibit improved or optimal kinetic and thermodynamic properties for blood gas O2 delivery. The engineered H-NOX proteins comprise mutations that impart altered O2 or NO ligand-binding relative to the corresponding wild-type H-NOX domain, and are operative as physiologically compatible mammalian blood O2 gas carriers. The invention also provides pharmaceutical compositions, kits, and methods that use wild-type or mutant H-NOX proteins for the treatment of any condition for which delivery of O2 is beneficial.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of nonprovisional patent application Ser. No. of 13/772,281, filed Feb. 20, 2013, which is a continuation of nonprovisional application Ser. No. 12/302,002, filed Jul. 26, 2010, which issued as U.S Pat. No. 8,404,631 on Mar. 26, 2013, and which is a National Phase application under 35 USC §371 of International Application No. PCT/US2007/012184, filed May 21, 2007, which claims the benefit of U.S. provisional application Ser. No. 60/921,505, filed May 22, 2006 by Michael A. Marletta, Stephen P. L. Cary, Elizabeth M. Boon, and Jonathan A. Winger, entitled “Engineering H-NOX Proteins for Therapeutic Nitric Oxide and Oxygen Delivery” (UC Case No. B06-084). This U.S. provisional application was converted from U.S. utility application Ser. No. 11/440,588, filed May 22, 2006, to a provisional application on May 1, 2007. The entire contents of each are hereby incorporated by reference in their entireties.
SUBMISSION OF SEQUENCE LISTING ON ASCII TEXT FILE
The content of the following submission on ASCII text file is incorporated herein by reference in its entirety: a computer readable form (CRF) of the Sequence Listing (file name: 627042000102SubSeqListing.txt, date recorded: May 12, 2015, size: 244 KB).


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This work was supported by Grant No. DE-AC03-76SF. The U.S. government may have rights in any patent issuing on this application.


TECHNICAL FIELD
This application pertains to H-NOX proteins and methods of using them to deliver oxygen. H-NOX proteins provide a new therapeutic tool for delivering O2 to humans and, for veterinary purposes, to animals.
BACKGROUND OF THE INVENTION
The current blood bank system has inherent risks and serious limitations. Blood typing errors, immunogenicity, transmission of bacterial agents, and viral infections such as HIV-1 and hepatitis, pose life threatening dangers to transfusion patients. In addition, the limited availability of donors, the requirement for specific blood types, the short shelf-life of red blood cells, and the need for refrigeration all limit the accessibility of transfusions to patients. Development of a stable blood substitute could eliminate the risks of the current blood bank system and increase the availability of transfusions to patients in most environments. Thus, the delivery of.
oxygen (O2) to organs and tissues to alleviate symptoms due to blood loss or hypoxia is a major therapeutic goal.
No hemoglobin-based therapies have been approved for use in humans in the U.S. Potential therapies include a variety of artificial O2 carriers (reviewed by Spahn, D. R. et al. (20.05). “Artificial O2 carriers: status in 2005,” Curr. Pharm. Des. 11(31):4099-4114), such as engineered hemoglobins (e.g., U.S. Pat. No. 6,022,849). However, some potential blood substitutes, such as hemoglobin-based blood substitutes, are limited due to their reactivity with nitric oxide (NO). In particular, NO acts as a chemical messenger in the control of many important processes in vivo, including neurotransmission, inflammation, platelet aggregation, and regulation of gastrointestinal and vascular smooth muscle tone. NO reacts directly with O2 that is bound to hemoglobin to form methemoglobin and nitrate. Both the heme iron and NO become oxidized by the bound oxygen atoms, and the reaction occurs so rapidly that no replacement of O2 by NO is observed (see, e.g., U.S. Pat. No. 6,455,676).
Since NO is produced and consumed on a continuous basis, there is a natural turnover of NO in vivo. When cell-free hemoglobin is administered, the balance between NO production and consumption is altered by reactions with cell-free hemoglobin. The oxidative reaction between NO and O2 bound to hemoglobin is irreversible, resulting in the destruction of NO, O2, and hemoglobin. NO binding to hemoglobin without O2 bound is effectively irreversible on physiologic timescales since the half-life for dissociation of nitrosylhemoglobin is 5-6 hours, thereby effectively inactivating hemoglobin as a cell-free O2 carrier.
Once an NO molecule reacts with hemoglobin, it is eliminated from the pool of signal molecules, thereby causing certain adverse conditions. For example, the binding of NO to hemoglobin (with or without O2 bound) can prevent vascular relaxation and potentially lead to hypertension, which is sometimes observed after the administration of certain extracellular hemoglobin solutions.
NO is also needed to mediate certain inflammatory responses. For example, NO produced by the endothelium inhibits platelet aggregation. Consequently, as NO is bound by cell-free hemoglobin (with or without O2 bound), platelet aggregation may increase. As platelets aggregate, they release potent vasoconstrictor compounds such as thromboxane A2 and serotonin. These compounds may act synergistically with the reduced NO levels caused by hemoglobin scavenging to produce significant vasoconstriction. In addition to inhibiting platelet aggregation, NO also inhibits neutrophil attachment to cell walls, which in turn can lead to cell wall damage. Endothelial cell wall damage has been observed with the infusion of certain hemoglobin solutions.
Another major drawback of hemoglobin-based blood substitutes is their high affinity for O2. This high affinity limits the ability of hemoglobin to release oxygen at a clinically useful rate in desired locations (such as peripheral tissues). Alternatively, the release of O2 by lower affinity hemoglobin-based blood substitutes in arteries before reaching microvascular beds may cause vasoconstriction due to a hyperoxic vasoconstrictor response (Winslow hypothesis). Additionally, hemoglobin-based blood substitutes are hindered by the rapid clearance of cell-free hemoglobin from plasma due the presence of receptors for hemoglobin that remove cell-free hemoglobin from plasma. Cell-free hemoglobin may also cause kidney toxicity, possibly due to NO depletion in glomeruli, causing constriction and subsequent dysfunction.
Due to the limitations of current blood substitutes and the chronic shortage of donated blood, there remains a significant interest in and need for additional or alternative therapies for delivering oxygen. In particular, blood substitutes with a lower NO reactivity and/or a longer plasma retention time are desired. Oxygen carriers with dissociation constants or off rates for O2 binding that are appropriate for particular clinical or industrial applications are also needed. An exemplary industry application for which O2 carriers are desirable includes the growth of cells in culture, which is often limited by the amount of O2 that reaches the cells.
BRIEF SUMMARY OF THE INVENTION
The present invention is based in part on the surprising discovery that wild-type and mutant H-NOX proteins have a much lower NO reactivity than hemoglobin and thus are desirable O2 carriers. If desired, mutations can be introduced into H-NOX proteins to alter their binding of O2 and NO ligands to further optimize the use of H-NOX proteins as O2 carriers.
In one aspect, the invention features mutant H-NOX proteins. Accordingly, in some-embodiments, the invention provides an isolated H-NOX protein having at least one mutation that alters the O2 dissociation constant or NO reactivity compared to that of a corresponding wild-type H-NOX protein. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is within 2 orders of magnitude of that of hemoglobin, and the NO reactivity of the mutant H-NOX protein is at least 10-fold lower than that of hemoglobin. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is between about 2 nM to about 50 μM at 20° C., about 50 nM to about 10 μM at 20° C., about 20 nM to about 2 μM at 20° C., about 100 nM to about 1.9 μM at 20° C., about 150 nM to about 1 μM at 20° C., or about 100 nM to about 255 nM at 20° C. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is less than about 80 nM at 20° C., such as between about 20 nM to about 75 nM at 20° C. In some embodiments, the NO reactivity of the mutant H-NOX protein is at least 100-fold lower than that of hemoglobin, such as at least 1,000-fold lower than that of hemoglobin. In some embodiments, the NO reactivity of the mutant H-NOX protein is less than about 700 s−1 at 20° C., such as less than about 600 s−1, 500 s−1, 400 s−1, 300 s−1, 200 s−1, 100 s−1, 75 s−1, 50 s−1, 25 s−1, 20 s−1, 10 s−1, 50 s−1, 3 s−1, 2 s−1, 1.8 s−1, 1.5 s−1, 1.2 s−1, 1.0 s−1, 0.8 s−1, 0.7 s−1, or 0.6 s−1 at 20° C. In some embodiments, the koff for oxygen of the mutant H-NOX protein is between about 0.01 to about 200 s−1 at 20° C., such as about 1.0 s−1 to about 16.0 s−1. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is between about 100 nM to about 1.9 μM at 20° C., and the koff for oxygen of the mutant H-NOX protein is between about 1.35 s−1 to about 14.5 s−1 at 20° C. In some embodiments, the rate of heme autoxidation of the mutant H-NOX protein is less than about 1 h−1 at 37° C. In some embodiments, the koff for oxygen of the mutant H-NOX protein is between about 1.35 s−1 to about 14.5 s−1 at 20° C., and the rate of heme autoxidation of the mutant H-NOX protein is less than about 1 h−1 at 37° C. In some embodiments, the koff for oxygen of the mutant H-NOX protein is between about 1.35 s−1 to about 14.5 s−1 at 20° C., and the NO reactivity of the mutant H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.). In some embodiments, the rate of heme autoxidation of the mutant H-NOX protein is less than about 1 h−1 at 37° C., and the NO reactivity of the mutant H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.).
In some embodiments, the invention features an isolated H-NOX protein having at least one mutation that alters the koff for oxygen or NO reactivity compared to that of a corresponding wild-type H-NOX protein. In some embodiments, the koff for oxygen of the mutant H-NOX protein is between about 0.01 to about 200 s−1 at 20° C., and the NO reactivity of the mutant H-NOX protein is at least 10-fold lower than that of hemoglobin. In some embodiments, the mutant H-NOX protein has a koff for oxygen that is less than or equal to about 0.65 s−1 at 20° C. (such as between about 0.21 s−1 to about 0.65 s−1 at 20° C.). In some embodiments, the mutant H-NOX protein derived from a T. tengcongensis protein and has koff for oxygen between about 1.35 s−1 to about 18 s−1 at 20° C. In some embodiments, the NO reactivity of the mutant H-NOX protein is at least 100-fold lower than that of hemoglobin, such as at least 1,000-fold lower than that of hemoglobin. In some embodiments, the NO reactivity of the mutant H-NOX protein is less than about 700 s−1 at 20° C., such as less than about 600 s−1, 500 s−1, 400 s−1, 300 s−1, 200 s−1, 100 s−1, 75 s−1, 50 s−1, 25 s−1, 20 s−1, 10 s−1, 50 s−1, 3 s−1, 2 s−1, 1.8 s−1, 1.5 s−1, 1.2 s−1, 1.0 s−1, 0.8 s−1, 0.7 s−1 or 0.6, s−1 at 20° C. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is between about 1 nM to about 1 mM at 20° C., between about 2 nM to about 50 μM at 20° C., between about 50 nM to about 10 μM at 20° C., or between about 100 nM to about 1.9 μM at 20° C. In some embodiments, the rate of heme autoxidation of the mutant H-NOX protein is less than about 1 h−1 at 37° C. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is between about 100 nM to about 1.9 μM at 20° C., and the rate of heme autoxidation of the mutant H-NOX protein is less than about 1 h−1 at 37° C. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is between about 100 nM to about 1.9 μM at 20° C., and the NO reactivity of the mutant H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.). In some embodiments, the rate of heme autoxidation of the mutant H-NOX protein is less than about 1 h−1 at 37° C., and the NO reactivity of the mutant H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.).
In various embodiments, the invention features an isolated H-NOX protein having at least one mutation that alters the O2 dissociation constant or NO reactivity compared to that of a corresponding wild-type H-NOX protein. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is within 2 orders of magnitude of that of hemoglobin, and the NO reactivity of the mutant H-NOX protein is at least 10-fold lower than that of hemoglobin. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is between about 100 nM. to about 255 nM at 20° C. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is less than 80 nM at 20° C., such as between about 20 nM to about 75 nM at 20° C. In some embodiments, the NO reactivity of the mutant H-NOX protein is at least 100-fold lower than that of hemoglobin, such as at least 1,000-fold lower than that of hemoglobin. In some embodiments, the mutant H-NOX protein has a koff for oxygen that is less than or equal to about 0.65 s−1 at 20° C. (such as between about 0.21 s−1 to about 0.65 s−1 at 20° C.). In some embodiments, the koff for oxygen of the mutant H-NOX protein is between about 1.35 s−1 to about 2.9 s−1 at 20° C. In some embodiments, the koff for oxygen of the mutant H-NOX protein is between about 5.8 s−1 to about 19 s−1 at 20° C. In some embodiments, the mutant H-NOX protein is stable at 4° C. in air.
In some embodiments, the invention features an isolated H-NOX protein having at least one mutation that alters the koff for oxygen or NO reactivity compared to that of a corresponding wild-type H-NOX protein. In some embodiments, the koff for oxygen of the mutant H-NOX protein is less than or equal to about 0.65 s−1 at 20° C., and the NO reactivity of the mutant H-NOX protein is at least 10-fold lower than that of hemoglobin. In some embodiments, the koff for oxygen of the mutant H-NOX protein is between about 0.21 s−1 to about 0.65 s−1 at 20° C. In some embodiments, the NO reactivity of the mutant H-NOX protein is at least 100-fold lower than that of hemoglobin, such as at least 1,000-fold lower than that of hemoglobin. In some embodiments, the NO reactivity of the mutant H-NOX protein is less than about 700 s−1 at 20. ° C., such as less than about 600 s−1, 500 s−1, 400 s−1, 300 s−1, 200 s−1, 100 s−1, 75 s−1, 50 s−1, 25 s−1, 20 s−1, 10 s−1, 50 s−1, 3 s−1, 2 s−1, 1.8 s−1, 1.5 s−1, 1.2 s−1, 1.0 s−1, 0.8 s−1, 0.7 s−1, or 0.6 s−1 at 20° C. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is between about 100 nM to about 1.9 μM at 20° C. In some embodiments, the rate of heme autoxidation of the mutant H-NOX protein is less than about 1 h−1 at 37° C. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is between about 100 nM to about 1.9 μM at 20° C., and the rate of heme autoxidation of the mutant H-NOX protein is less than about 1 h−1 at 37° C. In some embodiments, the O2 dissociation constant of the mutant H-NOX protein is between about 100 nM to about 1.9 μM at 20° C., and the NO reactivity of the mutant H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, 1.8 s−1, or 0.7 at 20° C.). In some embodiments, the rate of heme autoxidation of the mutant H-NOX protein is less than about 1 h−1 at 37° C., and the NO reactivity of the mutant H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, 1.8 s−1, or 0.7 at 20° C.).
In various embodiments, the invention features an isolated H-NOX protein selected from the group consisting of T. tengcongensis H-NOX I5A, T. tengcongensis H-NOX I5L, T. tengcongensis H-NOX I5L-P115A, T. tengcongensis H-NOX W9F, T. tengcongensis H-NOX W9F-Y140L, T. tengcongensis H-NOX W9F-Y140H T. tengcongensis H-NOX W9F-N74A, T. tengcongensis H-NOX W9Y, T. tengcongensis H-NOX W9N, T. tengcongensis H-NOX W9H, T. tengcongensis H-NOX N74E, T. tengcongensis H-NOX N74A, T. tengcongensis H-NOX N74H, T. tengcongensis H-NOX N74A-Y140H, T. tengcongensis H-NOX F78Y-Y140F, T. tengcongensis H-NOX P115A, T. tengcongensis H-NOX R135Q, T. tengcongensis H-NOX Y140F, T. tengcongensis H-NOX Y140H, T. tengcongensis H-NOX Y140A, T. tengcongensis I75F-His6, T. tengcongensis I75F, T. tengcongensis L144F-His6, T. tengcongensis L144F, L2 F9W-F142Y, D. desulfuricans H-NOX(728-899), D. desulfuricans H-NOX Y139L, β1 (1-385), β1(1-385) I145Y, β1 (1-385) I145H, β1 (1-194), β1(1-194) I145Y, β1(1-194) L9W-I145Y, β2(1-217), β2(1-217) I142Y, C. botulinum H-NOX(1-175), C. botulinum H-NOX(1-186), C. acetobutylicum H-NOX(1-197), C. acetobutylicum H-NOX(1-183), and C. elegans H-NOX GCY-35(1-252). In some embodiments, the β1 or β2 protein is derived from a R. norvegicus or H. sapiens β1 or β2 protein.
In various embodiments, the invention features an isolated H-NOX protein selected from the group consisting of T. tengcongensis H-NOX I5A, T. tengcongensis H-NOX I5L, T. tengcongensis H-NOX I5L-P115A, T. tengcongensis H-NOX W9F-Y140L, T. tengcongensis H-NOX W9F-Y140H, T. tengcongensis H-NOX W9F-N74A, T. tengcongensis H-NOX W9Y, T. tengcongensis H-NOX W9N, T. tengcongensis H-NOX W9H, T. tengcongensis H-NOX N74E, T. tengcongensis H-NOX N74A, T. tengcongensis H-NOX N74H, T. tengcongensis H-NOX N74A-Y140H, T. tengcongensis H-NOX F78Y-Y140F, T. tengcongensis H-NOX P115A, T. tengcongensis H-NOX R135Q, T. tengcongensis H-NOX Y140H, T. tengcongensis H-NOX Y140A, T. tengcongensis 175F-His6, T. tengcongensis 175F, T. tengcongensis L144F-His6, T. tengcongensis L144F, L. pneumophilia 2 F9W-F142Y, D. desulfuricans H-NOX(728-899), D. desulfuricans H-NOX Y139L, β1 (1-385) I145H, β1(1-194), β1 (1-194) I145Y, β1 (1-194) L9W-I145Y, β2(1-217), β2(1-217) I142Y, C. botulinum H-NOX(1-175), C. botulinum H-NOX(1-186), C. acetobutylicum H-NOX(1-197), C. acetobutylicum H-NOX(1-183), and C. elegans H-NOX GCY-35(1-252). In some embodiments, the β1 or β2 protein is derived from a R. norvegicus or H. sapiens β1 or β2. protein.
In some embodiments of the isolated H-NOX proteins, the O2 dissociation constant of the H-NOX protein is within 2 orders of magnitude of that of Homo sapiens hemoglobin alpha, such as an O2 dissociation constant between 0.1 to 10-fold or between 0.5 to 2-fold of that of Homo sapiens hemoglobin alpha. In some embodiments of the isolated H-NOX proteins, the NO reactivity of the H-NOX protein is at least 10-fold lower than that of Homo sapiens hemoglobin alpha, such as at least 100-fold or 1,000-fold lower than that of Homo sapiens hemoglobin alpha. In some embodiments of the isolated H-NOX proteins, the H-NOX protein contains one or more mutations (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mutations) compared to the H-NOX protein from which it was derived. In various embodiments of the isolated H-NOX proteins, the H-NOX protein contains less than 20, 15, 12, 10, 9, 8, 7, 6, 5, 4, 3, or 2 mutations compared to the H-NOX protein from which it was derived. In some embodiments of the isolated H-NOX proteins, the H-NOX protein has at least one distal pocket mutation. In some embodiments of the isolated H-NOX proteins, the H-NOX protein has at least one mutation that is not in the distal pocket. In some embodiments of the isolated H-NOX proteins, the H-NOX protein has at least one mutation in which a residue that corresponds to Ile5, Trp9, Asn74, Prol 15, or Arg135 of T. tengcongensis H-NOX or I145 of β1(1-385) is replaced by any other amino acid. In some embodiments of the isolated H-NOX proteins, the H-NOX protein has at least two mutations, wherein at least one mutation is the replacement of a residue that corresponds to Ile5, Trp9, Asn74, Prol 15, or Arg135 of T. tengcongensis H-NOX or 1145 of β31(1-385) by any other amino acid. In some embodiments of the isolated H-NOX proteins, the mutation in the H-NOX protein corresponds to a I5A mutation, a I5L mutation, a W9F mutation, a Y140F mutation, a Y140H mutation, a W9F Y140H double mutation, or a F78Y Y140F double mutation of T. tengcongensis or a I145 Y mutation of β1. In some embodiments of the isolated H-NOX proteins, the mutation in the H-NOX protein corresponds to a W9Y mutation, a W9H mutation, a W9N mutation, a N74H mutation, a N74E mutation, a N74A mutation, a P115A mutation, a R135Q mutation, a I5L P115A double mutant, a N74A Y140H double mutant, or a W9F N74A double of T. tengcongensis. In some embodiments of the isolated H-NOX proteins, at least one C-terminal amino acid (such as at least about 50 contiguous C-terminal amino acids or between about 25 to about 200 contiguous C-terminal amino acids) in the H-NOX protein has been removed compared to the corresponding wild-type protein.
In some embodiments of the isolated H-NOX proteins, the H-NOX protein is derived from a mammalian protein (e.g., a human protein such as β1). In various embodiments of the isolated H-NOX proteins, the H-NOX protein derived from a bacterial protein (e.g., a T. tengcongensis protein). In some embodiments of the isolated H-NOX proteins, the H-NOX protein is covalently bound to another molecule or moiety, such as polyethylene glycol. Herne may or may not be bound to the H-NOX protein. In some embodiments of the isolated H-NOX proteins, oxygen is bound to the H-NOX protein. In some embodiments of the isolated H-NOX proteins, the H-NOX protein is a fusion protein that includes an H-NOX domain and part or all of another protein, such as albumin (e.g., human serum albumin).
In some embodiments of the isolated H-NOX proteins, the H-NOX protein is not T. tengcongensis H-NOX Y40L, T. tengcongensis H-NOX F78Y/Y140L, wild-type T. tengcongensis H-NOX, or L. pneumophilia 2 H-NOX F142Y. In some embodiments of the isolated H-NOX proteins, the H-NOX protein is not R. norvegicus β2(1-217), R. norvegicus β1(1-194), R. norvegicus β1(1-385), or R. norvegicus β1 (1-385) I145Y. In some embodiments of the isolated H-NOX proteins, the H-NOX protein is not T. tengcongensis H-NOX W9F, T. tengcongensis H-NOX Y140F, or H. sapiens β1 H-NOX(1-385) I145Y. In some embodiments of the isolated H-NOX proteins, the H-NOX protein is not T. tengcongensis H-NOX Y140H, H. sapiens β1 I140Y, or H. sapiens β1 I145Y. In some embodiments of the isolated H-NOX proteins, the H-NOX protein is not T. tengcongensis H-NOX Y140F, wild-type L. pneumophilia 2 H-NOX, H. sapiens β1 H-NOX I140Y, wild-type H. sapiens β1 H-NOX, R. norvegicus sGC β1 H-NOX(1-385), R. norvegicus sGC β1 H-NOX(1-385) I145Y, R. norvegicus sGC β1 H-NOX H105G, R. norvegicus sGC β1 H-NOX H105F, R. norvegicus sGC β1 H-NOX I145Y, wild-type R. norvegicus β1 H-NOX, wild-type D. melangaster β1 H-NOX, wild-type D. melangaster CG14885-PA H-NOX, wild-type C. elegans GCY-35 H-NOX, wild-type N. punctiforme H-NOX, wild-type C. crescentus H-NOX, wild-type S. oneidensis H-NOX, or wild-type C. acetobutylicum H-NOX. In some embodiments of the isolated H-NOX proteins, the H-NOX protein is not T. tengcongensis H-NOX Y40L, T. tengcongensis H-NOX F78Y/Y140L, T. tengcongensis H-NOX W9F, T. tengcongensis H-NOX Y140F, wild-type. T. tengcongensis H-NOX, L. pneumophilia 2 H-NOX F142Y, wild-type L. pneumophilia 2 H-NOX, H. sapiens β1 H-NOX I140Y, H. sapiens B1 I145Y, wild-type H. sapiens β1 H-NOX, R. norvegicus sGC β1 H-NOX(1-385), R. norvegicus sGC β1 H-NOX(1-385) I145Y, R. norvegicus sGC β1 H-NOX H105G, R. norvegicus sGC β1 H-NOX H105F, R. norvegicus sGC β1 H-NOX I145Y, wild-type R. norvegicus β1 H-NOX, wild-type D. melangaster (31 H-NOX, wild-type D. melangaster CG14885-PA H-NOX, wild-type C. elegans GCY-35 H-NOX, wild-type N. punctiforme H-NOX, wild-type C. crescentus H-NOX, wild-type S. oneidensis H-NOX, or wild-type C. acetobutylicum H-NOX. In some embodiments of the isolated H-NOX proteins, the H-NOX protein is not any of the following H-NOX proteins that are listed by their gene name, followed by their species abbreviation and Genbank Identifiers (such as the following protein sequences available as of May 21, 2006; May 22, 2006; May 21, 2007; or May 22, 2007): Npun5905_Npu_23129606, alr2278_Ana_17229770, SO2144_Sone_24373702, Mdeg1343_Mde_23027521, VCA0720_Vch_15601476, CC2992_Ccr_16127222, Rsph2043_Rhsp_22958463 (gi:46192757), Mmc10739_Mcsp_22999020, Tar4_Tte_20807169, Ddes2822_Dde_23475919, CAC3243_Cac_15896488, gcy-31_Ce_17568389, CG14885_Dm_24647455, GUCY1B3_Hs_4504215, HpGCS-beta1_Hpull 4245738, Gycbeta100B_Dm_24651577, CG4154_Dm_24646993 (gi:NP_650424.2, gi:62484298), gcy-32_Ce_13539160, gcy-36_Ce_17568391 (gi:32566352, gi:86564713), gcy-35_Ce-17507861 (gi:71990146), gcy-37_Ce_17540904 (gi:71985505), GCY1α3_Hs_20535603, GCY1α2-Hs899477, or GYCα-99B_Dm_729270 (gi:68067738) (Lakshminarayan et al. (2003). “Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins,” BMG Genomics 4:5-13). The species abbreviations used in these names include Ana—Anabaena Sp; Ccr—Caulobacter crescentus; Cac—Clostridium acetobutylicum; Dde—Desulfovibrio desulfuricans; Mcsp—Magnetococcus sp.; Mde—Microbulbifer degradans; Npu—Nostoc punctifortne; Rhsp—Rhodobacter sphaeroides; Sone—Shewanella oneidensis; Tte—Thermoanaerobacter tengcongensis; Vch—Vibrio cholerae; Ce—Caenorhabditis elegans; Dm—Drosophila melanogaster; Hpul—Hemicentrotus pulcherrimus; Hs—Homo sapiens. In some embodiments of the isolated H-NOX proteins, the H-NOX protein is not any of the following H-NOX proteins that are listed by their organism name and Pfam database accession number (such as the following. protein sequences available as of May 21, 2006; May 22, 2006; May 17, 2007; May 21, 2007; or May 22, 2007): Caenorhabditis briggsae Q622M5_CAEBR, Caenorhabditis briggsae Q61P44_CAEBR, Caenorhabditis briggsae Q61R54_CAEBR, Caenorhabditis briggsae Q61V90_CAEBR, Caenorhabditis briggsae Q61A94_CAEBR, Caenorhabditis briggsae Q60TP4_CAEBR, Caenorhabditis briggsae Q60M10_CAEBR, Caenorhabditis elegans GCY37_CAEEL, Caenorhabditis elegans GCY31_CAEEL, Caenorhabditis elegans GCY36_CAEEL, Caenorhabditis elegans GCY32 CAEEL, Caenorhabditis elegans GCY35_CAEEL, Caenorhabditis elegans GCY34_CAEEL, Caenorhabditis elegans GCY33_CAEEL, Oryzias curvinotus Q7T040_ORYCU, Oryzias curvinotus Q75WF0_ORYCU, Oryzias latipes P79998_ORYLA, Oryzias latipes Q7ZSZ5_ORYLA, Tetraodon nigroviridis Q4SW38_TETNG, Tetraodon nigroviridis Q4RZ94_TETNG, Tetraodon nigroviridis Q4S6K5_TETNG, Fugu rubripes Q9OVY5_FUGRU, Xenopus laevis Q6INK9_XENLA, Homo sapiens Q5T8J7_HUMAN, Homo sapiens GCYA2_HUMAN, Homo sapiens GCYB2_HUMAN, Homo sapiens GCYB1HUMAN, Gorilla gorilla Q9N193_9 PRIM, Pongo pygmaeus Q5RAN8_PONPY, Pan troglodytes Q9N192_PANTR, Macaca mulatto Q9N194_MACMU, Hylobates lar Q9N191_HYLLA, Mus musculus Q8BXH3_MOUSE, Mus musculus GCYB1_MOUSE, Mus musculus Q3UTI4_MOUSE, Mus musculus Q3UH83_MOUSE, Mus musculus Q6XE41_MOUSE, Mus musculus Q80YP4_MOUSE, Rattus norvegicus Q8OWX7_RAT, Rattus norvegicus Q8OWX8_RAT, Rattus norvegicus Q920Q1_RAT, Rattus norvegicus Q54A43_RAT, Rattus norvegicus Q80WY0_RAT, Rattus norvegicus Q80WY4_RAT, Rattus norvegicus Q8CH85_RAT, Rattus norvegicus Q80WY5_RAT, Rattus norvegicus GCYB1_RAT, Rattus norvegicus Q8CH90_RAT, Rattus norvegicus Q91XJ7_RAT, Rattus norvegicus Q8OWX9_RAT, Rattus norvegicus GCYB2_RAT, Rattus norvegicus GCYA2_RAT, Canis familiaris Q4ZHR9_CANFA, Bos taurus GCYB1_BOVIN, Sus scrofa Q4ZHR7_PIG, Gryllus bimaculatus Q59HN5_GRYBI, Manduca sexta O77106_MANSE, Manduca sexta O76340_MANSE, Apis mellifera Q5UAFO_APIME, Apis mellifera Q5FANO_APIME, Apis mellifera Q6L5L6_APIME, Anopheles gambiae str PEST Q7PYK9_ANOGA, Anopheles gambiae str PEST Q7Q9W6_ANOGA, Anopheles gambiae str PEST Q7QF31_ANOGA, Anopheles gambiae str PEST Q7PS01_ANOGA, Anopheles gambiae str PEST Q7PFY2_ANOGA, Anopheles gambiae Q7KQ93_ANOGA, Drosophila melanogaster Q24086_DROME, Drosophila melanogaster GCYH_DROME, Drosophila melanogaster GCY8E_DROME, Drosophila melanogaster GCYDA_DROME, Drosophila melanogaster GCYDB_DROME, Drosophila melanogaster Q9VA09_DROME, Drosophila pseudoobscura Q29CE1_DROPS, Drosophila pseudoobscura Q296C7_DROPS, Drosophila pseudoobscura Q296C8_DROPS, Drosophila pseudoobscura Q29BU7_DROPS, Aplysia californica Q7YWK7_APLCA, Hemicentrotus pulcherrimus Q95NK5_HEMPU, Chlamydomonas reinhardtii, Q5YLC2_CHLRE, Anabaena sp Q8YUQ7_ANASP, Flavobacteria bacterium BBFL7 Q26GR8_9 BACT, Psychroflexus torquis ATCC 700755 Q1VQE5_9 FLAO, marine gamma proteobacterium HTCC2207 Q1YPJ5_9 GAMM, marine gamma proteobaoterium 1-1TCC2207 QlYTK4_9 GAMM, Caulobacter crescentus Q9A451_CAUCR, Acidiphilium cryptum JF-5 Q2DG60_ACICY, Rhodobacter sphaeroides Q3J0U9_RHOS4, Silicibacter pomeroyi Q5LPV1_SILPO, Paracoccus denitrificans PD1222, Q3PC67_PARDE, Silicibacter sp TM1040 Q3QNY2_9 RHOB, Jannaschia sp Q28ML8_JANSC, Magnetococcus sp MC-1 Q3XT27_9PROT, Legionella pneumophila Q5WXPO_LEGPL, Legionella pneumophila Q5WTZ5_LEGPL, Legionella pneumophila Q5X268_LEGPA, Legionella pneumophila Q5X2R2_LEGPA, Legionella pneumophila subsp pneumophila Q5ZWM9_LEGPH, Legionella pneumophila subsp pneumophila Q5ZSQ8_LEGPH, Colwellia psychrerythraea Q47Y43_COLP3, Pseudoalteromonas atlantica T6c Q3CSZ5_ALTAT, Shewanella oneidensis Q8EF49_SHEON, Saccharophagus degradans Q21E20_SACD2, Saccharophagus degradans Q21ER7_SACD2, Vibrio angustum S14 Q1ZWE5_9 VIBR, Vibrio vulnificus Q8DAE2_VIBVU, Vibrio alginolyticus 12G01 Q1 VCP6_VIBAL, Vibrio sp DAT722 Q2FA22_9 VIBR, Vibrio parahaemolyticus Q87NJ1_VIBPA, Vibrio fischeri Q5E1F5_VIBF1, Vibrio vulnificus Q7MJS8_VIBVY, Photobacterium sp SKA34 Q2C6Z5_9 GAMM, Hahella chejuensis Q2SFY7_HAHCH, Oceanospirillum sp MED92 Q2BKV0_9 GAMM, Oceanobacter sp RED65 Q1N035_9GAMM, Desulfovibrio desulfuricans Q310U7_DESDG, Halothermothrix orenii H 168 Q2AIW5_9 FIRM, Thermoanaerobacter tengcongensis Q8RBX6_THETN, Caldicellulosiruptor saccharolyticus DSM 8903 Q2ZH17_CALSA, Clostridium acetobutylicum Q97E73_CLOAB, Alkaliphilus metalliredigenes QYMF Q3C763_9 CLOT, Clostridium tetani Q899J9_CLOTE, and Clostridium beijerincki NCIMB 8052 Q2WVN0_CLOBE. In some embodiments of the isolated H-NOX proteins, the H-NOX protein is not R. norvegicus sGC β1 H-NOX C78S or R. norvegicus sGC β1 H-NOX C78E. In some embodiments of the isolated H-NOX proteins, the H-NOX protein does not have a mutation in the Y-S-R motif, which includes Tyr135, Ser137, and Arg139 of human H-NOX.
In one aspect, the invention features a recombinant nucleic acid encoding any one or more of the mutant H-NOX proteins described herein. In particular embodiments, the nucleic acid includes a segment of or the entire nucleic acid sequence of any of the nucleic acids shown in FIGS. 2-4D or 8A-8DD. In some embodiments, the nucleic acid encodes a fusion protein that includes an H-NOX domain and part or all of another protein, such as albumin (e.g., human serum albumin). In some embodiments, the nucleic acid includes at least about 50, 100, 150, 200, 300, 400, 500, 600, 700, 800, or more contiguous nucleotides from an H-NOX nucleic acid and contains one or more mutations (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mutations) compared to the H-NOX nucleic acid from which it was derived. In various embodiments, a mutant H-NOX nucleic acid contains less than about any of 20, 15, 12, 10, 9, 8, 7, 6, 5, 4, 3, or 2 mutations compared to the H-NOX nucleic acid from which it was derived. The invention also features degenerate variants of any nucleic acid encoding a mutant H-NOX protein.
In yet another aspect, the invention provides a vector that includes any one or more of the mutant H-NOX nucleic acids described herein. In another aspect, the invention features a cell that includes any one or more of the mutant H-NOX nucleic acids described herein. In one aspect, the invention features a cell that includes any vector described herein.
In one aspect, the invention features a method of producing an H-NOX protein. This method involves culturing a cell having a nucleic acid encoding any one or more of the mutant H-NOX proteins described herein under conditions suitable for production of the mutant H-NOX protein. In some embodiments, the invention further includes the step of purifying the mutant H-NOX protein.
In one aspect, the invention features pharmaceutical compositions that include one or more H-NOX proteins, such as any of the wild-type or mutant H-NOX proteins described herein. In some embodiments, the pharmaceutical composition includes a pharmaceutically acceptable amount of an H-NOX protein described herein and a pharmaceutically acceptable carrier. In some embodiments, the O2 dissociation constant of the H-NOX protein is between about 1 nM and about 1 mM at 20° C., and the NO reactivity of the H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.). In some embodiments, the O2 dissociation constant of the H-NOX protein is between about 20 nM to about 2 μM at 20° C., and the koff for oxygen of the H-NOX protein is between about 1.0 s−1 to about 16.0 s−1 at 20° C. In some embodiments, the O2 dissociation constant of the H-NOX protein is between about 20 nM to about 2 μM at 20° C., and the rate of heme autoxidation of the H-NOX protein is less than about 1 h−1 at 37° C. In some embodiments, the O2 dissociation constant of the H-NOX protein is between about 20 nM to about 2 μM at 20° C., and the NO reactivity of the H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.). In some embodiments, the koff for oxygen of the H-NOX protein is between about 1.0 s−1 to about 16.0 s−1 at 20° C., and the rate of heme autoxidation of the X protein is less than about 1 h−1 at 37° C. In some embodiments, the koff for oxygen of the H-NOX protein is between about 1.0 s−1 to about 16.0 s−1 at 20° C., and the NO reactivity of the H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.).
In some embodiments, the invention provides a pharmaceutical composition that includes a pharmaceutically acceptable amount of an H-NOX protein and a pharmaceutically acceptable carrier. In some embodiments, the O2 dissociation constant of the H-NOX protein is within 2 orders of magnitude of that of hemoglobin, and the NO reactivity of the H-NOX protein is at least 10-fold lower than that of hemoglobin. In some embodiments, the koff for oxygen of the H-NOX protein is between about 0.01 and about 200 s−1 at 20° C., wherein the NO reactivity of the H-NOX protein is at least 10-fold lower than that of hemoglobin.
In some embodiments of the pharmaceutical compositions, the O2 dissociation constant of the H-NOX protein is within 2 orders of magnitude of that of Homo sapiens hemoglobin alpha, such as an O2 dissociation constant between 0.1 to 10-fold or between 0.5 to 2-fold of that of Homo sapiens hemoglobin alpha. In some embodiments of the pharmaceutical compositions, the NO reactivity of the H-NOX protein is at least 10-fold lower than that of Homo sapiens hemoglobin alpha, such as at least 100-fold or 1,000-fold lower than that of Homo sapiens hemoglobin alpha. In some embodiments of the pharmaceutical compositions, the H-NOX protein is a wild-type protein. In some embodiments of the pharmaceutical compositions, the H-NOX protein is a mutant protein as described herein. In various embodiments of the pharmaceutical compositions, the H-NOX protein has at least one mutation that alters the O2 dissociation constant, the koff for oxygen, the rate of heme autoxidation, the NO reactivity, the NO stability, or any two or more of the foregoing compared to that of a corresponding wild-type protein. In some embodiments of the pharmaceutical compositions, the H-NOX protein is a selected from the group consisting of wild-type T. tengcongensis H-NOX, T. tengcongensis H-NOX I5A, T. tengcongensis H-NOX I5L, T. tengcongensis H-NOX I5L-P115A, T. tengcongensis H-NOX W9F, T. tengcongensis H-NOX W9F-Y140L, T. tengcongensis H-NOX W9F-Y140H, T. tengcongensis 11-NOX W9F-N74A, T. tengcongensis H-NOX W9Y, T. tengcongensis H-NOX W9N, T. tengcongensis H-NOX W9H, T. tengcongensis H-NOX N74E, T. tengcongensis H-NOX N74A, T. tengcongensis H-NOX N7411, T. tengcongensis H-NOX N74A-Y140H, T. tengcongensis H-NOX F78Y-Y140F, T. tengcongensis H-NOX F78Y/Y140L, T. tengcongensis H-NOX P115A, T. tengcongensis H-NOX R135Q, T. tengcongensis H-NOX Y140F, T. tengcongensis H-NOX Y40L, T. tengcongensis H-NOX Y140H, T. tengcongensis H-NOX Y140A, T. tengcongensis I75F-His6, T. tengcongensis I75F, T. tengcongensis L144F-His6, T. tengcongensis L144F, L. pneumophilia 2 H-NOX F142Y, wild-type L. pneumophilia 1 H-NOX, wild-type L. pneumophilia 2 H-NOX, L. pneumophilia 2 F9W-F142Y, wild-type D. desulfuricans H-NOX, D. desulfuricans H-NOX(728-899), D. desulfuricans H-NOX Y139L, wild-type H. sapiens β1 H-NOX, H. sapiens β1 I145Y, H. sapiens β1(1-385), H. sapiens β1(1-385) I145Y, H. sapiens β1(1-385) I145H, H. sapiens β1(1-194), H. sapiens β1(1-194) I145Y, H. sapiens β1(1-194) L9W-I145Y, H. sapiens β2(1-217), H. sapiens β2(1-217) I142Y, H. sapiens β1 H-NOX H105G, H. sapiens β1 H-NOX H105F, wild-type R. norvegicus β1 H-NOX, R. norvegicus β1(1-385), R. norvegicus β1(1-385) I145Y, R. norvegicus β1(1-385) I145H, R. norvegicus (1-194), R. norvegicus β1 (1-194) I145Y, R. norvegicus β1(1-194) L9W-I145Y, R. norvegicus β2(1-217), R. norvegicus β2(1-217), I142Y, R. norvegicus β1 H-NOX H105G, R. norvegicus β1 H-NOX H105F, C. botulinum H-NOX(1-175), C. botulinum H-NOX(1-186), wild-type C. acetobutylicum H-NOX, C. acetobutylicum H-NOX(1-197), C. acetobutylicum H-NOX(1-183), wild-type C. elegans GCY-35 H-NOX, C. elegans H-NOX GCY-35(1-252), wild-type D. melangaster β1 H-NOX, wild-type D. melangaster CG14885-PA, wild-type D. melangaster CG14886, wild-type D. melangaster CG4154; wild-type N. punctiforme H-NOX, wild-type C. crescentus H-NOX, wild-type S. oneidensis H-NOX, wild-type M. musculus H-NOX, wild-type C. familiaris H-NOX, wild-type B. T. aurus H-NOX, wild-type R. norvegicus; wild-type X. laevis H-NOX, wild-type C. latipes H-NOX, wild-type O. curivatus H-NOX, wild-type F. rubripes H-NOX, wild-type A. gambiae H-NOX, wild-type M. sexta H-NOX; wild-type C. elegans gcy-31, C. elegans gcy-32, wild-type C. elegans gcy-33, wild-type C. elegans gcy-34, wild-type C. elegans gcy-35, wild-type C. elegans gcy-36, wild-type C. elegans gcy-37; wild-type V. cholera H-NOX, wild-type V. fischerii H-NOX, and wild-type N. punctiforme H-NOX. In some embodiments of the pharmaceutical compositions, the pharmaceutical composition includes one or more liposomes or nanoparticles that include or encapsulate the H-NOX protein.
In some embodiments of the pharmaceutical compositions, the H-NOX protein is not T. tengcongensis H-NOX Y140H. In some embodiments of the pharmaceutical compositions, the H-NOX protein is not T. tengcongensis H-NOX Y40L, T. tengcongensis H-NOX F78Y/Y140L, wild-type T. tengcongensis H-NOX, or L. pneumophilia 2 H-NOX F142Y. In some embodiments of the pharmaceutical compositions, the H-NOX protein is not R. norvegicus β2(1-217), R. norvegicus β1(1-194), R. norvegicus β1(1-385), or R. norvegicus β1(1-385) I145Y. In some embodiments of the pharmaceutical compositions, the H-NOX protein is not T. tengcongensis H-NOX W9F, T. tengcongensis H-NOX Y140F, or H. sapiens β1 H-NOX(1-385) I145Y. In some embodiments, H-NOX protein is not T. tengcongensis H-NOX Y140H, H. sapiens β1 I140Y, or H. sapiens β1 I145Y. In some embodiments of the pharmaceutical compositions, the H-NOX protein is not T. tengcongensis H-NOX Y140F, wild-type L. pneumophilia 2 H-NOX, H. sapiens β1 H-NOX I140Y, wild-type H. sapiens β1 H-NOX, R. norvegicus sGC β1 H-NOX(1-385), R. norvegicus sGC β1 H-NOX(1-385) I145Y, R. norvegicus sGC β1 H-NOX H105G, R. norvegicus sGC β1 H-NOX H105F, R. norvegicus sGC β1 H-NOX I145Y, wild-type R. norvegicus β1 H-NOX, wild-type D. melangaster β1 H-NOX, wild-type D. melangaster CG14885-PA H-NOX, wild-type C. elegans GCY-35 H-NOX, wild-type N. punctiforme H-NOX, wild-type C. crescentus H-NOX, wild-type S. oneidensis H-NOX, or wild-type C. acetobutylicum H-NOX. In some embodiments of the pharmaceutical compositions, the H-NOX protein is not T. tengcongensis H-NOX Y40L, T. tengcongensis H-NOX F78Y/Y140L, T. tengcongensis H-NOXW9F, T. tengcongensis H-NOX Y140F, wild-type T. tengcongensis H-NOX, L. pneumophilia 2 H-NOX F142Y, wild-type L. pneumophilia 2 H-NOX, H. sapiens β1 H-NOX I140Y, H. sapiens β1 I145Y, wild-type H. sapiens β1 H-NOX, R. norvegicus sGC (31 H-NOX(1-385), R. norvegicus sGC β1 H-NOX(1-385) I145Y, R. norvegicus sGC H-NOX H105G, R. norvegicus sGC β1 H-NOX H105F, R. norvegicus sGC β1 H-NOX I145Y, wild-type R. norvegicus β1 H-NOX, wild-type D. melangaster β1 H-NOX, wild-type D. melangaster CG14885-PA H-NOX, wild-type C. elegans GCY-35 H-NOX, wild-type N. punctiforme H-NOX, wild-type C. crescentus H-NOX, wild-type S. oneidensis H-NOX, or wild-type C. acetobutylicum H-NOX. In some embodiments of the pharmaceutical compositions, the H-NOX protein is not any of the following H-NOX proteins that are listed by their gene name, followed by their species abbreviation and Genbank Identifiers (such as the following protein sequences available as of May 21, 2006; May 22, 2006; May 21, 2007; or May 22, 2007): Npun5905_Npu_23129606, alr2278_Ana_17229770, SO2144_Sone_24373702, Mdeg1343_Mde_23027521, VCA0720_Vch_15601476, CC2992_Ccr_16127222, Rsph2043_Rhsp_22958463 (gi:46192757), Mmc10739 Mcsp_22999020, Tar4_Tte_20807169, Ddes2822_Dde_23475919, CAC3243_Cac_15896488, gcy-31_Ce_17568389, CG14885_Dm_24647455, GUCY1B3_Hs_4504215, HpGCS-beta1_Hpull 4245738, Gycbeta100B_Dm_24651577, CG4154_Dm_24646993 (gi:NP_650424.2, gi:62484298), gcy-32_Ce_13539160, gcy-36_Ce_17568391 (gi:32566352, gi:86564713), gcy-35_Ce-17507861 (gi:71990146), gcy-37_Ce_17540904 (gi:71985505), GCY1α3_Hs_20535603, GCY1α2-Hs_899477, or GYCα-99B_Dm_729270 (gi:68067738) (Lakshminarayan et al. (2003). “Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins,” BMG Genomics 4:5-13). The species abbreviations used in these names include Ana—Anabaena Sp; Ccr—Caulobacter crescentus; Cac—Clostridium acetobutylicum; Dde—Desulfovibrio desulfuricans; Mcsp—Magnetococcus sp.; Mde—Microbulbifer degradans; Npu—Nostoc punctiforme; Rhsp—Rhodobacter sphaeroides; Sone—Shewanella oneidensis; Tte—Thermoanaerobacter tengcongensis; Vch—Vibrio cholerae; Ce—Caenorhabditis elegans; Dm—Drosophila melanogaster; Hpul—Hemicentrotus pulcherrimus; Hs—Homo sapiens. In some embodiments of the pharmaceutical compositions, the H-NOX protein is not R. norvegicus sGC β1 fl-NOX C78S or R. norvegicus sGC β1 H-NOX C78E. In some embodiments of the pharmaceutical compositions, the H-NOX protein is not any of the following H-NOX proteins that are listed by their organism name and Pfam database accession number (such as the following protein sequences available as of May 21, 2006; May 22, 2006; May 17, 2007; May 21, 2007; or May 22, 2007): Caenorhabditis briggsae Q622M5_CAEBR, Caenorhabditis briggsae Q61P44_CAEBR, Caenorhabditis briggsae Q61R54_CAEBR, Caenorhabditis briggsae Q61V90_CAEBR, Caenorhabditis briggsae Q61A94_CAEBR, Caenorhabditis briggsae Q60TP4_CAEBR, Caenorhabditis briggsae Q60M10_CAEBR, Caenorhabditis elegans GCY37_CAEEL, Caenorhabditis elegans GCY31_CAEEL, Caenorhabditis elegans GCY36_CAEEL, Caenorhabditis elegans GCY32_CAEEL, Caenorhabditis elegans GCY35_CAEEL, Caenorhabditis elegans GCY34_CAEEL, Caenorhabditis elegans GCY33_CAEEL, Oryzias curvinotus Q7T040_ORYCU, Oryzias curvinotus Q75WF0_ORYCU, Oryzias latipes P79998_ORYLA, Oryzias latipes Q7ZSZ5_ORYLA, Tetraodon nigroviridis Q4SW38_TETNG, Tetraodon nigroviridis Q4RZ94_TETNG, Tetraodon nigroviridis Q4S6K5_TETNG, Fugu rubripes Q9OVY5_FUGRU, Xenopus laevis Q61NK9_XENLA, Homo sapiens Q5T8J7_HUMAN, Homo sapiens GCYA2_HUMAN, Homo sapiens GCYB2_HUMAN, Homo sapiens GCYB1_HUMAN, Gorilla gorilla Q9N193_9 PRIM, Pongo pygmaeus Q5RAN8_PONPY, Pan troglodytes Q9N192_PANTR, Macaca mulatta Q9N194 MACMU, Hylobates lar Q9N191_HYLLA, Mus musculus Q8BXH3_MOUSE, Mus musculus GCYB1_MOUSE, Mus musculus Q3UTI4_MOUSE, Mus musculus Q3 U H83 MOUSE, Mus musculus Q6XE41_MOUSE, Mus musculus Q80YP4_MOUSE, Rattus norvegicus Q8OWX7RAT, Rattus norvegicus Q8OWX8RAT, Rattus norvegicus Q920Q1_RAT, Rattus norvegicus Q54A43_RAT, Rattus norvegicus Q80WY0_RAT, Rattus norvegicus Q80WY4_RAT, Rattus norvegicus Q8CH85_RAT, Rattus norvegicus Q80WY5_RAT, Rattus norvegicus GCYB1_RAT, Rattus norvegicus Q8CH90_RAT, Rattus norvegicus Q91XJ7_RAT, Rattus norvegicus Q8OWX9_RAT, Rattus norvegicus GCYB2_RAT, Rattus norvegicus GCYA2_RAT, Canis familiaris Q4ZHR9_CANFA, Bos taurus GCYB1_BOVIN, Sus scrofa Q4ZHR7_PIG, Gryllus bimaculatus Q59HN5_GRYBI, Manduca sexta O77106_MANSE, Manduca sexta O76340_MANSE, Apis mellifera Q5UAF0_APIME, Apis mellifera Q5FANO_APIME, Apis mellifera Q6L5L6_APIME, Anopheles gambiae str PEST Q7PYK9_ANOGA, Anopheles gambiae str PEST Q7Q9W6_ANOGA, Anopheles gambiae str PEST Q7QF31 ANOGA, Anopheles gambiae str PEST Q7PS01 ANOGA, Anopheles gambiae str PEST Q7PFY2_ANOGA, Anopheles gambiae Q7KQ93_ANOGA, Drosophila melanogaster Q24086_DROME, Drosophila melanogaster GCYH_DROME, Drosophila melanogaster GCY8E_DROME, Drosophila melanogaster GCYDA_DROME, Drosophila melanogaster GCYDB_DROME, Drosophila melanogaster Q9VA09_DROME, Drosophila pseudoobscura Q29CE1_DROPS, Drosophila pseudoobscura Q296C7_DROPS, Drosophila pseudoobscura Q296C8_DROPS, Drosophila pseudoobscura Q29BU7_DROPS, Aplysia californica Q7YWK7_APLCA, Hemicentrotus pulcherrimus Q95NK5_HEMPU, Chlamydomonas reinhardtii, Q5YLC2_CHLRE, Anabaena sp Q8YUQ7_ANASP, Flavobacteria bacterium BBFL7 Q26GR8_9 BACT, Psychroflexus torquis ATCC 700755 Q1VQE5_9 FLAO, marine gamma proteobacterium HTCC2207 Q1YPJ5_9 GAMM, marine gamma proteobacterium HTCC2207 QlYTK4_9 GAMM, Caulobacter crescentus Q9A451_CAUCR, Acidiphilium cryptum JF-5 Q2DG60_ACICY, Rhodobacter sphaeroides Q3J0U9_RHOS4, Silicibacter pomeroyi Q5LPV1_SILPO, Paracoccus denitrificans PD1222, Q3PC67_PARDE, Silicibacter sp TM1040 Q3QNY2_9 RHOB, Jannaschia sp Q28ML8_JANSC, Magnetococcus sp MC-1 Q3XT27_9 PROT, Legionella pneumophila Q5WXPO_LEGPL, Legionella pneumophila Q5WTZ5_LEGPL, Legionella pneumophila Q5X268_LEGPA, Legionella pneumophila Q5X2_R2 LEGPA, Legionella pneumophila subsp pneumophila Q5ZWM9_LEGPH, Legionella pneumophila subsp pneumophila Q5ZSQ8_LEGPH, Colwellia psychrerythraea Q47Y43_COLP3, Pseudoalteromonas atlantica T6c Q3CSZ5_ALTAT, Shewanella oneidensis Q8EF49_SHEON, Saccharophagus degradans Q21E20_SACD2, Saccharophagus degradans Q21ER7_SACD2, Vibrio angustum S14 Q1ZWE5_9 VIBR, Vibrio vulnificus Q8DAE2_VIBVU, Vibrio alginolyticus 12G01 Q1VCP6_VIBAL, Vibrio sp DAT722 Q2FA22_9 VIBR, Vibrio parahaemolyticus Q87NJ1_VIBPA, Vibrio fischeri Q5E1F5_VIBF1, Vibrio vulnificus Q7MJS8_VIBVY, Photobacterium sp SKA34 Q2C6Z5_9 GAMM, Hahella chejuensis Q2SFY7_HAHCH, Oceanospirillum sp MED92 Q2BKV0_9 GAMM, Oceanobacter sp RED65 Q1N035_9 GAMM, Desulfovibrio desulfuricans Q310U7_DESDG, Halothermothrix orenii H 168 Q2AIW5_9 FIRM, Thermoanaerobacter tengcongensis Q8RBX6_THETN, Caldicellulosiruptor saccharolyticus DSM 8903 Q2ZH17_CALSA, Clostridium acetobutylicum Q97E73_CLOAB, Alkaliphilus metalliredigenes QYMF Q3C763_9 CLOT, Clostridium tetani Q899J9_CLOTE, and Clostridium beijerincki NCIMB 8052 Q2WVN0_CLOBE. In some embodiments of the pharmaceutical compositions, the H-NOX protein does not have a mutation in the Y-S-R motif, which includes Tyr135, Ser137, and Arg139 of human H-NOX.
Unless otherwise explicitly noted or dictated by context, all wild-type and mutant H-NOX proteins described herein may be used in any of the pharmaceutical compositions described. herein. The H-NOX protein may or may not have heme and/or oxygen bound and may or may not be covalently bound to another molecule or moiety, such as polyethylene glycol. In some embodiments, the H-NOX protein is a fusion protein that includes an H-NOX domain and part or all of another protein, such as albumin (e.g., human serum albumin):
In one aspect, the invention provides methods of delivering oxygen to an individual (e.g., a mammal, such as a primate (e.g., a human, a monkey, a gorilla, an ape, a lemur, etc), a bovine, an equine, a porcine, a canine, or a feline) using an H-NOX protein. In some embodiments, the individual is suffering from or at risk for a cardiovascular disease, a neurological disease, tumor hypoxia, a loss of blood, or a wound. Exemplary cardiovascular indications include myocardial infarction (e.g., ST-segment elevation myocardial infarction), cardioplegia, sickle cell anemia, perioperative ischemia, peripheral vascular occlusion, and angioplasty. Exemplary neurological indications include ischemic stroke, traumatic brain injury, and spinal cord injury. For the treatment of tumor hypoxia, H-NOX proteins can be used, e.g., as a radiation therapy adjuvant in solid tumors (e.g., individuals with poor pre-metastatic prognoses) or as a PDT therapy adjuvant in surface tumors (e.g., colon, lung, or skin cancer, or cancer in another accessible surface or location). Applications of H-NOX proteins as a blood transfusion alternative include trauma (e.g., battlefield, disaster relief, or accidents), surgery (e.g., abdominal aneurysm-surgery, orthopedic surgery such as hip replacement surgery, or any other surgery that produces high blood loss), hemorrhages, hemorrhagic shock, hemodilution, and blood extension uses (e.g., supplementing auto-donation). Examples of wound repair applications include post-radiation wound repair (e.g., hyperbaric oxygen effect), post-surgical repair, diabetic ulcer repair, and burn wounds.
Accordingly, in some embodiments, the invention provides a method of delivering oxygen to an individual (e.g., a human) by administering to an individual in need thereof an H-NOX protein in an amount sufficient to deliver an effective amount of oxygen to the individual. In sortie embodiments, the O2 dissociation constant of the H-NOX protein is between about 1 nM to about 1 mM at 20° C., and the NO reactivity of the H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.). In some embodiments, the O2 dissociation constant of the H-NOX protein is within 2 orders of magnitude of that of hemoglobin, and the NO reactivity of the H-NOX protein is at least 10-fold lower than that of hemoglobin.
In some embodiments of the methods, oxygen is bound to the H-NOX protein prior to the administration of the H-NOX protein to the individual. In some embodiments of the methods, oxygen is not bound to the H-NOX protein prior to the administration of the H-NOX protein to the individual, and the H-NOX protein transports oxygen from one location in the individual to another location in the individual. In some embodiments of the methods, the H-NOX protein is administered to the blood of the individual. In some embodiments of the methods, the H-NOX protein is administered to the blood, a wound, a tumor, a hypoxic tissue, or a hypoxic organ of the individual. In some embodiments of the methods, the individual is suffering from or at risk for a loss of blood. In some embodiments of the methods, the H-NOX protein is administered to the individual at least twice.
In some embodiments of the methods, the O2 dissociation constant of the H-NOX protein is within 2 orders of magnitude of that of Homo sapiens hemoglobin alpha, such as an O2 dissociation constant between 0.1 to 10-fold or between 0.5 to 2-fold of that of Homo sapiens hemoglobin alpha. In some embodiments of the methods, the NO reactivity of the H-NOX protein is at least 10-fold lower than that of Homo sapiens hemoglobin alpha, such as at least 100-fold or 1,000-fold lower than that of Homo sapiens hemoglobin alpha. In some embodiments of the methods, the H-NOX protein is a wild-type protein. In some embodiments of the methods, the H-NOX protein is a mutant protein as described herein. In various embodiments of the methods, the H-NOX protein has at least one mutation that alters the O2 dissociation constant, the koff for oxygen, the rate of heme autoxidation, the NO reactivity, or any two or more of the foregoing compared to that of a corresponding wild-type protein. In some embodiments of the methods, the H-NOX protein is a selected from the group consisting of wild-type T. tengcongensis H-NOX, T. tengcongensis H-NOX I5A, T. tengcongensis H-NOX I5L, T. tengcongensis H-NOX I5L-P115A, T. tengcongensis H-NOX W9F, T. tengcongensis H-NOX W9F-Y140L, T. tengcongensis H-NOX-W9F-Y140H, T. tengcongensis H-NOX W9F-N74A, T. tengcongensis H-NOX W9Y, T. tengcongensis H-NOX W9N, T. tengcongensis H-NOX W9H, T. tengcongensis H-NOX N74E, T. tengcongensis H-NOX N74A, T. tengcongensis H-NOX N74H, T. tengcongensis H-NOX N74A-Y140H, T. tengcongensis H-NOX F78Y-Y140F, T. tengcongensis H-NOX F78Y/Y140L, T. tengcongensis H-NOX P115A, T. tengcongensis H-NOX R135Q, T. tengcongensis H-NOX Y140F, T. tengcongensis H-NOX Y40L, T. tengcongensis H-NOX Y140H, T. tengcongensis H-NOX Y140A, T. tengcongensis I75F-His6, T. tengcongensis I75F, T. tengcongensis L144F-His6, T. tengcongensis L144F, L. pneumophilia 2 H-NOX F142Y, wild-type L. pneumophilia 1 H-NOX, wild-type L. pneumophilia 2 H-NOX, L. pneumophilia 2 F9W-F142Y, wild-type D. desulfuricans H-NOX, D. desulfuricans H-NOX(728-899), D. desulfuricans H-NOX Y139L, wild-type H. sapiens β1 H-NOX, H. sapiens β1 I145Y, H. sapiens β1 (1-385), H. sapiens β1(1-385) I145Y, H. sapiens β1(1-385) I145H, H. sapiens β1(1-194), H. sapiens β1 (1-194) I145Y, H. sapiens β1 (1-194) L9W-I145Y, H. sapiens β2(1-217), H. sapiens β2(1-217) I142Y, H. sapiens β1 H-NOX H105G, H. sapiens β1 H-NOX H105F, wild-type R. norvegicus β1 H-NOX, R. norvegicus β1 (1-385), R. norvegicus β1 (1-385) I145Y, R. norvegicus β1 (1-385) I145H, R. norvegicus β1 (1-194), R. norvegicus β1 (1-194) I145Y, R. norvegicus β1(1-194) L9W-I145Y, R. norvegicus β2(1-217), R. norvegicus β2(1-217) I142Y, R. norvegicus β1 H-NOX H105G, R. norvegicus β1 H-NOX H105F, C. botulinum H-NOX(1-175), C. botulinum H-NOX(1-186), wild-type C. acetobutylicum H-NOX, C. acetobutylicum H-NOX(1-197), C. acetobutylicum H-NOX(1-183), wild-type C. elegans GCY-35 H-NOX, C. elegans H-NOX GCY-35(1-252), wild-type D. melangaster β1 H-NOX, wild-type D. melangaster CG14885-PA, wild-type D. melangaster CG14886, wild-type D. melangaster CG4154; wild-type N. punctiforme H-NOX, wild-type C. crescentus H-NOX, wild-type S. oneidensis H-NOX, wild-type M. musculus H-NOX, wild-type C. familiaris H-NOX, wild-type B. Taurus H-NOX, wild-type R. norvegicus; wild-type X. laevis H-NOX, wild-type O. latipes H-NOX, wild-type O. curivatus H-NOX, wild-type F. rubripes H-NOX, wild-type A. gambiae H-NOX, wild-type M. sexta H-NOX; wild-type C. elegans gcy-31, C. elegans gcy-32, wild-type C. elegans gcy-33, wild-type C. elegans gcy-34, wild-type C. elegans gcy-35, wild-type C. elegans gcy-36, wild-type C. elegans gcy-37; wild-type V. cholera H-NOX, wild-type V. fischerii H-NOX, and wild-type N. punctiforme H-NOX. In some embodiments of the methods, one or more liposomes or nanoparticles include or encapsulate the H-NOX protein.
In some embodiments of the methods, the H-NOX protein is not T. tengcongensis H-NOX Y140H. In some embodiments of the methods, the H-NOX protein is not T. tengcongensis H-NOX Y40L, T. tengcongensis H-NOX F78Y/Y140L, wild-type T. tengcongensis H-NOX, or L. pneumophilia 2 H-NOX F142Y. In some embodiments of the methods, the H-NOX protein is not R. norvegicus β2(1-217), R. norvegicus β1(1-194), R. norvegicus β1(1-385), or R. norvegicus β1(1-385) I145Y. In some embodiments of the methods, the H-NOX protein is not T. tengcongensis H-NOX W9F, T. tengcongensis H-NOX Y140F, or H. sapiens β1 H-NOX(1-385) I145Y. In some embodiments, H-NOX protein is not T. tengcongensis H-NOX Y140H, H. sapiens β1 I140Y, or H. sapiens β1 I145Y. In some embodiments of the methods, the H-NOX protein is not T. tengcongensis H-NOX Y140F, wild-type L. pneumophilia 2 H-NOX, H. sapiens β1 H-NOX I140Y, wild-type H. sapiens β1 H-NOX, R. norvegicus sGC β1 H-NOX(1-385), R. norvegicus sGC β1 H-NOX(1-385) I145Y, R. norvegicus sGC β1 H-NOX H105G, R. norvegicus sGC β1 H-NOX H105F, R. norvegicus sGC β1 H-NOX I145Y, wild-type R. norvegicus β1 H-NOX, wild-type D. melangaster β1 H-NOX, wild-type D. melangaster CG14885-PA H-NOX, wild-type C. elegans GCY-35 H-NOX, wild-type N. punctiforme H-NOX, wild-type C. crescentus H-NOX, wild-type S. oneidensis H-NOX, or wild-type C. acetobutylicum H-NOX. In some embodiments of the methods, the H-NOX protein is not T. tengcongensis H-NOX Y40L, T. tengcongensis H-NOX F78Y/Y140L, T. tengcongensis H-NOX W9F, T. tengcongensis H-NOX Y140F, wild-type T. tengcongensis H-NOX, L. pneumophilia 2 H-NOX F142Y, wild-type L. pneumophilia 2 H-NOX, H. sapiens β1 H-NOX I140Y, H. sapiens B1 I145Y, wild-type H. sapiens β1 H-NOX, R. norvegicus sGC β1 H-NOX(1-385), R. norvegicus sGC β1 H-NOX(1-385) I145Y, R. norvegicus sGC β1 H-NOX H105G, R. norvegicus sGC β1 H-NOX H105F, R. norvegicus sGC β1 H-NOX I145Y, wild-type R. norvegicus β1 H-NOX, wild-type D. melangaster β1 H-NOX, wild-type D. melangaster CG14885-PA H-NOX, wild-type C. elegans GCY-35 H-NOX, wild-type N. punctiforme H-NOX, wild-type C. crescentus H-NOX, wild-type S. oneidensis H-NOX, or wild-type C. acetobutylicum H-NOX. In some embodiments of the methods, the H-NOX protein is not any of the following H-NOX proteins that are listed by their gene name, followed by their species abbreviation and Genbank Identifiers (such as the following protein sequences available as of May 21, 2006; May 22, 2006; May 21, 2007; or May 22, 2007): Npun5905 Npu_23129606, alr2278_Ana 17229770, SO2144_Sone_24373702, Mdeg1343_Mde_23027521, VCA0720_Vch_15601476, CC2992_Ccr_16127222, Rsph2043_Rhsp_22958463 (gi:46192757), Mmc10739_Mcsp_22999020, Tar4_Tte_20807169, Ddes2822_Dde_23475919, CAC3243_Cac_15896488, gcy-31_Ce_17568389, CG14885_Dm_24647455, GUCY1B3_Hs_4504215, HpGCS-beta1_Hpul_14245738, Gycbeta100B_Dm_24651577, CG4154_Dm_24646993 (gi:NP_650424.2, gi:62484298), gcy-32_Ce_13539160, gcy-36_Ce_17568391 (gi:32566352, gi:86564713), gcy-35_Ce-17507861 (gi:71990146), gcy-37_Ce_17540904 (gi:71985505), GCY1α3_Hs_20535603, GCY1α2-Hs_899477, or GYCα-99B_Dm_729270 (gi:68067738) (Lakshminarayan et al. (2003). “Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins,” BMG Genomics 4:5-13). The species abbreviations used in these names include Ana—Anabaena Sp; Ccr—Caulobacter crescentus; Cac—Clostridium acetobutylicum; Dde—Desulfovibrio desulfuricans; Mcsp—Magnetococcus sp.; Mde—Microbulbifer degradans; Npu—Nostoc punctiforme; Rhsp—Rhodobacter sphaeroides; Sone—Shewanella oneidensis; Tte—Thermoanaerobacter tengcongensis; Vch—Vibrio cholerae; Ce—Caenorhabditis elegans; Dm—Drosophila melanogaster; Hpul—Hemicentrotus pulcherrimus; Hs—Homo sapiens. In some embodiments of the methods, the H-NOX protein is not any of the following H-NOX proteins that are listed by their organism name and Pfam database accession number (such as the following protein sequences available as of May 21, 2006; May 22, 2006; May 17, 2007; May 21, 2007; or May 22, 2007): Caenorhabditis briggsae Q622M5_CAEBR, Caenorhabditis briggsae Q61P44_CAEBR, Caenorhabditis briggsae Q61R54_CAEBR, Caenorhabditis briggsae Q61V90_CAEBR, Caenorhabditis briggsae Q61A94_CAEBR, Caenorhabditis briggsae Q60TP4_CAEBR, Caenorhabditis briggsae Q60M10_CAEBR, Caenorhabditis elegans GCY37_CAEEL, Caenorhabditis elegans GCY31_CAEEL, Caenorhabditis elegans GCY36_CAEEL, Caenorhabditis elegans GCY32_CAEEL, Caenorhabditis elegans GCY35_CAEEL, Caenorhabditis elegans GCY34. CAEEL, Caenorhabditis elegans GCY33_CAEEL, Oryzias curvinotus Q7T040_ORYCU, Oryzias curvinotus Q75WF0_ORYCU, Oryzias latipes P79998_ORYLA, Oryzias latipes Q7ZSZ5_ORYLA, Tetraodon nigroviridis Q4SW38_TETNG, Tetraodon nigroviridis Q4RZ94_TETNG, Tetraodon nigroviridis Q4S6K5_TETNG, Fugu rubripes Q9OVY5 FUGRU, Xenopus laevis Q6INK9_XENLA, Homo sapiens Q5T8J7 HUMAN, Homo sapiens GCYA2_HUMAN, Homo sapiens GCYB2_HUMAN, Homo sapiens GCYB1_HUMAN, Gorilla gorilla Q9N193_9 PRIM, Pongo pygmaeus Q5RAN8_PONPY, Pan troglodytes Q9N192_PANTR, Macaca mulatta Q9N194_MACMU, Hylobates lar Q9N191_HYLLA, Mus musculus Q8BXH3_MOUSE, Mus musculus GCYB1_MOUSE, Mus musculus Q3UTI4_MOUSE, Mus musculus Q3UH83_MOUSE, Mus musculus Q6XE41_MOUSE, Mus musculus Q80YP4_MOUSE, Rattus norvegicus Q8OWX7_RAT, Rattus norvegicus Q8OWX8_RAT, Rattus norvegicus Q920Q1_RAT, Rattus norvegicus Q54A43_RAT, Rattus norvegicus Q80WY0_RAT, Rattus norvegicus Q80WY4_RAT, Rattus norvegicus Q8CH85 RAT, Rattus norvegicus Q80WY5_RAT, Rattus norvegicus GCYB1_RAT, Rattus norvegicus Q8CH90_RAT, Rattus norvegicus Q91XJ7_RAT, Rattus norvegicus Q8OWX9_RAT, Rattus norvegicus GCYB2 RAT, Rattus norvegicus GCYA2_RAT, Canis familiaris Q4ZHR9_CANFA, Bos taurus GCYB1_BOVIN, Sus scrofa Q4ZHR7_PIG, Gryllus bimaculatus Q59HN5_GRYBI, Manduca sexta O77106_MANSE, Manduca sexta O76340_MANSE, Apis mellifera Q5UAFO_APIME, Apis mellifera Q5FANO_APIME, Apis mellifera Q6L5L6_APIME, Anopheles gambiae str PEST Q7PYK9_ANOGA, Anopheles gambiae str PEST Q7Q9W6_ANOGA, Anopheles gambiae str PEST Q7 QF31_ANOGA, Anopheles gambiae str PEST Q7PS01_ANOGA, Anopheles gambiae str PEST Q7PFY2_ANOGA, Anopheles gambiae Q7KQ93_ANOGA, Drosophila melanogaster Q24086_DROME, Drosophila melanogaster GCYH_DROME, Drosophila melanogaster GCY8E_DROME, Drosophila melanogaster GCYDA_DROME, Drosophila melanogaster GCYDB_DROME, Drosophila melanogaster Q9VA09_DROME, Drosophila pseudoobscura Q29CE1_DROPS, Drosophila pseudoobscura Q296C7_DROPS, Drosophila pseudoobscura Q296C8_DROPS, Drosophila pseudoobscura Q29BU7 DROPS, Aplysia californica Q7YWK7_APLCA, Hemicentrotus pulcherrimus Q95NK5_HEMPU, Chlamydomonas reinhardtii, Q5YLC2_CHLRE, Anabaena sp Q8YUQ7_ANASP, Flavobacteria bacterium BBFL7 Q26GR8_9 BACT, Psychroflexus torquis ATCC 700755 Q1VQE5_9 FLAO, marine gamma proteobacterium HTCC2207 Q1YPJ5_9 GAMM, marine gamma proteobacterium HTCC2207 Q1YTK4_9 GAMM, Caulobacter crescentus Q9A451_CAUCR, Acidiphilium cryptum JF-5 Q2DG60_ACICY, Rhodobacter sphaeroides Q3J0U9_RHOS4, Silicibacter pomeroyi Q5LPV1_SILPO, Paracoccus denitrificans PD1222, Q3PC67_PARDE, Silicibacter sp TM1040 Q3QNY2_9 RHOB, Jannaschia sp Q28ML8_JANSC, Magnetococcus sp MC-1 Q3XT27_9 PROT, Legionella pneumophila Q5WXPO_LEGPL, Legionella pneumophila Q5WTZ5_LEGPL, Legionella pneumophila Q5X268_LEGPA, Legionella pneumophila Q5X2R2_LEGPA, Legionella pneumophila subsp pneumophila Q5ZWM9_LEGPH, Legionella pneumophila subsp pneumophila Q5ZSQ8_LEGPH, Colwellia psychrerythraea Q47Y43_COLP3, Pseudoalteromonas atlantica T6c Q3CSZ5_ALTAT, Shewanella oneidensis Q8EF49_SHEON, Saccharophagus degradans Q21E20_SACD2, Saccharophagus degradans Q21ER7_SACD2, Vibrio angustum S14 Q1ZWE5_9VIBR, Vibrio vulnificus Q8DAE2_VIBVU, Vibrio alginolyticus 12G01 Q1VCP6_VIBAL, Vibrio sp DAT722 Q2FA22_9 VIBR, Vibrio parahaemolyticus Q87NJ1_VIBPA, Vibrio fischeri Q5E1F5_VIBF1, Vibrio vulnificus Q7MJS8_VIBVY, Photobacterium sp SKA34 Q2C6Z5_9 GAMM, Hahella chejuensis Q2SFY7_HAHCH, Oceanospirillum sp MED92 Q2BKV0_9 GAMM, Oceanobacter sp RED65 Q1N035_9 GAMM, Desulfovibrio desulfuricans Q310U7_DESDG, Halothermothrix orenii H 168 Q2AIW5_9 FIRM, Thermoanaerobacter tengcongensis Q8RBX6_THETN, Caldicellulosiruptor saccharolyticus DSM 8903 Q2ZH17_CALSA, Clostridium acetobutylicum Q97E73_CLOAB, Alkaliphilus metalliredigenes QYMF Q3C763_9 CLOT, Clostridium tetani Q899J9_CLOTE, and Clostridium beijerincki NCIMB 8052 Q2WVN0_CLOBE. In some embodiments of the methods, the H-NOX protein is not R. norvegicus sGC β1 H-NOX C78S or R. norvegicus sGC β1 H-NOX C78E. In some embodiments of the methods, the H-NOX protein does not have a mutation in the Y-S-R motif, which includes Tyr135, Ser137, and Arg139 of human H-NOX.
Unless otherwise explicitly noted or dictated by context, all wild-type and mutant proteins and all pharmaceutical compositions described herein may be used in any of the methods of delivering oxygen described herein. The H-NOX protein may or may not have heme and/or oxygen bound and may or may not be covalently bound to another molecule or moiety, such as polyethylene glycol. In some embodiments, the H-NOX protein is a fusion protein that includes an H-NOX domain and part or all of another protein, such as albumin (e.g., human serum albumin).
In one aspect, the invention features kits that include one or more H-NOX proteins. In some embodiments, the invention provides a kit that includes an H-NOX protein and instructions for using the kit to deliver oxygen to an individual. In some embodiments, the O2 dissociation constant of the H-NOX protein is between about 1 nM to about 1 mM at 20° C., and the NO reactivity of the H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.). In some embodiments, the O2 dissociation constant of the H-NOX protein is within 2 orders of magnitude of that of hemoglobin, and the NO reactivity of the H-NOX protein is at least 10-fold lower than that of hemoglobin. In some embodiments, the O2 dissociation constant of the H-NOX protein is between about 1 nM to about 1 mM at 20° C., and the NO reactivity of the H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.). In some embodiments, the H-NOX protein is not T. tengcongensis H-NOX Y140H. Unless otherwise explicitly noted or dictated by context, all wild-type and mutant proteins and all pharmaceutical compositions described herein may be used in any of the kits described herein. The H-NOX protein may or may not have heme and/or oxygen bound and may or may not be covalently bound to another molecule or moiety, such as polyethylene glycol. In some embodiments, the H-NOX protein is a fusion protein that includes an H-NOX domain and part or all of another protein, such as albumin (e.g., human serum albumin).
In one aspect, the invention features an H-NOX protein (such as any of the wild-type or mutant proteins described herein) for use as a medicament. In some embodiments, the invention features an H-NOX protein for use in a method of delivering oxygen to an individual. In some embodiments, the H-NOX protein is used to treat any condition for which delivery of O2 is beneficial, such as a cardiovascular disease, a neurological disease, tumor hypoxia, a loss of blood, or a wound.
In some embodiments, the invention features the use of an H-NOX protein (such as any of the wild-type or mutant proteins described herein) for the manufacture of a medicament, such as a medicament for delivering oxygen to an individual. In some embodiments, the invention features the use of an H-NOX protein for delivering oxygen to an individual. In some embodiments, the H-NOX protein is used to treat any condition for which delivery of O2 is beneficial, such as a cardiovascular disease, a neurological disease, tumor hypoxia, a loss of blood, or a wound.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1A is a picture of the three dimensional structure of distal pocket residues of NO-binding and O2-binding H-NOX proteins (above heme). Herne coordination residues of NO-binding and O2-binding H-NOX proteins are also shown (below heme). FIG. 1A is based on the three-dimensional structure of T. tengcongensis H-NOX reported by Pellicena, P. et al. (Aug. 31, 2004). “Crystal Structure of An Oxygen-Binding Heme Domain Related to Soluble Guanylate Cyclases,” Proc Natl. Acad Sci USA 101(35):12854-12859.
FIG. 1B is a stereo side view of the three dimensional structure of T. tengcongensis HNOX illustrating structural features of the H-NOX domain. The protein fold is represented by ribbon diagrams. The heme, dioxygen ligand, and proximal histidine are shown as ball-and-stick models. α-helices are labeled A-G according to the nomenclature shown in FIG. 5B. β-strands are labeled 1-4. FIG. 1B is from Pellicena, P. et al. (Aug. 31, 2004). “Crystal Structure of An Oxygen-Binding Heme Domain Related to Soluble Guanylate Cyclases,” Proc Natl. Acad Sci USA 101(35):12854-12859.
FIGS. 1C-1H are pictures of the three dimensional structure of T. tengcongensis HNOX illustrating exemplary distal pocket residues in T. tengcongensis HNOX. The following residues depicted in FIGS. 1C-1H are the main residues comprising the H-NOX distal pocket: Thr4, Ile5, Thr8, Trp9, Trp67, Asn74, Ile75, Phe78, Phe82, Tyr140, and Leu144, which are contained within helices A, D, E, and G. FIGS. 1C-1H were created using PYMOL (DeLano Scientific, LLP).
FIG. 2 is a sequence alignment of the following H-NOX proteins that bind or are predicted to bind O2 and NO: Majority (SEQ ID NO:1); Ce. gcy-31 (SEQ ID NO:2); Ce. gcy-33 (SEQ ID NO:3); Ce. gcy-35 (SEQ ID NO:4); Dm. CG14885 HNOX (SEQ ID NO:5); Dm. CG4154 HNOX (SEQ ID NO:6); Ms. Beta3 H-NOX (SEQ ID NO:7); Tt HNOX (SEQ ID NO:8); and Ca HNOX (SEQ ID NO:9). These H-NOX proteins are predicted to bind O2 as well as NO because they have a tyrosine at the position corresponding to Y140 of T. tengcongensis H-NOX. The amino acid numbering used in FIG. 2 starts with the first amino acid in the H-NOX domain or full-length protein as residue number 1. The alignment was generated using the default parameters in the program MegAlign. The abbreviations used in FIG. 2 are described below with respect to FIGS. 4A-4D.
FIG. 3A-3D are a sequence alignment of the following H-NOX proteins that bind or are predicted to bind NO but not O2: Majority (SEQ ID NO:10); Dm. sGC beta1 protein (SEQ ID NO:11); sGC beta1 protein (SEQ ID NO:12); hs. sGC beta1 protein (SEQ ID NO:13); hs. beta2 protein (SEQ ID NO:14); Ms. sGC beta1 protein (SEQ ID NO:15); Mm. sGC beta1 protein (SEQ ID NO:16); Np. beta1 HD-like (SEQ ID NO:17); Tr. sGC beta1 protein (SEQ ID NO:18); Anopheles_gambiae|XP_310919 (SEQ ID NO:19); Apis_mellifera|NP_001011632 (SEQ ID NO:20); Bt. sGC beta1 protein (SEQ ID NO:21); Chlamydomonas_reinhardtii|AAR02 (SEQ ID NO:22); Oryzias_curvinotus|BAC98396 (SEQ ID NO:23); Oryzias_latipes|BAA76691 (SEQ ID NO:24); Strongylocentrotus_purpuratus|X (SEQ ID NO:25); and Sus scrofa beta1|NP_001018042+(SEQ ID NO:26). The alignment was generated using the default parameters in the program MegAlign. The abbreviations used in FIGS. 3A-3D are described below with respect to FIG. 4.
FIGS. 4A-4D are a sequence alignment of H-NOX proteins from FIGS. 2 and 3A-3D: Majority (SEQ ID NO:27); Dm. sGC beta1 protein (SEQ ID NO:11); sGC beta1 protein (SEQ ID NO:12); hs. sGC beta1 protein (SEQ ID NO:13); hs. beta2 protein (SEQ ID NO:14); Mm. sGC beta1 protein (SEQ ID NO:16); Np. beta1 HD-like (SEQ ID NO:17); Tr. sGC beta1 protein (SEQ ID NO:18); Chlamydomonas_reinhardtii|AAR02 (SEQ ID NO:22); Oryzias_curvinotus|BAC98396 (SEQ ID NO:23); Strongylocentrotus_purpuratus|X (SEQ ID NO:25); Sus scrofa beta1|NP_001018042 (SEQ ID NO:26); gcy-31a (SEQ ID NO:2); gcy-33 (SEQ ID NO:3); Ca. HNOX (SEQ ID NO:9); T. beta1HD-like (SEQ ID NO:8); Ms. sGc beta 3 protein (SEQ ID NO:7); CG14885 (SEQ ID NO:5); and Dm. sGC short variant (SEQ ID NO:6). The alignment was generated using the default parameters in the program MegAlign. For FIGS. 2-4D, “Dm. sGC beta1 protein” denotes Drosophila melanogaster β1 H-NOX; “sGC beta1 protein” denotes Rattus norvegicus β1 H-NOX; “hs. sGC beta1 protein” denotes Homo sapiens β1 H-NOX; “hs. beta2 protein” denotes Homo sapiens β2 H-NOX; “Mm. sGC beta1 protein” denotes Mus musculus β1 H-NOX; “Np. beta1 HD-like” denotes Nostoc punctiforme H-NOX; “Tr. sGC beta1 protein” denotes Takifugu rubripes β1 H-NOX; “Anopheles_gambiae|XP_310919” denotes Anopheles gambiae β1 H-NOX; “Apis_mellifera|NP_001011632” denotes Apis mellifera β1 H-NOX; “Bt. sGC beta1 protein” denotes Bos taurus β1 H-NOX; “Chlamydomonas_reinhardtii|AAR02” denotes Chlamydornonas reinhardtii β1 H-NOX; “Oryzias_curvinotus|BAC98396 denotes Oryzias curvinotus β1 H-NOX; “Oryzias_latipes|BAA76691” denotes Oryzias latipes β1 H-NOX; “Strongylocentrotus_purpuratus|X” denotes Strongylocentrotus purpuratus β1 H-NOX; “Sus scrofa beta1|NP_001018042+” denotes Sus scrofa β1 H-NOX; “gcy-31a” denotes Caenorhabditis elegans Gcy-31a H-NOX; “gcy-33” denotes Caenorhabditis elegans Gcy-33 H-NOX; “gcy-35” denotes Caenorhabditis elegans Gcy-35 H-NOX; “Ca. H-NOX” denotes Clostridium acetobutiylicum H-NOX; “T. beta1 HD-like” denotes Thermoanaerobacter tengcongensis H-NOX; “Ms. sGc beta 3 protein” denotes Manduca sexta β3 H-NOX; “CG14885” denotes Drosophila melanogaster CG14885 H-NOX; “Dm. sGC short variant” denotes Drosophila melanogaster Gcy-88-E-S H-NOX, and “Dm. CG4154 HNOX” denotes Drosophila melanogaster CG4154 H-NOX.
FIG. 5A is a sequence alignment of members of the H-NOX family. The sequence numbering is that of T. tengcongensis H-NOX. Invariant residues are indicated by a “V”, very highly conserved residues are indicated by “s”. Y140 of T. tengcongensis H-NOX is indicated by a “H.” Predicted distal pocket tyrosine residues that may stabilize an FeII—O2 complex in other H-NOX proteins are: position 70 for Caenorhabditis elegans GCY-35; position 140 in Drosophila melanogaster CG14885-PA; position 138 of Caenorhabditis elegans GCY-35; position 140 of Clostridium acetobutylicum; numbered according to Thermoanaerobacter tengcongensis. Accession numbers are: Homo sapiens β1 [gi:2746083] (SEQ ID NO:28), Rattus norvegicus β1 [gi:27127318] (SEQ ID NO:29), Drosophila melangaster β1 [gi:861203] (SEQ ID NO:30), Drosophila melangaster CG14885-PA [gi:23171476] (SEQ ID NO:31), Caenorhabditis elegans GCY-35 [gi:52782806] (SEQ ID NO:32), Nostoc punctiforme [gi:23129606] (SEQ ID NO:33), Caulobacter crescentus [gi:16127222] (SEQ ID NO:34), Shewanella oneidensis [gi:24373702] (SEQ ID NO:35), Legionella pneumophila (ORF 2) [CUCGC_272624] (SEQ ID NO:36), Clostridium acetobutylicum [gi:15896488] (SEQ ID NO:37), and Thermoanaerobacter tengcongensis [gi:20807169] (SEQ ID NO:38). Alignments were generated using the program MegAlign, Lasergene, DNA Star, (see, the world-wide web at “dnastar.com/productsimegalign.php”). Clustal-W default parameters were used.
FIG. 5B is a sequence alignment of exemplary H-NOX domains. The secondary structure annotations and the numbering on top of the alignment correspond to the H-NOX domain from T. tengcongensis. α-helices are represented by spirals, and β-strands by arrows. The distal pocket is defined by α-helices αA, αD, αE, and αG. Pubmed/NCBI accession numbers are as follows: Ther_tengcongensis gi 120807169| (SEQ ID NO:39), Clos_acetobutylicum gi |15896488| (SEQ ID NO:40), Clos_tetani GI:75543266 (SEQ ID NO:41), Desu_desulfuricans gi |23475919| (SEQ ID NO:42), Vibr_vulnificus gi |27361734| (SEQ ID NO:43), Caul_crescentus gi |16127222| (SEQ ID NO:44), Micr_degradans gi |23027521| (SEQ ID NO:45), Vibr_cholerae gi |15601476| (SEQ ID NO:46), Shew_oneidensis gi |24373702| (SEQ ID NO:47), Rat_beta1_sGC gi |27127318| (SEQ ID NO:48), Rat_beta2 sGC gi |21956635| (SEQ ID NO:49), Nost_punctiforme gi |23129606| (SEQ ID NO:50), and Nost_sp. gi |17229770| (SEQ ID NO:51). The consensus sequence is shown a the bottom of FIG. 5B (SEQ ID NO:52). The alignments were generated using the program MULTALIN (Corpet, F. (1988) Nucleic Acids Res. 16:10881-10890), and FIG. 5B was prepared using the program ESPRIPT (Gouet, P. et al. (1999) Bioinformatics 15: 305-308.).
FIGS. 6A and 6B are pictures of the three dimensional structure of the heme environment of the T. tengcongensis H-NOX domain. FIGS. 6A and 6B are from Pellicena, P. et al. (Aug. 31, 2004). “Crystal Structure of An Oxygen-Binding Heme Domain Related to Soluble Guanylate Cyclases,” Proc Natl. Acad Sci USA 101(35):12854-12859.
FIGS. 7A-7F are graphs of the UV-visible spectroscopy of H-NOX proteins after anaerobic reduction (FeII unligated complexes; top line in each graph) before and after being exposed to air (FeII—O2 complexes; bottom line in each graph) for Tt H-NOX (FIG. 7A), Tt Y140L (FIG. 7B), Tt W9F-Y140L (FIG. 7C), Tt F78Y-Y140L (FIG. 7D), L2 H-NOX and L2 F142Y (FIG. 7E), and β1(1-385) and β1(1-385) I145Y (FIG. 7F). In addition to the FeII and FeII—O2 complexes of L2 F142Y and β1(1-385) I145Y, the spectrum of wild-type L2 H-NOX and β1-(1-385) H-NOX after reduction and exposure to air are shown in the middle line in FIGS. 7E and 7F, respectively, to demonstrate that these proteins do not bind O2 before the addition of a distal pocket tyrosine. The two or three numbers written in the upper left corner of each panel represent the wavelength for the peak of the lines in the graph. The numbers are written vertically in the order in which the corresponding lines appear vertically in the graph. For example, the 430 nm value in FIG. 7A denotes the peak of the wavelength for the top line in the graph (which represents a FeII unligated complex), and the 416 nm value in FIG. 7A denotes the peak of the wavelength for the bottom line in the graph (which represents a FeII—O2 complex). A shift in the wavelength in the presence of air indicates that the protein binds O2. The formation of a double peak between 500 and 600 nm in the presence of air is also indicative of O2 binding. FIGS. 7A-7F are from Boon, E. M. et al. (2005). “Molecular Basis For NO Selectivity in Soluble Guanylate Cyclase,” Nature Chem. Biol. 1:53-59.
FIGS. 8A-8DD contain polynucleotide sequences of exemplary nucleic acids that encode H-NOX proteins and the amino acid sequences of the corresponding H-NOX proteins (SEQ ID NOS:53-162).



DETAILED DESCRIPTION OF THE INVENTION
The present invention is based in part on the surprising discovery that H-NOX proteins have a much lower NO reactivity than hemoglobin. This intrinsic low NO reactivity (and high NO stability) makes wild-type and mutant H-NOX proteins desirable blood substitutes because of the lower probability of inactivation of H-NOX proteins by endogenous NO and the lower probability of scavenging of endogenous NO by H-NOX proteins. Importantly, the presence of a distal pocket tyrosine in some H-NOX proteins (Pellicena, P. et al. (Aug. 31, 2004). “Crystal Structure of An Oxygen-Binding Heme Domain Related to Soluble Guanylate Cyclases,” Proc Natl. Acad Sci USA 101(35):12854-12859) is suggestive of undesirable, high NO reactivity, contraindicating use as a blood substitute. For example, by analogy, a Mycobacterium tuberculosis hemoglobin protein, with a structurally analogous distal pocket tyrosine, reacts extremely rapidly with NO, and is used by the Mycobacterium to effectively scavenge and avoid defensive NO produced by an infected host (Ouellet, H. et al. (Apr. 30, 2002). “Truncated Hemoglobin HbN Protects Mycobacterium Bovis From Nitric Oxide,” Proc. Natl. Acad. Sci. USA 99(9):5902-5907). However, we surprisingly discovered that H-NOX proteins actually have a much lower NO reactivity than that of hemoglobin making their use as blood substitutes possible.
Additionally, it was surprising discovered that H-NOX proteins that bind NO but not O2 can be converted to H-NOX proteins that bind both NO and O2 by the introduction of a single amino acid mutation. Thus, the affinity of H-NOX proteins for O2 and NO and the ability of H-NOX proteins to discriminate between O2 and NO ligands can be altered by the introduction of one or more amino acid mutations, allowing H-NOX proteins to be tailored to bind O2 or NO with desired affinities. Additional mutations can be introduced to further alter the affinity for O2 and/or NO. The H-NOX protein family can therefore be manipulated to exhibit improved or optimal kinetic and thermodynamic properties for O2 delivery. For example, mutant H-NOX proteins have been generated with altered dissociation constants and/or off rates for O2 binding that improve the usefulness of H-NOX proteins for a variety of clinical and industrial applications. The ability to tune H-NOX proteins to bind and deliver O2 is a therapeutic avenue that addresses and overcomes the central shortcomings of current O2 carriers. Accordingly, the present invention provides proteins, compositions, kits, and methods for the delivery of oxygen.
There are numerous benefits of using H-NOX proteins for O2 delivery. The principle role of blood transfusion following trauma and surgery is to deliver O2. An ideal blood substitute avoids the challenges of conventional blood: viral contamination, typing requirements, limited shelf-life, and limited availability. The major limitations of hemoglobin-based blood substitutes are their high affinity for O2 and their propensity to react with NO. As mentioned above, destruction of even low levels of NO can have serious effects on the tonic resting state of the vasculature and organs and leads to hypertension and gastrointestinal distress. Additionally, in the process of reacting with NO, the hemoglobin loses it ability to deliver O2 on a clinically relevant timeframe. Numerous attempts have been made to minimize the toxicity of first generation hemoglobin-based oxygen carriers (HBOCs), including intra- and inter-molecular cross-linking (“Blood Substitutes,” R. Winslow ed. Academic Press, 2006). While these modifications overcame some of the severe toxicity issues related to extravasation of hemoglobin, the destruction of oxygen binding due to high NO reactivity remained. These second generation HBOCs exhibit reduced oxygen affinity, with p50 values close to the p50 value of erythrocytes, yet they have failed in clinical trials. An alternate hypothesis as been proposed by Winslow and colleagues: a low p50 HBOC with an appropriate viscosity and colloidal osmotic pressure is more appropriate for cell-free oxygen delivery than a high p50 HBOC (Tsai, A. G. et al. (2003). “Targeted O2 Delivery by low-P50 hemoglobin: A New Basis for O2 Therapeutics,” Am. J. Physiol. Heart Circ. Physiol. 285:H1411-H1419; Winslow (2007). “Red Cell Substitutes,” Seminars in Hematology 44:51-59). Whether the NO reactivity of such an HBOC becomes an issue in clinical trials remains to be seen. Engineering H-NOX proteins to bind and deliver O2 with minimal NO reactivity provides a new blood gas O2 carrier for use in blood substitutes where the H-NOX proteins deliver O2 without scavenging NO or being inactivated as O2 carriers by NO. These H-NOX proteins, compositions, kits, and methods are described further herein.
H-NOX Proteins
Overview of H-NOX Protein Family
Unless otherwise indicated, any wild-type or mutant H-NOX protein can be used in the compositions, kits, and methods as described herein. As used herein, an “H-NOX protein” means a protein that has an H-NOX domain (named for Heme-Nitric oxide and OXygen binding domain). An H-NOX protein may or may not contain one or more other domains in addition to the H-NOX domain. H-NOX proteins are members of a highly-conserved, well-characterized family of hemoproteins (Iyer, L. M. et al. (Feb. 3, 2003). “Ancient Conserved Domains Shared by Animal Soluble Guanylyl Cyclases And Bacterial Signaling Proteins,” BMC Genomics 4(1):5; Karow, D. S. et al. (Aug. 10, 2004). “Spectroscopic Characterization of the Soluble Guanylate Cyclase-Like Heme Domains From Vibrio Cholerae And Thermoanaerobacter Tengcongensis,” Biochemistry 43(31):10203-10211; Boon, E. M. et at (2005). “Molecular Basis For NO Selectivity in Soluble Guanylate Cyclase,” Nature Chem. Biol. 1:53-59; Boon, E. M. et al. (October 2005). “Ligand Discrimination in Soluble Guanylate Cyclase and the H-NOX Family of Heme Sensor Proteins,” Curr. Opin. Chem. Biol. 9(5):441-446; Boon, E. M. et al. (2005). “Ligand Specificity of H-NOX Domains: From sGC to Bacterial NO Sensors,” J. Inorg. Biochem. 99(4):892-902). H-NOX proteins are also referred to as Pfam 07700 proteins or HNOB proteins (Pfam—A database of protein domain family alignments and Hidden Markov Models, Copyright (C) 1996-2006 The Pfam Consortium; GNU LGPL Free Software Foundation, Inc., 59 Temple Place—Suite 330, Boston, Mass. 02111-1307, USA). In some embodiments, an H-NOX protein has, or is predicted to have, a secondary structure that includes six alpha-helices, followed by two beta-strands, followed by one alpha-helix, followed by two beta-strands. An H-NOX protein can be an apoprotein that is capable of binding heme or a holoprotein with heme bound. An H-NOX protein can covalently or non-covalently bind a heme group. Some H-NOX proteins bind NO but not O2, and others bind both NO and O2. H-NOX domains from facultative aerobes that have been isolated bind NO but not O2. H-NOX proteins from obligate aerobic prokaryotes, C. elegans, and D. melanogaster bind NO and O2. Mammals have two H-NOX proteins: β1 and β2. An alignment of mouse, rat, cow, and human H-NOX sequences shows that these species share >99% identity. In some embodiments, the H-NOX domain of an H-NOX protein or the entire H-NOX protein is at least about any of 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 95, 97, 98, 99, or 99.5% identical to that of the corresponding region of a naturally-occurring Thermoanaerobacter tengcongensis H-NOX protein or a naturally-occurring sGC protein (e.g., a naturally-occurring sGC β1 protein). As discussed further herein, an H-NOX protein may optionally contain one or more mutations relative to the corresponding naturally-occurring H-NOX protein. In some embodiments, the H-NOX protein includes one or more domains in addition to the H-NOX domain. In particular embodiments, the H-NOX protein includes one or more domains or the entire sequence from another protein. For example, the H-NOX protein may be a fusion protein that includes an H-NOX domain and part or all of another protein, such as albumin (e.g., human serum albumin). In some embodiments, only the H-NOX domain is present.
A crystal structure of a prokaryotic O2-binding H-NOX from Thermoanaerobacter tengcongensis (Nioche, P. et al. (Nov. 26, 2004). “Femtomolar Sensitivity of a NO Sensor From Clostridium Botulinum,” Science 306(5701):1550-1551; Pellicena, P. et al. (Aug. 31, 2004). “Crystal Structure of An Oxygen-Binding Heme Domain Related to Soluble Guanylate Cyclases,” Proc Natl. Acad Sci USA 101(35):12854-12859) shows that a tyrosine side chain hydroxyl group makes a critical H-bond to the FeII—O2 moiety. This distal pocket hydrogen-bonding network, involving principally Y140, stabilizes an FeII—O2 complex (FIG. 6B). This tyrosine is not present in H-NOX proteins that discriminate against O2 and only bind NO. For example, this hydrogen-bonding network is predicted to be absent in the H-NOX proteins from sGCs and aerobic prokaryotes, suggesting this as a key molecular factor in the remarkable ligand selectivity against O2 displayed by these heme proteins. FIGS. 7A-7G clearly demonstrate that the addition of a tyrosine in the distal pocket of a wild-type H-NOX protein that binds NO but not O2 can enable the mutant H-NOX protein to bind O2. Thus, a tyrosine in the distal heme pocket of the H-NOX heme fold acts like a switch to turn on or off O2 binding.
As illustrated in FIGS. 6A and 6B, the structure of the porphyrin is highly distorted. As illustrated in FIG. 6A, the conserved Y-S-R motif makes hydrogen-bonding interactions with the propionic acid side chains of the heme group. FIG. 6B, the conserved H102 is the proximal ligand to the heme (FIG. 6B).
As used herein, a “protein” includes proteins and fragments of proteins whether isolated from natural sources, produced by recombinant techniques, or chemically synthesized. A protein may have one or more modifications, such as a post-translational modification (e.g., glycosylation, etc) or any other modification (e.g., PEGylation, etc). The protein may contain one or more non-naturally-occurring amino acids (e.g., such as an amino acid with a side chain modification). In various embodiments, the H-NOX protein has at least about 50, 100, 150, 181, 200, 250, 300, 350, 400, or more amino acids. In some embodiments, the H-NOX proteins may include from about 50 to about 600 amino acids, such as about 100 to about 500 amino acids, about 150 to about 400 amino acids, about 150 to about 300 amino acids, or about 175 to about 200 amino acids.
Sources of H-NOX Proteins
H-NOX proteins from any genus or species can be used in the compositions, kits, and methods described herein. In various embodiments, the H-NOX protein is a protein from a mammal (e.g., a primate (e.g., human, monkey, gorilla, ape, lemur, etc), a bovine, an equine, a porcine, a canine, or a feline), an insect, a yeast, or a bacteria or is derived from such a protein. Exemplary mammalian H-NOX proteins include wild-type human and rat soluble guanylate cyclase (such as the β1 subunit). Examples of H-NOX proteins include wild-type mammalian H-NOX proteins, e.g. H. sapiens, M. musculus, C. familiaris, B. taurus and R. norvegicus; and wild-type non-mammalian vertebrate H-NOX proteins, e.g., X. laevis, O. latipes, O. curivatus, and F. rubripes. Examples of non-mammalian wild-type NO-binding H-NOX proteins include wild-type H-NOX proteins of D. melanogaster, A. gambiae, and M. sexta; examples of non-mammalian wild-type O2-binding H-NOX proteins include wild-type H-NOX proteins of C. elegans gcy-31, gcy-32, gcy-33, gcy-34, gcy-35, gcy-36, and gcy-37; D. melanogaster CG14885, CG14886, and CG4154; and M. sexta beta-3; examples of prokaryotic wild-type H-NOX proteins include T. tengcongensis, V. cholera, V. Jischerii, N. punctiforme, D. desulfuricans, L. pneumophila 1, L. pneumophila 2, and C. acetobutylicum. 
NCBI Accession numbers for exemplary H-NOX proteins include the following: Homo sapiens β1 [gi:2746083], Rattus norvegicus [gi:27127318], Drosophila melangaster β1 [gi:861203], Drosophila melangaster CG14885-PA [gi:23171476], Caenorhabditis elegans GCY-35 [gi:52782806], Nostoc punctiforme [gi:23129606], Caulobacter crescentus [gi:16127222], Shewanella oneidensis [gi:24373702], Legionella pneumophila (ORF 2) [CUCGC_272624], Clostridium acetobutylicum [gi:15896488], and Thermoanaerobacter tengcongensis [gi:20807169].
Exemplary H-NOX protein also include the following H-NOX proteins that are listed by their gene name, followed by their species abbreviation and Genbank Identifiers (such as the following protein sequences available as of May 21, 2006; May 22, 2006; May 21, 2007; or May 22, 2007, which are each hereby incorporated by reference in their entireties): Npun5905 Npu_23129606, alr2278_Ana_17229770, SO2144_Sone_24373702, Mdeg1343_Mde_23027521, VCA0720_Vch_15601476, CC2992_Ccr_16127222, Rsph2043_Rhsp_22958463 (gi:46192757), Mmc10739_Mcsp_22999020, Tar4_Tte_20807169, Ddes2822_Dde_23475919, CAC3243_Cac_15896488, gcy-31_Ce_17568389, CG14885_Dm_24647455, GUCY1B3_Hs_4504215, HpGCS-beta1_Hpul_14245738, Gycbeta100B_Dm_24651577, CG4154_Dm_24646993 (gi:NP_650424.2, gi:62484298), gcy-32_Ce_13539160, gcy-36_Ce_17568391 (gi:32566352, gi:86564713), gcy-35_Ce-17507861 (gi:71990146), gcy-37_Ce_17540904 (gi:71985505), GCY1a3_Hs_20535603, GCY1a2-Hs_899477, or GYCa-99B_Dm_729270 (gi:68067738) (Lakshminarayan et al. (2003). “Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins,” BMG Genomics 4:5-13). The species abbreviations used in these names include Ana—Anabaena Sp; Ccr—Caulobacter crescentus; Cac—Clostridium acetobutylicum; Dde—Desulfovibrio desulfuricans; Mcsp—Magnetococcus sp.; Mde—Microbulbifer degradans; Npu—Nostoc punctiforme; Rhsp—Rhodobacter sphaeroides; Sone—Shewanella oneidensis; Tte—Thermoanaerobacter tengcongensis; Vch—Vibrio cholerae; Ce—Caenorhabditis elegans; Dm—Drosophila melanogaster; Hpul—Hemicentrotus pulcherrimus; Hs—Homo sapiens. 
Other exemplary H-NOX proteins include the following H-NOX proteins that are listed by their organism name and Pfam database accession number (such as the following protein sequences available as of May 21, 2006; May 22, 2006; May 17, 2007; May 21, 2007; or May 22, 2007, which are each hereby incorporated by reference in their entireties): Caenorhabditis briggsae Q622M5_CAEBR, Caenorhabditis briggsae Q61P44_CAEBR, Caenorhabditis briggsae Q61R54_CAEBR, Caenorhabditis briggsae Q61V90_CAEBR, Caenorhabditis briggsae Q61A94_CAEBR, Caenorhabditis briggsae Q60TP4_CAEBR, Caenorhabditis briggsae Q60M10_CAEBR, Caenorhabditis elegans GCY37_CAEEL, Caenorhabditis elegans GCY31_CAEEL, Caenorhabditis elegans GCY36_CAEEL, Caenorhabditis elegans GCY32_CAEEL, Caenorhabditis elegans GCY35_CAEEL, Caenorhabditis elegans GCY34CAEEL, Caenorhabditis elegans GCY33_CAEEL, Oryzias curvinotus Q7T040_ORYCU, Oryzias curvinotus Q75WF0_ORYCU, Oryzias latipes P79998_ORYLA, Oryzias latipes Q7ZSZ5_ORYLA, Tetraodon nigroviridis Q4SW38_TETNG, Tetraodon nigroviridis Q4RZ94_TETNG, Tetraodon nigroviridis Q4S6K5_TETNG, Fugu rubripes Q9OVY5_FUGRU, Xenopus laevis Q6INK9_XENLA, Homo sapiens Q5T8J7_HUMAN, Homo sapiens GCYA2 HUMAN, Homo sapiens GCYB2_HUMAN, Homo sapiens GCYB1_HUMAN, Gorilla gorilla Q9N193_9 PRIM, Pongo pygmaeus Q5RAN8_PONPY, Pan troglodytes Q9N192PANTR, Macaca mulatta Q9N194_MACMU, Hylobates lar Q9N191_HYLLA, Mus musculus Q8BXH3_MOUSE, Mus musculus GCYB1_MOUSE, Mus musculus Q3UTI4_MOUSE, Mus musculus Q3UH83_MOUSE, Mus musculus Q6XE41_MOUSE, Mus musculus Q80YP4_MOUSE, Rattus norvegicus Q8OWX7_RAT, Rattus norvegicus Q8OWX8_RAT, Rattus norvegicus Q920Q1_RAT, Rattus norvegicus Q54A43_RAT, Rattus norvegicus Q80WY0_RAT, Rattus norvegicus Q80WY4_RAT, Rattus norvegicus Q8CH85_RAT, Rattus norvegicus Q80WY5_RAT, Rattus norvegicus GCYB1_RAT, Rattus norvegicus Q8CH90 RAT, Rattus norvegicus Q91XJ7_RAT, Rattus norvegicus Q8OWX9_RAT, Rattus norvegicus GCYB2_RAT, Rattus norvegicus GCYA2_RAT, Canis familiaris Q4ZHR9 CANFA, Bos taurus GCYB1_BOVIN, Sus scrofa Q4ZHR7_PIG, Gryllus bimaculatus Q59HN5_GRYBI, Manduca sexta O77106 MANSE, Manduca sexta O76340_MANSE, Apis mellifera Q5UAFO_APIME, Apis mellifera Q5FAN0_APIME, Apis mellifera Q6L5L6_APIME, Anopheles gambiae str PEST Q7PYK9_ANOGA, Anopheles gambiae str PEST Q7Q9W6_ANOGA, Anopheles gambiae str PEST Q7QF31_ANOGA, Anopheles gambiae str PEST Q7PS01_ANOGA, Anopheles gambiae str PEST Q7PFY2_ANOGA, Anopheles gambiae Q7KQ93_ANOGA, Drosophila melanogaster Q24086_DROME, Drosophila melanogaster GCYH_DROME, Drosophila melanogaster GCY8E_DROME, Drosophila melanogaster GCYDA_DROME, Drosophila melanogaster GCYDB_DROME, Drosophila melanogaster Q9VA09_DROME, Drosophila pseudoobscura Q29CE1_DROPS, Drosophila pseudoobscura Q296C7_DROPS, Drosophila pseudoobscura Q296C8_DROPS, Drosophila pseudoobscura Q29BU7_DROPS, Aplysia californica Q7YWK7_APLCA, Hemicentrotus pulcherrimus Q95NK5_HEMPU, Chlamydomonas reinhardtii, Q5YLC2_CHLRE, Anabaena sp Q8YUQ7_ANASP, Flavobacteria bacterium BBFL7 Q26GR8_9 BACT, Psychroflexus torquis ATCC 700755 Q1VQE5_9 FLAO, marine gamma proteobacterium HTCC2207 Q1YPJ5_9 GAMM, marine gamma proteobacterium HTCC2207 QlYTK4_9 GAMM, Caulobacter crescentus Q9A451_CAUCR, Acidiphilium cryptum JF-5 Q2DG60_ACICY, Rhodobacter sphaeroides Q3J0U9_RHOS4, Silicibacter pomeroyi Q5LPV1_SILPO, Paracoccus denitrificans PD1222, Q3PC67_PARDE, Silicibacter sp TM1040 Q3QNY2_9 RHOB, Jannaschia sp Q28ML8 JANSC, Magnetococcus sp MC-1 Q3XT27_9 PROT, Legionella pneumophila Q5WXPO_LEGPL, Legionella pneumophila Q5WTZ5_LEGPL, Legionella pneumophila Q5X268_LEGPA, Legionella pneumophila Q5X2R2_LEGPA, Legionella pneumophila subsp pneumophila Q5ZWM9_LEGPH, Legionella pneumophila subsp pneumophila Q5ZSQ8_LEGPH, Colwellia psychrerythraea Q47Y43_COLP3, Pseudoalteromonas atlantica T6c Q3CSZ5_ALTAT, Shewanella oneidensis Q8EF49_SHEON, Saccharophagus degradans Q21E20_SACD2, Saccharophagus degradans Q21ER7_SACD2, Vibrio angustum S14 Q1ZWE5_9 VIBR, Vibrio vulnificus Q8DAE2_VIBVU, Vibrio alginolyticus 12G01 Q1VCP6_VIBAL, Vibrio sp DAT722 Q2FA22_9VIBR, Vibrio parahaemolyticus Q87NJ1_VIBPA, Vibrio fischeri Q5E1F5_VIBF1, Vibrio vulnificus Q7MJS8_VIBVY, Photobacterium sp SKA34 Q2C6Z5_9 GAMM, Hahella chejuensis Q2SFY7_HAHCH, Oceanospirillum sp MED92 Q2BKV0_9 GAMM, Oceanobacter sp RED65 Q1N035_9 GAMM, Desulfovibrio desulfuricans Q310U7_DESDG, Halothermothrix orenii H 168 Q2AIW5_9 FIRM, Thermoanaerobacter tengcongensis Q8RBX6_THETN, Caldicellulosiruptor saccharolyticus DSM 8903 Q2ZH17_CALSA, Clostridium acetobutylicum Q97E73_CLOAB, Alkaliphilus metalliredigenes QYMF Q3C763_9 CLOT, Clostridium tetani Q899J9_CLOTE, and Clostridium beijerincki NCIMB 8052 Q2WVN0_CLOBE. These sequences are predicted to encode H-NOX proteins based on the identification of these proteins as belonging to the H-NOX protein family using the Pfam database as described herein.
Additional H-NOX proteins and nucleic acids, which may be suitable for use in the pharmaceutical compositions and methods described herein, can be identified using standard methods. For example, standard sequence alignment and/or structure prediction programs can be used to identify additional H-NOX proteins and nucleic acids based on the similarity of their primary and/or predicted protein secondary structure with that of known H-NOX proteins and nucleic acids. For example, the Pfam database uses defined alignment algorithms and Hidden Markov Models (such as Pfam 21.0) to categorize proteins into families, such as the H-NOX protein family (Pfam—A database of protein domain family alignments and Hidden Markov Models, Copyright (C) 1996-2006 The Pfam Consortium; GNU LGPL Free Software Foundation, Inc., 59 Temple Place—Suite 330, Boston, Mass. 02111-1307, USA). Standard databases such as the swissprot-trembl database (world-wide web at “expasy.org”, Swiss Institute of Bioinformatics Swiss-Prot group CMU—1 rue Michel Servet CH-1211 Geneva 4, Switzerland) can also be used to identify members of the H-NOX protein family. The secondary and/or tertiary structure of an H-NOX protein can be predicted using the default settings of standard structure prediction programs, such as PredictProtein (630 West, 168 Street, BB217, New York, N.Y. 10032, USA). Alternatively, the actual secondary and/or tertiary structure of an H-NOX protein can be determined using standard methods.
In some embodiments, the H-NOX protein has the same amino acid in the corresponding position as any of following distal pocket residues in T. tengcongensis H-NOX: Thr4, Ile5, Thr8, Trp9, Trp67, Asn74, Ile75, Phe78, Phe82, Tyr140, Leu144, or any combination of two or more of the foregoing. In some embodiments, the H-NOX protein has a proline or an arginine in a position corresponding to that of Pro115 or Arg135 of T. tengcongensis H-NOX, respectively, based on sequence alignment of their amino acid sequences. In some embodiments, the H-NOX protein has a histidine that corresponds to His105 of R. norvegicus β1 H-NOX. In some embodiments, the H-NOX protein has or is predicted to have a secondary structure that includes six alpha-helices, followed by two beta-strands, followed by one alpha-helix, followed by two beta-strands. This secondary structure has been reported for H-NOX proteins.
If desired, a newly identified H-NOX protein can be tested to determine whether it binds heme using standard methods. The ability of an H-NOX protein to function as an O2 carrier can be tested by determining whether the H-NOX protein binds O2 using standard methods, such as those described herein. If desired, one or more of the mutations described herein can be introduced into the H-NOX protein to optimize its characteristics as an O2 carrier. For example, one or more mutations can be introduced to alter its O2 dissociation constant, koff for oxygen, rate of heme autoxidation, NO reactivity, NO stability or any combination of two or more of the foregoing. Standard techniques such as those described herein can be used to measure these parameters.
As discussed herein, mutant H-NOX proteins (e.g., class I and class II mutants discussed below) may be derived by mutagenesis from these or other natural wild-type source sequences (e.g., the sequences listed in FIG. 2-4D or 8A-8DD or any other sequence described herein). As used herein, “derived from” refers to the source of the protein into which one or more mutations is introduced. For example, a protein that is “derived from a mammalian protein” refers to protein of interest that results from introducing one or more mutations into the sequence of a wild-type (i.e., a sequence occurring in nature) mammalian protein.
Mutant H-NOX Proteins
As discussed further herein, an H-NOX protein may contain one or more mutations, such as a mutation that alters the O2 dissociation constant, the koff for oxygen, the rate of heme autoxidation, the NO reactivity, the NO stability, or any combination of two or more of the foregoing compared to that of the corresponding wild-type protein. Panels of engineered H-NOX proteins may be generated by random mutagenesis followed by empirical screening for requisite or desired dissociation constants, dissociation rates, NO-reactivity, stability, physio-compatibility, or any combination of two or more of the foregoing in view of the teaching provided herein using techniques as described herein and, additionally, as known by the skilled artisan. Alternatively, mutagenesis can be selectively targeted to particular regions or residues such as distal pocket residues apparent from the experimentally determined or predicted three-dimensional structure of an H-NOX protein (FIG. 1A herein; and see, for example, Boon, E. M. et al. (2005). “Molecular Basis For NO Selectivity in Soluble Guanylate Cyclase,” Nature Chemical Biology 1:53-59, which is hereby incorporated by reference in its entirety, particularly with respect to the sequences of wild-type and mutant H-NOX proteins) or evolutionarily conserved residues identified from sequence alignments (FIGS. 2-4 herein; and see, for example, Boon E. M. et al. (2005). “Molecular Basis For NO Selectivity in Soluble Guanylate Cyclase,” Nature Chemical Biology 1:53-59, which is hereby incorporated by reference in its entirety, particularly with respect to the sequences of wild-type and mutant H-NOX proteins).
As used herein, a “mutant protein” means a protein with one or more mutations compared to a protein occurring in nature. In one embodiment, the mutant protein has a sequence that differs from that of all proteins occurring in nature. In various embodiments, the amino acid sequence of the mutant protein is at least about any of 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 95, 97, 98, 99, or 99.5% identical to that of the corresponding region of a protein occurring in nature. In some embodiments, the mutant protein is a protein fragment that contains at least about any of 25, 50, 75, 100, 150, 200, 300, or 400 contiguous amino acids from a full-length protein. Sequence identity can be measured, for example, using sequence analysis software with the default parameters specified therein (e.g., Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705). This software program matches similar sequences by assigning degrees of homology to various. amino acids replacements, deletions, and other modifications.
As used herein, a “mutation” means an alteration in a reference nucleic acid or amino acid sequence occurring in nature. Exemplary nucleic acid mutations include an insertion, deletion, frameshift mutation, silent mutation, nonsense mutation, or missense mutation. In some embodiments, the nucleic acid mutation is not a silent mutation. Exemplary protein mutations include the insertion of one or more amino acids (e.g., the insertion of 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids), the deletion of one or more amino acids (e.g., a deletion of N-terminal, C-terminal, and/or internal residues, such as the deletion of at least about any of 5, 10, 15, 25, 50, 75, 100, 150, 200, 300, or more amino acids or a deletion of about any of 5, 10, 15, 25, 50, 75, 100, 150, 200, 300, or 400 amino acids), the replacement of one or more amino acids (e.g., the replacement of 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids), or combinations of two or more of the foregoing. An exemplary functional truncation of an H-NOX protein includes residues 1-385 of the 131 sequence. In some embodiments, a mutant protein has at least one amino acid alteration compared to a protein occurring in nature. In some embodiments, a mutant nucleic acid sequence encodes a protein that has at least one amino acid alteration compared to a protein occurring in nature. In some embodiments, the nucleic acid is not a degenerate version of a nucleic acid occurring in nature that encodes a protein with an amino acid sequence identical to a protein occurring in nature. The nomenclature used in referring to a particular amino acid mutation first identifies the wild-type amino acid, followed by the residue number and finally the substitute amino acid. For example, Y140L means that tyrosine has been replaced by a leucine at residue number 140.
An “evolutionary conserved mutation” is the replacement of an amino acid in one protein by an amino acid in the corresponding position of another protein in the same protein family. Exemplary evolutionary conserved mutations (also denoted class I mutations) are listed in Table 1A. In Table 1A, mutations are numbered/annotated according to the sequence of human β1 H-NOX, but are analogous for all H-NOX sequences. Thus, the corresponding position in any other H-NOX protein can be mutated to the indicated residue. For example, Phe4 of human β1 H-NOX can be mutated to a tyrosine since other H-NOX proteins have, a tyrosine in this position. The corresponding phenylalanine residue can be mutated to a tyrosine in any other H-NOX protein. In particular embodiments, the one or more mutations are confined to evolutionarily conserved residues. in some embodiments, the one or more mutations may include at least one evolutionarily conserved mutation and at least one non-evolutionarily conserved mutation. If desired, these mutant H-NOX proteins are subjected to empirical screening for NO/O2 dissociation constants, NO-reactivity, stability, and physio-compatibility in view of the teaching provided herein.







TABLE 1A





Exemplary Class I H-NOX mutations targeting


evolutionary conserved residues



















F4Y
Q30G
I145Y



F4L
E33P
I145H



H7G
N61G
K151E



A8E
C78H
I157F



L9W
A109F
E183F










In some embodiments, the mutation is a distal pocket mutation, such as mutation of a residue in alpha-helix A, D, E, or G (Pellicena, P. et al. (Aug. 31, 2004). “Crystal Structure of An Oxygen-Binding Heme Domain Related to Soluble Guanylate Cyclases,” Proc Natl. Acad Sci USA 101(35):12854-12859). Exemplary distal pocket mutations (also denoted class II mutations) are listed in Table 1B. In Table 1B, mutations are numbered/annotated according to the sequence of human β1 H-NOX, but are analogous for all H-NOX sequences. Because several substitutions provide viable mutations at each recited residue, the residue at each indicated position can be changed to any other naturally or non-naturally-occurring amino acid (denoted “X”). Such mutations can produce H-NOX proteins with a variety of desired affinity, stability, and reactivity characteristics.







TABLE 1B





Exemplary Class II H-NOX mutations


targeting distal pocket residues



















V8X
M73X
I145X



L9X
F77X
I149X



F70X
C78X










In particular embodiments, the mutation is a heme distal pocket mutation. As described herein, a crucial molecular determinant that prevents O2 binding in NO-binding members of the H-NOX family is the lack of a H-bond donor in the distal pocket of the heme. Accordingly, in some embodiments, the mutation alters H-bonding between the H-NOX domain and the ligand within the distal pocket. In some embodiments, the mutation disrupts an H-bond donor of the distal pocket and/or imparts reduced O2 ligand-binding relative to the corresponding wild-type H-NOX domain. Exemplary distal pocket residues include hr4, Ile5, Thr8, Trp9, Trp67, Asn74, Ile75, Phe78, Phe82, Tyr140, and Leu144 of T. tengcongensis H-NOX and the corresponding residues in any other H-NOX protein.
Residues that are not in the distal pocket can also affect the three-dimensional structure of the heme group; this structure in turn affects the binding of O2 and NO to iron in the heme group. Accordingly, in some embodiments, the H-NOX protein has one or more mutations outside of the distal pocket. Examples of residues that can be mutated but are not in the distal pocket include Pro115 and Arg135 of T. tengcongensis H-NOX. In some embodiments, the mutation is in the proximal pocket which includes His105 as a residue that ligates to the heme iron.
In some embodiments when two or more mutations are present; at least one mutation is in the distal pocket, and at least one mutation is outside of the distal pocket (e.g., a mutation in the proximal pocket). In some embodiments, all the mutations are in the distal pocket.
In some embodiments, the amino acid sequence of the H-NOX protein is not identical to the sequence of a protein that is produced by an organism in nature. In some embodiments, the amino acid sequence of the H-NOX protein is not identical to a sequence found in any database on May 21, 2006 or May 22, 2006 (such as all known sequences predicted or known to be an H-NOX nucleic acid or amino acid sequence). In some embodiments, the amino acid sequence of the H-NOX protein is not identical to a sequence found in any database on May 21, 2007 or May 22, 2007 (such as all known sequences predicted or known to be an H-NOX nucleic acid or amino acid sequence).
To reduce the immunogenicity of H-NOX proteins derived from sources other than humans, amino acids in an H-NOX protein can be mutated to the corresponding amino acids in a human H-NOX. For example, one or more amino acids on the surface of the tertiary structure of a non-human H-NOX protein can be mutated to the corresponding amino acid in a human H-NOX proteins. In some variations, mutation of one or more surface amino acids may be combined with mutation of two or more distal pocket residues, mutation of one or more residues outside of the distal pocket (e.g., a mutation in the proximal pocket), or combinations of two or more of the foregoing.
Exemplary mutations are shown in Table 2. In addition, any of the residues listed in Table 2 can be mutated to any other amino acid. The invention also relates to any combination of mutation described herein, such as double, triple, or higher multiple mutations. For example, combinations of any of the mutations described herein can be made in the same H-NOX protein. Note that mutations in equivalent positions in other mammalian or non-mammalian H-NOX proteins are also encompassed by this invention. If desired, residues other than the ones mentioned in Table 2 can also be mutated. Exemplary mutant H-NOX proteins comprise one or more mutations that impart altered O2 or NO ligand-binding relative to the corresponding wild-type H-NOX domain and are operative as a physiologically compatible mammalian O2 blood gas carrier.
In Table 2 and all subsequent tables, the residue number for a mutation indicates the position in the sequence of the particular H-NOX protein being described. For example, T. tengcongensis 15A refers to the replacement of isoleucine by alanine at the fifth position in T. tengcongensis H-NOX. The same isoleucine to alanine mutation can be made in the corresponding residue in any other H-NOX protein (this residue may or may not be the fifth residue in the sequence of other H-NOX proteins). Since the amino acid sequences of mammalian β1 H-NOX domains differ by at most two amino acids, mutations that produce desirable mutant H-NOX proteins when introduced into wild-type rat β1 H-NOX proteins are also expected to produce desirable mutant H-NOX proteins when introduced into wild-type β1 H-NOX proteins from other mammals, such as humans.







TABLE 2







Exemplary H—NOX mutants from T. tengcongensis (Tt), L. pneumophila (Lp),


D. desulfuricans (Dd), V. cholera (Vc), N. punctiforme (Np),


C. botulinium (Cb), C. acetobutylicum, (Ca), rat, human, C. elegans (Ce).
















Other





Tt
Lp
Dd
Bacteria
Rat
Human
Worm





Tt H—NOX
L2 H—NOX
Dd H—NOX
Vc H—NOX
β1(1-385)
β1(1-385)
Ce GCY-




(728-



35(1-252)




899)


Tt H—NOX
L2 F142Y
Dd Y139L
Np H—NOX
β1(1-385)
β1(1-385)


His6



I145Y
I145Y


Tt I5A
L2 F9W-

Cb H—NOX
β1(1-385)
β1(1-385)



F142Y

(1-
I145H
I145H





175)


Tt I5L
L1 H—NOX

Cb H—NOX
β1(1-385)
β1(1-385)





(1-
C78Y
C78Y





186)


Tt I5L-
L1 F142Y

Ca H—NOX
β1(1-194)
β1(1-194)


P115A


(1-





197)


Tt W9F


Ca H—NOX
β1 H105F
β1 H105F





(1-





183)


Tt W9F-



β1 H105G
β1 H105G


Y140L


Tt W9F-



β1(1-194)
β1(1-194)


Y140H



I145Y
I145Y


Tt W9F-



β1(1-194)
β1(1-194)


N74A



L9W-I145Y
L9W-







I145Y


Tt W9Y



β2(1-217)
β2(1-217)


Tt W9N



β2(1-217)
β2(1-217)






I142Y
I142Y


Tt W9H


Tt N74E


Tt N74A


Tt N74H


Tt N74A-


Y140H


Tt I75F


His6


Tt F78Y-


Y140L


Tt F78Y-


Y140F


Tt P115A


Tt R135Q


His6


Tt Y140F


Tt Y140L


Tt Y140H


Tt Y140A


Tt L144F


His6









Modifications to H-NOX Proteins

Any of the wild-type or mutant H-NOX proteins can be modified and/or formulated using standard methods to enhance therapeutic or industrial applications. For example, and particularly as applied to heterologous engineered H-NOX proteins, a variety of methods are known in the art for insulating such agents from immune surveillance, including crosslinking, PEGylation, carbohydrate decoration, etc. (e.g., Rohlfs, R. J. et al. (May 15, 1998). “Arterial Blood Pressure Responses to Cell-Free Hemoglobin Solutions And The Reaction With Nitric Oxide,” J. Biol. Chem. 273(20):12128-12134; Migita, R. et al. (June 1997). “Blood Volume And Cardiac Index in Rats After Exchange Transfusion With Hemoglobin-Based Oxygen Carriers,” J. Appl. Physiol. 82(6):1995-2002; Vandegriff, K. D. et al. (Aug. 15, 2004). “Kinetics of NO and O2 Binding to a Maleimide Poly(ethylene glycol)-Conjugated Human Haemoglobin,” Biochem 382(Pt 1):183-189, which are each hereby incorporated by reference in their entireties, particularly with respect to the modification of proteins) as well as other techniques known to the skilled artisan. Fusing an H-NOX protein with a human protein such as human serum albumin can increase the serum half-life, viscosity, and colloidal oncotic pressure. In some embodiments, an H-NOX protein is modified during or after its synthesis to decrease its immunogenicity and/or to increase its plasma retention time. H-NOX proteins can also be encapsulated (such as encapsulation within liposomes or nanoparticles).
Characteristics of Wild-type and Mutant H-NOX Proteins
As described herein, a large number of diverse H-NOX mutant proteins providing ranges of NO and O2 dissociation constants, O2 koff, NO reactivity, and stability have been generated. To provide operative blood gas carriers, the H-NOX proteins may be used to functionally replace or supplement endogenous O2 carriers, such as hemoglobin. Accordingly, in some embodiments, an H-NOX protein has a similar or improved O2 association rate, O2 dissociation rate, dissociation constant for O2 binding, NO stability, NO reactivity, autoxidation rate, plasma retention time, or any combination of two or more of the foregoing compared to an endogenous O2 carrier, such as hemoglobin.
As used herein, “hemoglobin” means a protein or a mutant thereof from the well-characterized family of hemoglobins, which are iron-containing O2-transport metalloproteins in red blood cells. Purified, stroma-free, human hemoglobin has a kinetic KD for O2 of about 200-500 nM. This value is subunit dependent.
As used herein, a “koff” means a dissociation rate, such as the rate of release of O2 or NO from a protein. A lower numerical lower koff indicates a slower rate of dissociation. In various embodiments, the koff for O2 for an H-NOX protein is between about 0.01 to about 200 s−1 at 20° C., such as about 0.1 to about 200 s−1, about 0.1 to 100 s−1, about 1.0 to about 16.0 s−1, about 1.35 to about 23.4 s−1, about 1.34 to about 18 s−1, about 1.35 to about 14.5 s−1, about 0.21 to about 23.4 s−1, about 1.35 to about 2.9 s−1, about 2 to about 3 s−1, about 5 to about 15 s−1, or about 0.1 to about 1 s−1. In some embodiments, the H-NOX protein has a koff for oxygen that is less than or equal to about 0.65 s−1 at 20° C. (such as between about 0.21 s−1 to about 0.65 s−1 at 20° C.).
By a “kon” is meant an association rate, such as the rate of binding of O2 or NO to a protein. A lower numerical lower kon indicates a slower rate of association. In various embodiments, the kon for O2 for an H-NOX protein is between about 0.14 to about 60 μM−1 s−1 at 20° C., such as about 6 to about 60 μM−1 s−1, about 6 to 12 μM−1 s−1, about 15 to about 60 μM−1 s−1, about 5 to about 18 μM−s−1, or about 6 to about 15 μM−1 s−1.
By “dissociation constant” is meant a “kinetic dissociation constant” or a “calculated dissociation constant.” A “kinetic dissociation constant” or “KD” means a ratio of kinetic off-rate (koff) to kinetic on-rate (kon), such as a KD value determined as an absolute value using standard methods (e.g., standard spectroscopic, stopped-flow, or flash-photolysis methods) including methods known to the skilled artisan and/or described herein. “Calculated dissociation constant” or “calculated KD” refers to an approximation of the kinetic dissociation constant based on a measured koff. A value for the kon is derived via the correlation between kinetic KD and koff as described herein.
In various embodiments, the kinetic or calculated KD for O2 binding by an H-NOX protein is between about 1 nM to 1 mM, such as about 2 nM to about 2 μM, about 2 μM to about 1 mM, about 100 nM to about 1 μM, about 9 μM to about 50 μM, about 100 μM to about 1 mM, about 50 nM to about 10 μM, about 2 nM to about 50 μM, about 100 nM to about 1.9 μM, about 150 nM to about 1 μM, or about 100 nM to about 255 nM, about 20 nM to about 2 μM, 20 nM to about 75 nM, about 1 μM to about 2 μM, about 2 μM to about 10 μM, about 2 μM to about 9 μM, or about 100 nM to 500 nM at 20° C. In some embodiments, the kinetic or calculated KD for O2 binding is less than about any of 100 nM, 80 nM, 50 nM, 30 nM, 25 nM, 20 nM, or 10 nM at 20° C.
In various embodiments, the kinetic or calculated KD for O2 binding by an H-NOX protein is within about 0.01 to about 100-fold of that of hemoglobin under the same conditions (such as at 20° C.), such as between about 0.1 to about 10-fold or between about 0.5 to about 2-fold of that of hemoglobin under the same conditions (such as at 20° C.). In various embodiments, the kinetic or calculated KD for NO binding by an H-NOX protein is within about 0.01 to about 100-fold of that of hemoglobin under the same conditions (such as at 20° C.), such as between about 0.1 to about 10-fold or between about 0.5 to about 2-fold of that of hemoglobin under the same conditions (such as at 20° C.).
As used herein, “oxygen affinity” is a qualitative term that refers to the strength of oxygen binding to the heme moiety of a protein. This affinity is affected by both the koff and kon for oxygen. A numerically lower oxygen KD value means a higher affinity. “NO affinity” is a qualitative term that refers to the strength of NO binding to a protein (such as binding to a heme group or to an oxygen bound to a heme group associated with a protein). This affinity is affected by both the koff and kon for NO. A numerically lower NO KD value means a higher affinity.
As used herein, “NO stability” refers to the stability or resistance of a protein to oxidation by NO in the presence of oxygen. For example, the ability of the protein to not be oxidized when bound to NO in the presence of oxygen is indicative of the protein's NO stability. In some embodiments, less than about any of 50, 40, 30, 10, or 5% of an H-NOX protein is oxidized after incubation for about any of 1, 2, 4, 6, 8, 10, 15, or 20 hours at 20° C.
As used herein, “NO reactivity” refers to the rate at which iron in the heme of a heme-binding protein is oxidized by NO in the presence of oxygen at a concentration of 2 μM protein. A lower numerical value for NO reactivity in units of s−1 indicates a lower NO reactivity. In various embodiments, the NO reactivity of an H-NOX protein is less than about 700 s−1 at 20° C., such as less than about 600 s−1, 500 s−1, 400 s−1, 300 s−1, 200 s−1, 100 s−1, 75 s−1, 50 s−1, 25 s−1, 20 s−1, 10 s−1, 50 s−1, 3 s−1, 2 s−1, 1.8 s−1, 1.5 s−1, 1.2 s−1, 1.0 s−1, 0.8 s−1, 0.7 s−1, or 0.6 s−1 at 20° C. In various embodiments, the NO reactivity of an H-NOX protein is between about 0.1 to about 600 s−1 at 20° C., such as between about 0.5 to about 400 s−1, about 0.5 to about 100 s−1, about 0.5 to about 50 s−1, about 0.5 to about 10 s−1, about 1 to about 5 s−1, or about 0.5 to about 2.1 s−1 at 20° C. In various embodiments, the reactivity of an H-NOX protein is at least about 10, 100, 1,000, or 10,000 fold lower than that of hemoglobin under the same conditions, such as at 20° C.
As used herein, an “autoxidation rate” refers to the rate at which iron in the heme of a heme-binding protein is autoxidized. A lower numerical autoxidation rate in units of indicates a lower autoxidation rate. In various embodiments, the rate of heme autoxidation of an H-NOX protein is less than about 1.0 h−1 at 37° C., such as less than about any of 0.9 h−1, 0.8 h−1, 0.7 h−1, 0.6 h−1, 0.5 h−1, 0.4 h−1, 0.3 h−1, 0.2 h−1, 0.1 h−1, or 0.05 h−1 at 37° C. In various embodiments, the rate of heme autoxidation of an H-NOX protein is between about 0.006 to about 5.0 h−1 at 37° C., such as about 0.006 to about 1.0 h−1, 0.006 to about 0.9 h−1, or about 0.06 to about 0.5 h−1 at 37° C.
In various embodiments, a mutant H-NOX protein has (a) an O2 or NO dissociation constant, association rate (kon for O2 or NO), or dissociation rate (koff for O2 or NO) within 2 orders of magnitude of that of hemoglobin, (b) has an NO affinity weaker (e.g., at least about 10-fold, 100-fold, or 1000-fold weaker) than that of sGC β1, respectively, (c) an NO reactivity with bound O2 at least 1000-fold less than hemoglobin, (d) an in vivo plasma retention time at least 2, 10, 100, or 1000-fold higher than that of hemoglobin, or (e) any combination of two or more of the foregoing.
Exemplary suitable O2 carriers provide dissociation constants within two orders of magnitude of that of hemoglobin, i.e. between about 0.01 and 100-fold, such as between about 0.1 and 10-fold, or between about 0.5 and 2-fold of that of hemoglobin. A variety of established techniques may be used to quantify dissociation constants, such as the techniques described herein (Boon, E. M. et al. (2005). “Molecular Basis For NO Selectivity in Soluble Guanylate Cyclase,” Nature Chem. Biol. 1:53-59; Boon, E. M. et al. (October 2005). “Ligand Discrimination in Soluble Guanylate Cyclase and the H-NOX Family of Heme Sensor Proteins,” Curr. Opin. Chem. Biol. 9(5):441-446; Boon, E. M. et al. (2005). “Ligand Specificity of H-NOX Domains: From sGC to Bacterial NO Sensors,” J. Inorg. Biochem. 99(4):892-902), Vandegriff, K. D. et al. (Aug. 15, 2004). “Kinetics of NO and O2 Binding to a Maleimide Poly(ethylene glycol)-Conjugated Human Haemoglobin,” Biochem J. 382(Pt 1):183-189, which are each hereby incorporated by reference in their entireties, particularly with respect to the measurement of dissociation constants), as well as those known to the skilled artisan. Exemplary O2 carriers provide low or minimized NO reactivity of the H-NOX protein with bound O2, such as an NO reactivity lower than that of hemoglobin. In some embodiments, the NO reactivity is much lower, such as at least about 10, 100, 1,000, or 10,000-fold lower than that of hemoglobin. A variety of established techniques may be used to quantify NO reactivity (Boon, E. M. et al. (2005). “Molecular Basis For NO Selectivity in Soluble Guanylate Cyclase,” Nature Chem. Biol. 1:53-59; Boon, E. M. et al. (October 2005). “Ligand Discrimination in Soluble Guanylate Cyclase and the H-NOX Family of Heme Sensor Proteins,” Curr. Opin. Chem. Biol. 9(5):441-446; Boon, E. M. et al. (2005). “Ligand Specificity of H-NOX Domains: From sGC to Bacterial NO Sensors,” J. Inorg. Biochem. 99(4):892-902), Vandegriff, K. D. et al. (Aug. 15, 2004). “Kinetics of NO and O2 Binding to a Maleimide Poly(ethylene glycol)-Conjugated Human Haemoglobin,”. Biochem J. 382(Pt 1):183-189, which are each hereby incorporated by reference in their entireties, particularly with respect to the measurement of NO reactivity) as well as those known to the skilled artisan. Because wild-type T. tengcongensis H-NOX has such a low NO reactivity, other wild-type H-NOX proteins and mutant H-NOX proteins may have a similar low NO reactivity. For example, T. tengcongensis H-NOX Y140H has an NO reactivity similar to that of wild-type T. tengcongensis H-NOX.
In addition, suitable O2 carriers provide high or maximized stability, particularly in vivo stability. A variety of stability metrics may be used, such as oxidative stability (e.g., stability to autoxidation or oxidation by NO), temperature stability, and in vivo stability. A variety of established techniques may be used to quantify stability, such as the techniques described herein (Boon, E. M. et al. (2005). “Molecular Basis For NO Selectivity in Soluble Guanylate Cyclase,” Nature Chem. Biol. 1:53-59; Boon, E. M. et al. (October 2005). “Ligand Discrimination in Soluble Guanylate Cyclase and the H-NOX Family of Heme Sensor Proteins,” Curr. Opin. Chem. Biol. 9(5):441-446; Boon, E. M. et al. (2005). “Ligand Specificity of H-NOX Domains: From sGC to Bacterial NO Sensors,” J. Inorg. Biochem. 99(4):892-902), as well as those known to the skilled artisan. For in vivo stability in plasma, blood, or tissue, exemplary metrics of stability include retention time, rate of clearance, and half-life. H-NOX proteins from thermophilic organisms are expected to be stable at high temperatures. In various embodiments, the plasma retention times are at least about 2-, 10-, 100-, or 1000-fold greater than that of hemoglobin (e.g. Bobofchak, K. M. et al. (August 2003). “A Recombinant Polymeric Hemoglobin With Conformational, Functional, And Physiological characteristics of an in vivo O2 transporter,” Am. J. Physiol. Heart Circ. Physiol. 285(2):H549-H561). As will be appreciated by the skilled artisan, hemoglobin-based blood substitutes are limited by the rapid clearance of cell-free hemoglobin from plasma due the presence of receptors for hemoglobin that remove cell-free hemoglobin from plasma. Since there are no receptors for H-NOX proteins in plasma, wild-type and mutant H-NOX proteins are expected to have a longer plasma retention time than that of hemoglobin. If desired, the plasma retention time can be increased by PEGylating or crosslinking an H-NOX protein or fusing an H-NOX protein with another protein using standard methods (such as those described herein and those known to the skilled artisan).
In various embodiments, the H-NOX protein has an O2 dissociation constant between about 1 nM to about 1 mM at 20° C. and a NO reactivity at least about 10-fold lower than that of hemoglobin under the same conditions, such as at 20° C. In some embodiments, the H-NOX protein has an O2 dissociation constant between about 1 nM to about 1 mM at 20° C. and a NO reactivity less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.). In some embodiments, the H-NOX protein has an O2 dissociation constant within 2 orders of magnitude of that of hemoglobin and a NO reactivity at least about 10-fold lower than that of hemoglobin under the same conditions, such as at 20° C. In some embodiments, the H-NOX protein has a koff for oxygen between about 0.01 to about 200 s−1 at 20° C. and an NO reactivity at least about 10-fold lower than that of hemoglobin under the same conditions, such as at 20° C. In some embodiments, the H-NOX protein has a koff for oxygen that is less than about 0.65 s−1 at 20° C. (such as between about 0.21 s−1 to about 0.64 s−1 at 20° C.) and a NO reactivity at least about 10-fold lower than that of hemoglobin under the same conditions, such as at 20° C. In particular embodiments, the O2 dissociation constant of the H-NOX protein is between about 2 nM to about 50 μM, about 50 nM to about 10 μM, about 100 nM to about 1.9 μM, about 150 nM to about 1 μM, or about 100 nM to about 255 nM at 20° C. In various embodiments, the O2 dissociation constant of the H-NOX protein is less than about 80 nM at 20° C., such as between about 20 nM to about 75 nM at 20° C. In some embodiments, the NO reactivity of the H-NOX protein is at least about 100-fold lower or about 1,000 fold lower than that of hemoglobin, under the same conditions, such as at 20° C. In some embodiments, the NO reactivity of the H-NOX protein is less than about 700 s−1 at 20° C., such as Less than about 600 s−1, 500 s−1, 400 s−1, 300 s−1, 200 s−1, 100 s−1, 75 s−1, 50 s−1, 25 s−1, 20 s−1, 10 s−1, 50 s−1, 3 s−1, 2 s−1, 1.8 s−1, 1.5 s−1, 1.2 s−1, 1.0 s−1, 0.8 s−1, 0.7 s−1, or 0.6 s−1 at 20° C. In some embodiments, the koff for oxygen of the H-NOX protein is between 0.01 to 200 s−1 at 20° C., such as about 0.1 to about 200 s−1, about 0.1 to 100 s−1, about 1.35 to about 23.4 s−1, about 134 to about 18 s−1, about 1.35 to about 14.5 s−1, about 0.21 to about 23.4 s−1, about 2 to about 3 s−1, about 5 to about 15 s−1, or about 0.1 to about 1 s−1. In some embodiments, the O2 dissociation constant of the H-NOX protein is between about 100 nM to about 1.9 μM at 20° C., and the koff for oxygen of the H-NOX protein is between about 1.35 s−1 to about 14.5 s−1 at 20° C. In some embodiments, the rate of heme autoxidation of the H-NOX protein is less than about 1 h−1 at 37° C., such as less than about any of 0.9 h−1, 0.8 s−1,0.7 h−1, 0.6 h−1, 0.5 h−1, 0.4 h−1, 0.3 h−1, 0.2 h−1, or 0.1 s−1. In some embodiments, the koff for oxygen of the H-NOX protein is between about 1.35 s−1 to about 14.5 s−1 at 20° C., and the rate of heme autoxidation of the H-NOX protein is less than about 1 h−1 at 37° C. In some embodiments, the koff for oxygen of the H-NOX protein is between about 1.35 s−1 to about 14.5 s−1 at 20° C., and the NO reactivity of the H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 s−1, or 1.8 s−1 at 20° C.). In some embodiments, the rate of heme autoxidation of the H-NOX protein is less than about 1 h−1 at 37° C., and the NO reactivity of the H-NOX protein is less than about 700 s−1 at 20° C. (e.g., less than about 600 s−1, 500 s−1, 100 s−1, 20 or 1.8 s−1 at 20° C.).
In some embodiments, the viscosity of the H-NOX protein solution is between 1 and 4 centipoise (cP). In some embodiments, the colloid oncotic pressure of the H-NOX protein solution is between 20 and 50 mm Hg.
Table 3 lists exemplary sizes, oxygen affinities, autoxidation stabilities, NO reactivity rates, and modifications for wild-type and mutant H-NOX proteins. In Table 3, the vehicle size refers to the molecular weight of a modified (e.g., PEGylated) or unmodified H-NOX protein.







TABLE 3







Exemplary Embodiments for H—NOX proteins













Stability
NO reactivity
Particle


Vehicle size
Oxygen Affinity
(autoxidation)
(s−1)
decoration





>1 MD
<1 nM
1 hour
0.01 to 0.1 
Cross-liking


 0.5 kD to 1 MD
 1 nM to 100 nM
 1 h to 12 h
0.1 to 1  
PEGylation


 0.1 kD to 0.5 kD
100 nM to 1 uM
12 h to 48 h
1 to 10
Encapsulation


0.01 kD to 0.1 kD
 1 uM to 10 uM
48 h to 2 weeks
10 to 100









Exemplary data for particular mutants are reported in Tables 4-12. In Tables 4-12, β1 and B2 refer to proteins derived from rat H-NOX proteins. Since the amino acid sequences of mammalian β1 H-NOX domains differ by at most two amino acids, similar results are expected for the corresponding mutations in other mammalian β1 H-NOX proteins, such as human β1. As shown in Table 4, introducing one or more mutations into wild-type H-NOX proteins allows the autoxidation rate and O2 dissociation rate to be altered. If desired, the autoxidation rate or O2 dissociation rate can be further altered by combining any of the single or double mutations listed in Table 4 or by introducing one or more additional mutations into an H-NOX protein, as described herein.







TABLE 4







Stability to autoxidation, O2-binding properties (such as rate of


O2 dissociation) and distal pocket H-bonding residues are listed


for wild-type and class II mutant H—NOX proteins










Protein
Stability
O2-binding activityb
Distal pocket residues










Tt H—NOX, a prokaryotic H—NOX and a strong O2 binder










Tt H—NOX
kox ~0c
koff = 1.22
Trp9, Phe78, Tyr140


Tt Y140F
kox = 0.05
koff = 15.7d
Trp9, Phe78, Phe140


Tt Y140L
kox = 0.19
koff = 20.d
Trp9, Phe78, Leu140


Tt Y140H
kox = 0.87
koff = 5.03
Trp9, Phe78, His140


Tt Y140A
Stablea
Partial complexd,e
Trp9, Phe78, Ala140


Tt W9F
kox ~0c
koff = 1.84
Phe9, Phe78, Tyr140


Tt W9F-Y140L
kox = 0.12
No complex formed
Phe9, Phe78, Leu140


Tt W9F-Y140H
kox = 0.11
koff = 23.4
Phe9, Phe78, His140


Tt F78Y-Y140L
kox ~0c
koff = 0.83
Trp9, Tyr78, Leu140


Tt F78Y-Y140F
kox ~0c
koff = 1.48
Trp9, Tyr78, Phe140







Prokaryotic H—NOX proteins for which the wild-type protein does not bind O2










L2 H—NOX
Stablea
No complex formed
Phe9, Phe78, Phe142


L2 F142Y
Stablef
koff = 3.68
Phe9, Phe78, Tyr142


L2 F9W-F142Y
Stablef
Binds O2e
Trp9, Phe78, Tyr142


L1 H—NOX
kox = 0.31
No complex formed
Leu9, Leu78, Phe142


L1 F142Y
kox = 1.8
koff = 1.73d
Leu9, Leu78, Tyr142







Eukaryotic H—NOX for which the wild-type protein does not bind O2










β2(1-217)
kox = 0.18
No complex formed
Leu9, Cys76, Ile142


β2(1-217) I142Y

g
Leu9, Cys76, Tyr142


β1(1-194)
kox = 4.3
No complex formed
Leu9, Cys78, Ile145


β1(1-194) I145Y
kox = 2.8
g
Leu9, Cys78, Tyr145


β1(1-194) L9W-I145Y
kox ~10
g
Trp9, Cys78, Tyr145


β1(1-385)
Stablee
No complex found
Leu9, Cys78, Ile145


β1(1-385) I145Y
kox = 0.72
koff = 2.69
Leu9, Cys78, Tyr145


β1(1-385) I145H


Leu9, Cys78, His145


β1(1-385) C78Y


Leu9, Tyr78, Ile145







Other H—NOX predicted to bind O2 as the wild-type construct










Dd H—NOX(728-899)
kox = 0.98
koff = 5.80
Phe9, Phe75, Tyr139


Dd Y139L


Phe9, Phe75, Leu139


Cb H—NOX(1-175)
Not stable
g
Trp9, Phe78, Tyr140



constructh


Cb H—NOX(1-186)
Slightly more
g
Trp9, Phe78, Tyr140



stablei


Ca H—NOX(1-197)
Not stable
g
Trp9, Phe78, Tyr140



constructh


Ca H—NOX(1-183)
Slightly more
g
Trp9, Phe78, Tyr140



stablei


Ce GCY-35(1-252)
Stable
Binds O2e
Phe9, Thr78, Tyr144





aThe construct is stable to oxidation (evaluated by the rate of autoxidation, kox [h−1] at 37° C.) and/or heme loss.


bO2-binding activity was evaluated by the rate of O2 dissociation from the heme at 20° C. (s−1).


cAfter 24 hours at 37° C., there is still no indication of autoxidation.


dOnly a small portion of the protein forms a complex with O2, the rate reported represents the kinetics for this population.


eThe protein binds O2 but the koff was not determined.


fAlthough relatively stable, this protein precipitated as it oxidized, making it difficult to measure kox.


gNot applicable due to instability or rapid oxidation.


h“Not stable construct” means the protein oxidizes immediately under the conditions tested.


i“Slightly more stable” means the protein oxidizes over a period of minutes to hours, but does not remain stable beyond 24 hours under the conditions tested.






Table 5 illustrates the alteration of the O2 association rate (kon), O2 dissociation rate (koff), O2 dissociation constant (KD), and autoxidation rate (kox) in fl-NOX proteins by the introduction of one or more mutations. In some embodiments, any of the single or double mutations listed in Table 5 are combined with another mutation (such as another mutation in Table 5 or any other mutation described herein) to further alter the O2 association rate, O2 dissociation rate, O2 dissociation constant, autoxidation rate, or combinations of two or more of the foregoing.







TABLE 5







O2-binding kinetic constants for histidyl-ligated FeII heme proteins












Protein
KDa
konb
koffc
koxd
Ref.





Tt H—NOX
89.7 ± 6.2
13.6 ± 1.0
1.22 ± 0.09
e
i


Tt P115A
21.2 ± 2.1
10.4 ± 1.1
0.22 ± 0.01
e
j


Tt I5A
~80

0.82 ± 0.03
0.7
j


Tt I5L
~1000

9.50 ± 0.64
0.6
j


Tt I5L-
~30

0.28 ± 0.01
0.6
j


P115A


Tt W9F
305 ± 31
 6.02 ± 0.62
1.84 ± 0.17
e
i


Tt Y140F
f
15.7 ± 1.4
15.7 ± 9.8 
0.05
j


Tt Y140L
~2000
Geminal
20.1 ± 2.0 
0.19
i


Tt Y140H
~500

5.03 ± 0.69
0.87
j


Tt W9F-
~2500

23.4 ± 3.7 
0.11
j


Y140H










Tt W9F-
No complex with O2 observed
0.12
i


Y140L












Tt F78Y-
~150

1.48 ± 0.33
e
j


Y140F


Tt F78Y-
~80

0.83 ± 0.17
e
i


Y140L


Tt W9F-
Millimolar
very slow


j


N74A


Dd
Millimolar
very slow
7.13 ± 0.45
0.14
j


H—NOX










Dd Y139L
No complex with O2 observed

j












β1(1-385)
70,000,00
0.00004
2.69 ± 0.61
0.72
i


I145Y


L2 F142Y
 9200 ± 3000
 0.40 ± 0.14
3.68 ± 0.71

i


Hs Hb beta
267
60
16

n


Hs Hb alpha
560
50
28

k


Sw Mb
880
17
15
0.006
k


Bj FixL
140,000
0.14
20
2.7
l


HemAT-B
720
32
23
0.06
m





adissociation constant at 20° C. (nM);


brate of O2 association to the heme at 20° C. (μM−1s−1);


crate of O2 dissociation from the heme at 20° C. (s−1);


drate of heme autoxidation (h−1) at 37° C.;


eafter 24 hours at 37° C., still no indication of autoxidation;


fonly a small portion of the protein forms a complex with O2, although the kinetics for this population could be measured;


iBoon, E. M. et al. (June 2005). “Molecular Basis For NO Selectivity in Soluble Guanylate Cyclase,” Nature Chemical Biology 1(1): 53-59,


junpublished data;


kSpringer, B. A. et al. (1994) “Family Physicians Key Partners in Preventing Suicide Among Youth,” Chem. Rev. 94: 699-714;


lGilles-Gonzalez et al. (1994) “Heme-Based Sensors, Exemplified by the Kinase FixL, are a New Class of Heme Protein with Distinctive Ligand Binding and Autoxidation,” Biochemistry 33: 8067-8073.


mAono, S. et al. (2002) “Resonance Raman and Ligand Binding Studies of the Oxygen-Sensing Signal Transducer Protein HemAT from Bacillus Subtilis,” J. Biol. Chem. 277: 13528-13538.


nAntonini, E. et al. (1971). “Hemoglobin and Myoglobin in Their Reactions with Ligands,” North-Holland Publ., Amsterdam.






Table 6 illustrates that the O2 association rate, O2 dissociation rate, O2, autoxidation rate, NO reactivity, and stability of FeII—O2 complexes in H-NOX proteins may be altered by the introduction of one or more mutations. In some embodiments, any of the single or double mutations listed in Table 6 are combined with another mutation (such as another mutation in Table 6 or any other mutation described herein) to further alter the O2 association rate, O2 dissociation rate, O2, autoxidation rate, NO reactivity, or stability of FeII—O2 complexes in an H-NOX protein. As will be appreciated by the skilled artisan, introduction of one or more additional mutations, such as those described herein, may be used to further alter these values.







TABLE 6







O2 association rate, O2 dissociation rate, O2, autoxidation rate,


NO reactivity, and stability of FeII—O2 complexes in H—NOX proteins.

















stability of FeII—O2


Protein
kona
Koffb
koxc
NO reactivityd
complex
















Hs Hb
23
11
0.006
<0.001
s
oxidizes o/n in air at RT,






(~7,000
s−1)e
stable at 4° C. in air,








stable anaerobic


Tt H—NOX
13.6
1.22
Very
0.54 ± 0.07
s−1
Always stable





slow


Tt Y140H
~10
5.03
0.87
1.7 ± 0.4
s−1
oxidizes o/n in air at RT,








stable at 4° C. in air,








stable anaerobic












β1(1-385)
~105
2.69
0.72
slow to FeIII—NO
oxidizes o/n in air at RT,


I145Y




stable at 4° C. in air,







stable anaerobic





arate of O2 association to the heme at 20° C. (μM−1s−1);


brate of O2 dissociation from the heme at 20° C. (s−1);


crate of heme autoxidation (h−1) at 37° C.;


dFor determination of NO reactivities: purified proteins (Tt WT HNOX, Tt Y140H HNOX, Homo sapiens hemoglobin (Hs Hb)) were prepared at 2 μM in buffer A and nitric oxide (NO) was prepared at 200 μM in Buffer A (Buffer A: 50 mM Hepes, pH 7.5, 50 mM NaCl) at 20° C. Using stopped flow spectroscopy, the protein was rapidly mixed with NO in a 1:1 ratio with an integration time of 0.00125 seconds. The wavelengths of maximum change were fit to a single exponential, essentially measuring the rate-limiting step of oxidation by NO. The end products of the reaction were ferric-NO for the HNOX proteins and ferric-aquo for Hs Hb.


eFor Hs Hb, the reaction of the protein with NO was so fast that the reaction was completed within the dead time of the experiment (0.001 seconds). The NO reactivity for hemoglobin is approximately 7,000 s−1 at 20° C. based on Eich, R. F. et al. (1996) “Mechanism of NO-Induced Oxidation of Myoglobin and Hemoglobin,” Biochemistry 35: 6976-6983.






Table 7 demonstrates that the dissociation constant for O2 binding can be significantly changed by mutating one or more residues in H-NOX proteins. The kinetic KD values for these exemplary H-NOX proteins range from 21.20 nM to 1000000.00 nM at 20° C. If desired, the dissociation constant for O2 binding can be further altered by combining any of the single or double mutations listed in Table 7 or by introducing one or more additional mutations into an H-NOX protein, as described herein.







TABLE 7







Wild-type and mutant H—NOX proteins and reference proteins


arranged by the value of the dissociation constant for O2 binding













Kinetic KD

Calculated KD



Protein
(nM)
±
(nM)
















Tt P115A
21.2
2.1




Tt N74H


27



Tt I5L-P115A


30



Tt N74A


32



Tt I5A


80



Tt F78Y-Y140L


80



Tt H—NOX His6


89



Tt H—NOX
89.7
6.2



Tt wt


90



Tt F78Y-Y140F


150



Tt W9Y


218



Tt R135Q His6


252



Hs Hb beta


267



Tt W9F
305
31



Tt W9H


456



Tt Y140H


500



Hs Hb alpha


560



Tt W9N


573



Tt I75F-His6


713-773



HemAT-B


720



Sw Mb


880



Tt I5L


1000



Tt L144F-His6


1092-1185



Tt Y140L


2000



Tt W9F-Y140H


2500



L2 F142Y
9200
3000



Bj FixL


140000



Tt W9F-N74A


1000000



Dd H—NOX


1000000



β1(1-385) I145Y


1000000










Table 8 demonstrates that the dissociation rates for O2 binding can be significantly changed by mutating one or more residues in H-NOX proteins. The dissociation rates for these exemplary H-NOX proteins range from 0.21 s−1 to 23.4 s−1 at 20° C. If desired, the dissociation rate for O2 binding can be further altered by combining any of the single or double mutations listed in Table 8 or by introducing one or more additional mutations into an H-NOX protein, as described herein.







TABLE 8







Wild-type and mutant H—NOX proteins and reference proteins


arranged by the value of the dissociation rate for O2 binding











Protein
koff (s−1)
±















Tt N74A
0.21
0.004



Tt P115A
0.22
0.01



Tt I5L-P115A
0.28
0.03



Tt N74E
0.38
0.01



Tt N74H
0.44
0.01



Tt I5A
0.82
0.03



Tt F78Y-
0.83
0.17



Y140L



Tt H—NOX His6
1.2
0.02



Tt H—NOX
1.22
0.09



Tt F78Y-Y140F
1.48
0.33



L1 F142Y
1.73



Tt W9F
1.84
0.17



β1(1-385)
2.69
0.61



I145Y



Tt W9Y
3.07
0.1



Tt R135Q His6
3.56
0.08



L2 F142Y
3.68
0.71



Tt Y140H
5.03
0.69



Tt W9H
6.42
0.11



Dd H—NOX
7.13
0.45



Tt W9N
8.09
0.14



Tt I5L
9.5
0.64



Tt I75F-His6
10.48
0.12



Sw Mb
15



Tt Y140F
15.7
9.8



Hs Hb beta
16



Tt L144F-His6
16.06
0.21



Bj FixL
20



Tt Y140L
20.1
2



HemAT-B
23



Tt W9F-Y140H
23.4
3.7



Hs Hb alpha
28










Table 9 demonstrates that the association rates for O2 binding can be significantly changed by mutating one or more residues in H-NOX proteins. The association rates for these exemplary H-NOX proteins range from 60 μM−1 s−1 to 0.14 μM−1 s−1 at 20° C. If desired, the association rate for O2 binding can be further altered by combining any of the single or double mutations listed in Table 9 or by introducing one or more additional mutations into an H-NOX protein, as described herein.







TABLE 9







Wild-type and mutant H—NOX proteins and reference proteins


arranged by the value of the association rate for O2 binding











Protein
kon (μM−1s−1)
±















Hs Hb beta
60




Hs Hb alpha
50



HemAT-B
32



Sw Mb
17



Tt Y140F
15.7
1.4



Tt H—NOX
13.6
1



Tt P115A
10.4
1.1



Tt W9F
6.02
0.62



L2 F142Y
0.4
0.14



Bj FixL
0.14



Tt W9F-N74A
very slowa



Dd H—NOX
very slowa



β1(1-385) I145Y
very slowa







aBy “very slow” is meant slower than hemoglobin, such as approximately one to two orders of magnitude slower than hemoglobin.






Table 10 illustrates the effect of exemplary H-NOX mutations on O2 and NO-binding. Each number listed in Table 10 for the Fe-unligated form is for a single peak (which is listed in between the p and a columns). When O2 or NO binds, this single peak splits into two peaks, β and α (which are listed below the β and a columns, respectively). If desired, O2 or NO-binding can be further altered by combining any of the single or double mutations listed in Table 10 or by introducing one or more additional mutations into an H-NOX protein, as described herein.







TABLE 10







UV-visible peak positionsa for some histidyl-ligated


FeII heme protein complexes












Protein
Soret
β
α











FeII unligated complex












sGC
431
555




β1(1-385) I145Y
429
549



Tt H—NOX
431
565



Tt W9F-Y140L
430
560



Vc H—NOX
429
568



Np H—NOX
430
555



L2 H—NOX
428
557



L2 F142Y
428
557



Tt I75F-His6
431
569



Tt L144F-His6
433
564



Hb
430
555







FeII—NO complex












sGC
398
537
572



β1(1-385) I145Y
399/416
542
574



Tt H—NOX
420
547
575



Tt W9F-Y140L
423
540
573



Vc H—NOX
398
540
573



Np H—NOX
416/400
543
576



L2 H—NOX
399/416
544
575



L2 F142Y
417
544
578



Tt I75F-His6
418
545
574



Tt L144F-His6
416
544
574



Hb
418
545
575







FeII—O2 complex











sGC
No complex observed













β1(1-385) I145Y
416
541
575



Tt H—NOX
416
556
591











Tt W9F-Y140L
No complex observed




Vc H—NOX
No complex observed



Np H—NOX
No complex observed



L2 H—NOX
No complex observed












L2 F142Y
417
542
577



Tt I75F-His6
416
552
589



Tt L144F-His6
416
544
574



Hb
415
541
577







anm (at 20° C.)






Table 11 contains UV-visible peak positions for some Fe(II), Fe(III), Fe(II)-NO, and Fe(II)-O2 complexes. When a hemoglobin or H-NOX protein is anaerobic, it has a Soret peak at 431 nm, and it is in an unligated state. If the H-NOX protein does not bind O2, then the Soret peak will not change when O2 is added. If the H-NOX protein does bind O2, then its Soret peak will shift to between 414 nm and 418 nm when O2 is added, which is the same shift that occurs in hemoglobin, indicative of O2 bound to the heme. Soret peaks for oxidized H-NOX (Fe(III)) or H-NOX bound to NO in a 6 coordinate state may be relevant to the state of the H-NOX protein after storage or use. If the H-NOX protein does not bind NO, then the Soret peak will not change when NO is added. If the H-NOX protein binds NO and forms a 6-coordinate ferrous-nitrosyl complex, then its Soret peak will shift to between 420 nm and 424 nm when NO is added. If the H-NOX protein binds NO and forms a 5-coordinate ferrous-nitrosyl complex, the Soret peak will shift to 399 nm. If desired, O2 or NO-binding can be further altered by combining any of the single or double mutations listed in Table 11 or by introducing one or more additional mutations into an H-NOX protein, as described herein.







TABLE 11







UV-visible peak positions for some Fe (II), Fe (III),


Fe(II)—NO, and Fe(II)—O2 complexes.













Complex
Protein
Soret

α










β




Fe (II)
Tt wt
430
563




Tt W9Y
430
569




Tt N74A
433
558




Tt N74H
431
561




Tt N74A-Y140H
430
567




Tt W9H
431
563




Tt N74E
433
559




Tt W9N
431
569




Tt wt His6
430
565






βa



Fe (III)
Tt wt
413
550
585




Tt W9Y
409
N.A.




Tt N74A
416
554
586




Tt N74H
408
N.A.




Tt N74A-Y140H
407
N.A.




Tt W9H
407
N.A.




Tt N74E
408
N.A.




Tt W9N
408
N.A.




Tt wt His6
413
550
586






β



Fe(II)—NO
Tt wt
420
550
578




Tt W9Y
420
552
576




Tt N74A
421
572




Tt N74H
424
562




Tt N74A-Y140H
421
549
576




Tt W9H
420
548
575




Tt N74E
422
544
571




Tt W9N
421
541
576




Tt wt His6
420
547
576



Fe(II)—O2
Tt wt
416
556
591




Tt W9Y
416
555
590




Tt N74A
418
553
589




Tt N74H
418
553
589




Tt N74A-Y140H
414
555
584




Tt W9H
418
556
589




Tt N74E
417
555
587




Tt W9N
416
588
553




Tt wt His6
416
556
591







a“N.A.” denotes nonassignable α and β bands due to low signal at longer wavelengths.






Table 12 contains autoxidation rates for exemplary T. tengcongensis H-NOX proteins. If desired, the autoxidation rate can be further altered by combining any the mutations listed in Table 12 or by introducing one or more additional mutations into an H-NOX protein, as described herein. The 2 nm and 3 nm values mean in Table 12 refer to a shift in the UV-V is Soret peak by 2 to 3 nm over the time period of the observation; this extremely small change may be due to autoxidation.







TABLE 12







Autoxidation rates for T. tengcongensis (Tt) H—NOX proteins











Autoxidation Rate



Protein
(25° C., hr−1)a







Tt wt
Stable



Tt W9Y
Stable



Tt N74A
Stable



Tt N74H
stable at 4° C., very




slow at RT (2 nm)



Tt W9H
Stable



Tt N74E
very slow at 4° C.




(2 nm), slow at RT



Tt W9N
stable at 4° C., very




slow at RT (3 nm)



Tt wt His6
Stable



Tt I75F-His6
Stable



Tt L144F-His6
Stable







a“Stable” denotes lack of heme oxidation after at least 24 hours.



“RT” denotes room temperature.






H-NOX Nucleic Acids

The invention also features nucleic acids encoding any of the mutant H-NOX proteins described herein. As used herein, a “nucleic acid” refers to two or more deoxyribonucleotides and/or ribonucleotides in either single or double-stranded form, and unless otherwise limited, encompasses known analogs of naturally-occurring nucleotides that hybridize to nucleic acids in a manner similar to nucleotides occurring in nature. In some embodiments, the nucleic acid is a recombinant nucleic acid. By “recombinant nucleic acid” means a nucleic acid of interest that is free of one or more nucleic acids (e.g., genes) which, in the genome occurring in nature of the organism from which the nucleic acid of interest is derived, flank the nucleic acid of interest. In some embodiments, an H-NOX nucleic acid is operably linked to another nucleic acid encoding all or a portion of another protein such that the recombinant nucleic acid encodes a fusion protein that includes an H-NOX protein (e.g., an H-NOX domain with or without another domain from an H-NOX protein) and all or part of another protein, such as human serum albumin. The term therefore includes, for example, a recombinant DNA which is incorporated into a vector, into an autonomously replicating plasmid or virus, or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA, a genomic DNA fragment, or a cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences.
The invention also features vectors with one more nucleic acids encoding any of the mutant H-NOX proteins that are described herein. As used herein, a “vector” means a construct that is capable of delivering, and optionally expressing one or more nucleic acids of interest in a host cell. Examples of vectors include, but are not limited to, plasmids, viral vectors, DNA or RNA expression vectors, cosmids, and phage vectors. In some embodiments, the vector contains a nucleic acid under the control of an expression control sequence. An “expression control sequence” means a nucleic acid sequence that directs transcription of a nucleic acid of interest. An expression control sequence can be a promoter, such as a constitutive or an inducible promoter, or an enhancer. The expression control sequence is operably linked to the nucleic acid segment to be transcribed.
In particular embodiments, the nucleic acid includes a segment of or the entire nucleic acid sequence of any of the nucleic acids shown in FIGS. 2-4D or 8A-8DD. In some embodiments, the nucleic acid includes at least about 50, 100, 150, 200, 300, 400, 500, 600, 700, 800, or more contiguous nucleotides from a H-NOX nucleic acid and contains one or more mutations (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mutations) compared to the H-NOX nucleic acid from which it was derived. In various embodiments, a mutant H-NOX nucleic acid contains less than about 20, 15, 12, 10, 9, 8, 7, 6, 5, 4, 3, or 2 mutations compared to the H-NOX nucleic acid from which it was derived. The invention also features degenerate variants of any nucleic acid encoding a mutant H-NOX protein.
The invention also includes a cell or population of cells containing at least one nucleic acid encoding a mutant H-NOX protein described herein. Exemplary cells include insect, plant, yeast, bacterial, and mammalian cells. These cells are useful for the production of mutant H-NOX proteins using standard methods, such as those described herein.
Formulations of H-NOX Proteins
Any wild-type or mutant H-NOX protein described herein may be used for the formulation of pharmaceutical or non-pharmaceutical compositions. As discussed further below, these formulations are useful in a variety of therapeutic and industrial applications.
In some embodiments, the pharmaceutical composition includes one or more wild-type or mutant H-NOX proteins (such as any of the H-NOX wild-type or mutant proteins described herein) and a pharmaceutically acceptable carrier. In various embodiments, the H-NOX protein is an isolated or purified protein. By “pharmaceutically acceptable carrier” is meant any material which, when combined with an active ingredient, allows the ingredient to retain biological activity and does not provoke an unacceptable immune response (e.g., a severe allergy or anaphylactic shock) based on the knowledge of a skilled practitioner. Examples include, but are not limited to, any of the standard pharmaceutical carriers such as phosphate buffered saline solutions, water, emulsions such as oil/water emulsion, and various types of wetting agents. Exemplary diluents for aerosol or parenteral administration are phosphate buffered saline or normal (0.9%) saline. Compositions comprising such carriers are formulated by well known conventional methods (see, for example, Remington's Pharmaceutical Sciences, 18th edition, A. Gennaro, ed., Mack Publishing Co., Easton, Pa., 1990; and Remington, The Science and Practice of Pharmacy 20th Ed. Mack Publishing, 2000, which are each hereby incorporated by reference in their entireties, particularly with respect to formulations).
While any suitable carrier known to those of ordinary skill in the art may be employed in the pharmaceutical compositions of this invention, the type of carrier will vary depending on the mode of administration. Compositions can be formulated for any appropriate manner of administration, including, for example, intravenous, intra-arterial, intravesicular, inhalation, intraperitoneal, intrapulmonary, intramuscular, subcutaneous, intra-tracheal, transmucosal, intraocular, intrathecal, or transdermal administration. For parenteral administration, such as subcutaneous injection, the carrier may include, e.g., water, saline, alcohol, a fat, a wax, or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, or magnesium carbonate, may be employed. Biodegradable microspheres (e.g., polylactate polyglycolate) may also be used as carriers.
In some embodiments, the pharmaceutical or non-pharmaceutical compositions include a buffer (e.g., neutral buffered saline, phosphate buffered saline, etc), a carbohydrate (e.g., glucose, mannose, sucrose, dextran, etc), an antioxidant, a chelating agent (e.g., EDTA, glutathione, etc.), a preservative, another compound useful for binding and/or transporting oxygen, an inactive ingredient (e.g., a stabilizer, filler, etc), or combinations of two or more of the foregoing. In some embodiments, the composition is formulated as a lyophilizate. H-NOX proteins may also be encapsulated within liposomes or nanoparticles using well known technology. Other exemplary formulations that can be used for H-NOX proteins are described by, e.g., U.S. Pat. Nos. 6,974,795, and 6,432,918, which are each hereby incorporated by reference in their entireties, particularly with respect to formulations of proteins.
The compositions described herein may be administered as part of a sustained release formulation (e.g., a formulation such as a capsule or sponge that produces a slow release of compound following administration). Such formulations may generally be prepared using well known technology and administered by, for example, oral, rectal or subcutaneous implantation, or by implantation at the desired target site. Sustained-release formulations may contain an H-NOX protein dispersed in a carrier matrix and/or contained within a reservoir surrounded by a rate controlling membrane. Carriers for use within such formulations are biocompatible, and may also be biodegradable. In some embodiments, the formulation provides a relatively constant level of H-NOX protein release. The amount of H-NOX protein contained within a sustained release formulation depends upon the site of implantation, the rate and expected duration of release, and the nature of the condition to be treated or prevented.
In some embodiments, the pharmaceutical composition contains an effective amount of a wild-type or mutant H-NOX protein. The term “effective amount” intends such amount of one or more proteins described herein which in combination with its parameters of efficacy and toxicity should be effective in a given therapeutic form based on the knowledge of the practicing specialist. As is understood in the art, an effective amount can be in one or more doses. As is understood in the clinical context, an effective dosage of a pharmaceutical composition may or may not be achieved in conjunction with another drug, compound, or pharmaceutical composition. Thus, an effective amount can be considered in the context of administering one or more therapeutic agents, and a single agent can be considered to be given in an effective amount if, in conjunction with one or more other agents, a desirable or beneficial result can be or is achieved.
An exemplary dose of hemoglobin as a blood substitute is from about 10 mg to about 5 grams or more of extracellular hemoglobin per kilogram of patient body weight. Thus, in some embodiments, an effective amount of an H-NOX protein for administration to a human is between a few grams to over about 350 grams. Other exemplary doses of an H-NOX protein include about any of 4.4, 5, 10, or 13 G/DL (where G/DL is the concentration of the H-NOX protein solution prior to infusion into the circulation) at an appropriate infusion rate, such as about 0.5 ml/min (see, for example, Winslow, R. Chapter 12 In Blood Substitutes). It will be appreciated that the unit content of active ingredients contained in an individual dose of each dosage form need not in itself constitute an effective amount since the necessary effective amount could be reached by the combined effect of a plurality of administrations. The selection of the amount of an H-NOX protein to include in a pharmaceutical composition depends upon the dosage form utilized, the condition being treated, and the particular purpose to be achieved according to the determination of the ordinarily skilled artisan in the field.
Exemplary compositions include genetically engineered, recombinant H-NOX proteins, which may be isolated or purified, comprising one or more mutations that collectively impart altered O2 or NO ligand-binding relative to the corresponding wild-type H-NOX protein, and operative as a physiologically compatible mammalian blood gas carrier. For example, mutant H-NOX proteins as described herein.
The invention also provides blood substitutes comprising or consisting essentially of one or more wild-type or mutant H-NOX proteins. Suitable buffers and other ingredients for formulating blood substitutes are known in the art.
To reduce or prevent an immune response in human subjects who are administered a pharmaceutical composition, human H-NOX proteins (either wild-type human proteins or human proteins into which one or more mutations have been introduced) or other non-antigenic H-NOX proteins (e. g., mammalian H-NOX proteins) can be used. To reduce or eliminate the immunogenicity of H-NOX proteins derived from sources other than humans, amino acids in an H-NOX protein can be mutated to the corresponding amino acids in a human H-NOX. For example, one or more amino acids on the surface of the tertiary structure of a non-human H-NOX protein can be mutated to the corresponding amino acid in a human H-NOX protein.
Therapeutic Applications of H-NOX Proteins
Any of the wild-type or mutant H-NOX proteins (e.g., isolated or purified H-NOX proteins) or pharmaceutical compositions described herein may be used in therapeutic applications. Particular H-NOX proteins can be selected for such applications based on the desired O2 association rate, O2 dissociation rate, dissociation constant for O2 binding, NO stability, NO reactivity, autoxidation rate, plasma retention time, or any combination of two or more of the foregoing for the particular indication being treated. H-NOX proteins can be used to treat cardiovascular disease, neurological disease, tumor hypoxia, loss of blood, or wounds. For example, an O2-binding H-NOX protein can be used in most situations where red blood cells or plasma expanders are currently utilized. Specifically, H-NOX protein can be used as red blood cell substitutes for the treatment of trauma (e.g., battlefield, disaster relief, or accidents), hemorrhages, hemorrhagic shock, surgery (e.g., abdominal aneurysm-surgery, orthopedic surgery such as hip replacement surgery, or any other surgery that produces high blood loss), hemodilution, blood extension uses (e.g., supplementing auto-donation), and any other situation where blood volume is lost or O2 carrying capacity is reduced. Examples of wound repair applications include post-radiation wound repair (e.g., hyperbaric oxygen effect), post-surgical repair, diabetic ulcer repair, and burn wounds.
An oxygen-binging H-NOX-can also be used to temporarily augment O2 delivery during or after pre-donation of autologous blood prior to the return of the autologous blood to the individual (such as a replacement for blood that is removed during surgical procedures where the individual's blood is removed and saved for reinfusion at the end of surgery or during recovery). In some embodiments, the H-NOX proteins also function as simple volume expanders that provide oncotic pressure due to the presence of the large H-NOX protein molecule.
Because the distribution in the vasculature of extracelluar H-NOX proteins is not limited by the size of the red blood cells, H-NOX proteins of the present invention can be used to deliver O2 to areas that red blood cells cannot penetrate. These areas can include any tissue areas that are located downstream of obstructions to red blood cell flow, such as areas downstream of one or more thrombi, sickle cell occlusions, arterial occlusions, peripheral vascular occlusions, angioplasty balloons, surgical instruments, tissues that are suffering from oxygen starvation or are hypoxic, and the like. Additionally, all types of tissue ischemia can be treated using H-NOX proteins. Such tissue ischemias include, for example, perioperative ischemia, stroke, emerging stroke, transient ischemic attacks, myocardial stunning and hibernation, acute or unstable angina, emerging angina, and myocardial infarction (e.g., ST-segment elevation myocardial infarction). Other exemplary cardiovascular indications that can be treated using H-NOX proteins include cardioplegia and sickle cell anemia. Exemplary target indications include conditions of functional hemoglobin deficiency, such as where a blood substitute or O2 carrier is indicated, including blood loss, hypoxia, etc.
H-NOX proteins can also be used as an adjunct with radiation or chemotherapy for the treatment of cancer. In some embodiments, an H-NOX protein is used as a radiation therapy adjuvant in solid tumors (e.g., individuals with poor pre-metastatic prognoses) or as a PDT therapy adjuvant in surface tumors (e.g., colon, lung, or skin cancer, or cancer in another accessible surface or location). H-NOX proteins can be used to treat anemia by providing additional oxygen-carrying capacity in a patient who is suffering from anemia. Exemplary neurological indications include ischemic stroke, traumatic brain injury, and spinal cord injury. The methods and compositions are applicable to both acute (providing rapid oxygen to tissues or a specific site, e.g. acute myocardial infarction, acute local or systemic tissue oxygenation, or blood transfusion), and chronic situations (e.g. post-acute recovery from cardiac infarction).
In various embodiments, the invention features a method of delivering O2 to an individual (e.g., a mammal, such as a primate (e.g., a human, a monkey, a gorilla, an ape, a lemur, etc), a bovine, an equine, a porcine, a canine, or a feline) by administering to an individual in need thereof a wild-type or mutant H-NOX protein in an amount sufficient to deliver O2 to the individual. In some embodiments, the invention provides methods of carrying or delivering blood gas to an individual such as a mammal, comprising the step of delivering (e.g., transfusing, etc) to the blood of the individual (e.g., a mammal) one or more of H-NOX compositions. Methods for delivering O2 carriers to blood or tissues (e.g., mammalian blood or tissues) are known in the art. In various embodiments, the H-NOX protein is an apoprotein that is capable of binding heme or is a holoprotein with heme bound. The H-NOX protein may or may not have heme bound prior to the administration of the H-NOX protein to the individual. In some embodiments, O2 is bound to the H-NOX protein before it is delivered to the individual. In other embodiments, O2 is not bound to the H-NOX protein prior to the administration of the protein to the individual, and the H-NOX protein transports O2 from one location in the individual to another location in the individual.
The methods of the present invention can be used to treat any individual. For use herein, unless clearly indicated otherwise, “an individual” as used herein intends a mammal, including but not limited to, a primate (e.g., a human, monkey, gorilla, ape, lemur, etc.), a bovine, an equine, a porcine, a canine, and a feline. Thus, the invention finds use in both human medicine and in the veterinary context, including use in agricultural animals and domestic pets. The individual may have been diagnosed with, is suspected of having, or is at risk of developing an indication, such as a cardiovascular disease, a neurological disease, hypoxia (e.g., tumor hypoxia), a loss of blood, or a wound. The individual may exhibit one or more symptoms associated with the indication. The individual can be genetically or otherwise predisposed to developing such a condition.
As used herein, “in need thereof” includes individuals who have a condition or disease (such as a cardiovascular disease, a neurological disease, hypoxia such as tumor hypoxia, a loss of blood, or a wound) or are “at risk” for the condition or disease. As used herein, an “at risk” individual is an individual who is at risk of development of a condition, such as a cardiovascular disease, a neurological disease, hypoxia (e.g., tumor hypoxia), a loss of blood, or a wound. An individual “at risk” may or may not have a detectable disease or condition, and may or may not have displayed detectable disease prior to the treatment methods described herein. “At risk” denotes that an individual has one or more so-called risk factors, which are measurable parameters that correlate with development of a disease or condition and are known in the art. An individual having one or more of these risk factors has a higher probability of developing the disease or condition than an individual without these risk factor(s). These risk factors include, but are not limited to, age, sex, race, diet, history of previous disease, presence of precursor disease, genetic (i.e., hereditary) considerations, and environmental exposure. Surgery, presence in or near a military or war zone, or conditions that predispose an individual to blood loss (such as hemophilia) are exemplary risk factors for blood loss.
These methods can be used to treat or delay any condition for which delivery of O2 is beneficial. By “treatment” or “treating” is meant an approach for obtaining a beneficial or desired result, including clinical results. For purposes of this invention, beneficial or desired results include, but are not limited to, alleviation of symptoms associated with a condition (such as, but not limited to, a cardiovascular disease, a neurological disease, hypoxia such as tumor hypoxia, a loss of blood, or a wound), diminishment of the extent of the symptoms associated with a condition, or prevention of a worsening of the symptoms associated with a condition. In some embodiments, treatment with a one or more proteins disclosed herein is accompanied by no or fewer side effects than are associated with currently available therapies.
As used herein, “delaying” development of a disease or condition means to defer, hinder, slow, retard, stabilize and/or postpone development of the disease or condition, such as a cardiovascular disease, a neurological disease, hypoxia (e.g., tumor hypoxia), a loss of blood, or a wound. This delay can be of varying lengths of time, depending on the history of the disease and/or individual being treated. As is evident to one skilled in the art, a sufficient or significant delay can, in effect, encompass prevention, in that the individual does not develop the disease or condition. For example, the method may reduce the probability of disease development in a given time frame and/or reduce the extent of the disease in a given time frame, when compared to not using the method. In some embodiments, such comparisons are based on clinical studies using a. statistically significant number of subjects. Disease development can be detectable using standard clinical techniques. Development may also refer to disease progression that can be initially undetectable and includes occurrence, recurrence, and onset.
Wild-type and mutant H-NOX proteins with a relatively low KD for O2 (such as less than about 80 nM or less than about 50 nM) are expected to be particularly useful to treat tissues with low oxygen tension (such as tumors, some wounds, or other areas where the oxygen tension is very low, such as a p50 below 1 mm Hg). The high affinity of such H-NOX proteins for O2 may increase the length of time the O2 remains bound to the H-NOX protein, thereby reducing the amount of O2 that is released before the H-NOX protein reaches the tissue to be treated.
While not intending to be bound by a particular theory, the utility of a cell-free red cell substitute as a resuscitation fluid is believed to be influenced by the p50 of the O2 carrier. For example, a PEGylated hemoglobin-based O2 carrier called MP4 appears to deliver O2 more effectively to the microvasculature than some lower affinity hemoglobin-based O2 carriers. MP4 is reported to have a p50 of  ̃5 mmHg, (perhaps 100 to 200 nm KD), and the p50 of stroma-free hemoglobin is 14 mm Hg ( ̃400 nm Kr)). Since MP4 is capable of oxygen delivery in tissues (PO2  ̃5 to 10 mm Hg), it is likely that the appropriate O2 affinity for vehicles to deliver O2 to hypoxic tissues is less than about 5 mm Hg, and perhaps less than about 2 mm Hg, which roughly corresponds to a KD less than about 80 nm. These values indicate that MP4 has been engineered with a higher O2 affinity (lower p50) than native hemoglobin. From an equilibrium perspective, this suggests that high-affinity O2-binding proteins may be more successful in delivering O2 to areas of low O2 tension, such as the peripheral vasculature.
In some embodiments for the direct delivery of an H-NOX protein with bound O2 to a particular site in the body (such as a tissue, organ, wound, or tumor), the koff for O2 is more important than the KD value because O2 is already bound to the protein (making the kon less important) and oxygen needs to be released at or near a particular site in the body (at a rate influenced by the koff). In some embodiments, the koff may also be important when H-NOX proteins are in the presence of red cells in the circulation, where they facilitate diffusion of O2 from red cells, and perhaps prolonging the ability of diluted red cells to transport O2 to further points in the vasculature.
In some embodiments for the delivery of an H-NOX protein that circulates in the bloodstream of an individual, the H-NOX protein binds O2 in the lungs and releases O2 at one or more other sites in the body. For some of these applications, the KD value is more important than the koff since O2 binding is at or near equilibrium. In some embodiments for extreme hemodilution, the KD more important than the koff when the H-NOX protein is the primary O2 carrier because the H-NOX protein will bind and release O2 continually as it travels through the circulation. Since hemoglobin has a p50 of 14 mm Hg, red cells (which act like capacitors) have a p50 of 30 mm Hg, and HBOCs have been developed with ranges between 5 mm Hg and 90 mm Hg, the optimal KD range for H-NOX proteins may therefore be between 2 mm Hg to 100 mm Hg for some applications.
H-NOX proteins can also be used for imaging. In particular, light imaging (e.g., optical coherence tomography; see, for example, Villard, J. W. (2002). “Use of a Blood Substitute to Determine Instantaneous Murine Right Ventricular Thickening with Optical Coherence Tomography,” Circulation 105:1843-1849, which is incorporated by reference in its entirety particularly with respect to optical coherence tomography) is obfuscated by erythrocytes. Perfusion with an H-NOX solution allows for clearer images of the circulation and vessel walls because the H-NOX protein is much smaller than erythrocytes.
H-NOX proteins and pharmaceutical compositions of the invention can be administered to an individual by any conventional means such as by oral, topical, intraocular, intrathecal, intrapulmonary, intra-tracheal, or aerosol administration; by transdermal or mucus membrane adsorption; or by injection (e.g., subcutaneous, intravenous, intra-arterial, intravesicular, or intramuscular injection). H-NOX proteins may also be included in large volume parenteral solutions for use as blood substitutes. In exemplary embodiments, the H-NOX protein is administered to the blood (e.g., administration to a blood vessel such as a vein, artery, or capillary), a wound, a tumor, a hypoxic tissue, or a hypoxic organ of the individual.
In some embodiments, a sustained continuous release formulation of the composition is used. Administration of an H-NOX protein can occur, e.g., for a period of seconds to hours depending on the purpose of the administration. For example, as a blood delivery vehicle, an exemplary time course of administration is as rapid as possible. Other exemplary time courses include about any of 10, 20, 30, 40, 60, 90, or 120 minutes. Exemplary infusion rates for H-NOX solutions as blood replacements are from about 30 mL/hour to about 13,260 mL/hour, such as about 100 mL/hour to about 3,000 mL/hour. An exemplary total dose of*H-NOX protein is about 900 mg/kg administered over 20 minutes at 13,260 mL/hour. An exemplary total dose of H-NOX protein for a swine is about 18.9 grams.
Exemplary dosing frequencies include, but are not limited to, at least 1, 2, 3, 4, 5, 6, or 7 times (i.e., daily) a week. In some embodiments, an H-NOX protein is administered at least 2, 3, 4, or 6 times a day. The H-NOX protein can be administered, e.g., over a period of a few days or weeks. In some embodiments, the H-NOX protein is administrated for a longer period, such as a few months or years. The dosing frequency of the composition may be adjusted over the course of the treatment based on the judgment of the administering physician.
As noted above, the selection of dosage amounts for H-NOX proteins depends upon the dosage form utilized, the frequency and number of administrations, the condition being treated, and the particular purpose to be achieved according to the determination of the ordinarily skilled artisan in the field. In some embodiments, an effective amount of an H-NOX protein for administration to human is between a few grams to over 350 grams.
In some embodiments, two or more different H-NOX proteins are administered simultaneously, sequentially, or concurrently. In some embodiments, another compound or therapy useful for the delivery of O2 is administered simultaneously, sequentially, or concurrently with the administration of one or more H-NOX proteins.
Other exemplary therapeutic applications for which H-NOX proteins can be used are described by, e.g., U.S. Pat. Nos. 6,974,795, and 6,432,918, which are each hereby incorporated by reference in their entireties, particularly with respect to therapeutic applications for O2 carriers.
Industrial Applications of H-NOX Proteins
The H-NOX proteins and composition described herein can also be used for a number of in vitro or industrial applications (see, e.g., U.S. Pat. No. 6,455,676, which is hereby incorporated by reference in its entirety, particularly with respect to in vitro or industrial applications). Particular H-NOX proteins can be selected for such applications based on the desired O2 association rate, O2 dissociation rate, dissociation constant for O2 binding, NO stability, NO reactivity, autoxidation rate, half-life, or any combination of two or more of the foregoing for the particular application. In various embodiments of industrial applications, the H-NOX protein is an apoprotein that is capable of binding heme or is a holoprotein with heme bound.
H-NOX proteins can be used, for example, as reference standards for analytical instrumentation needing such reference standards. The delivery of O2 by H-NOX proteins can be used for the enhancement of cell growth in cell culture by maintaining or increasing O2 levels in vitro. For these applications, H-NOX proteins can be added to a cell culture medium to deliver O2 to the medium (and to cells in the medium). In some embodiments, O2 is bound to the H-NOX protein before it is added to the cell culture medium. In other embodiments, O2 is not bound to the H-NOX protein prior to its addition to the cell culture medium, and the H-NOX protein transports O2 from one location in the medium to another location in the medium.
Alternatively, cells can be genetically modified to encode an H-NOX protein to increase the amount of O2 obtained by the cells. For example, cells that express a compound of interest (such as a small molecule or protein useful in pharmaceutical applications) can be genetically modified to also produce a H-NOX protein that facilitates growth of the cells, especially under low O2 conditions (Sullivan et al. (2006). “Targeted Oxygen Delivery within Hepatic Hollow Fiber Bioreactors via Supplementation of Hemoglobin-Based Oxygen Carriers,” Biotechnol. Prog. 22:1374-87; Frey et al. (2001). “Dissection of Central Carbon Metabolism of Hemoglobin-Expressing Escherichia Coli by 13C Nuclear Magnetic Resonance Flux distribution Analysis in Microaerobic Bioprocesses,” Applied and Environmental Biology 67(2):680-687). Moreover, the H-NOX proteins can be used to remove O2 from solutions requiring the removal of O2.
Kits with H-NOX Proteins
Also provided are articles of manufacture and kits that include any of the H-NOX proteins described herein and suitable packaging. In some embodiments, the invention includes a kit with (i) an H-NOX protein (such as a wild-type or mutant H-NOX protein described herein or formulations thereof as described herein) and (ii) instructions for using the kit to deliver O2 to an individual. In various embodiments, the invention features a kit with (i) an H-NOX protein (such as a wild-type or mutant H-NOX protein described herein or formulations thereof as described herein) and (ii) instructions for using the kit for any of the industrial uses described herein (e.g., use of an H-NOX protein as a reference standard for analytical instrumentation needing such a reference standard, enhancement of cell growth in cell culture by maintaining or increasing O2 levels in vitro, addition of O2 to a solution, or removal of O2 from a solution).
Suitable packaging for compositions described herein are known in the art, and include, for example, vials (e.g., sealed vials), vessels, ampules, bottles, jars, flexible packaging (e.g., sealed Mylar or plastic bags), and the like. These articles of manufacture may further be sterilized and/or sealed. Also provided are unit dosage forms comprising the compositions described herein. These unit dosage forms can be stored in a suitable packaging in single or multiple unit dosages and may also be further sterilized and sealed. Instructions supplied in the kits of the invention are typically written instructions on a label or package insert (e.g., a paper sheet included in the kit), but machine-readable instructions (e.g., instructions carried on a magnetic or optical storage disk) are also acceptable. The instructions relating to the use of H-NOX proteins generally include information as to dosage, dosing schedule, and route of administration for the intended treatment or industrial use. The kit may further comprise a description of selecting an individual suitable or treatment.
The containers may be unit doses, bulk packages (e.g., multi-dose packages) or sub-unit doses. For example, kits may also be provided that contain sufficient dosages of H-NOX proteins disclosed herein to provide effective treatment for an individual for an extended period, such as about any of a week, 2 weeks, 3 weeks, 4 weeks, 6 weeks, 8 weeks, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, or more. Kits may also include multiple unit doses of H-NOX proteins and instructions for use and packaged in quantities sufficient for storage and use in pharmacies, for example, hospital pharmacies and compounding pharmacies. In some embodiments, the kit includes a dry (e.g., lyophilized) composition that can be reconstituted, resuspended, or rehydrated to form generally a stable aqueous suspension of H-NOX protein.
Exemplary Methods for Production of H-NOX Proteins
The present invention also provides methods for the production of any of the mutant H-NOX proteins described herein. In some embodiments, the method involves culturing a cell that has a nucleic acid encoding a mutant H-NOX protein under conditions suitable for production of the mutant H-NOX protein. In various embodiments, the mutant H-NOX is also purified (such as purification of the H-NOX protein from the cells or the culture medium).
As noted above, the sequences of several wild-type H-NOX proteins and nucleic acids are known and can be use to generate mutant H-NOX proteins and nucleic acids of the present invention. Techniques for the mutation, expression, and purification of recombinant H-NOX proteins have been described by, e.g., Boon, E. M. et al. (2005). “Molecular Basis For NO Selectivity in Soluble Guanylate Cyclase,” Nature Chemical Biology 1:53-59 and Karow, D. S. et al. (Aug. 10, 2004). “Spectroscopic Characterization of The Soluble Guanylate Cyclase-Like Heme Domains From Vibrio Cholerae And Thermoanaerobacter Tengcongensis,” Biochemistry 43(31):10203-10211, which is hereby incorporated by reference in its entirety, particularly with respect to the mutation, expression, and purification of recombinant H-NOX proteins. These techniques or other standard techniques can be used to generate any mutant H-NOX protein.
In particular, mutant H-NOX proteins described herein can be generated a number of methods that are known in the art. Mutation can occur at either the amino acid level by chemical modification of an amino acid or at the codon level by alteration of the nucleotide sequence that codes for a given amino acid. Substitution of an amino acid at any given position in a protein can be achieved by altering the codon that codes for that amino acid. This can be accomplished by site-directed mutagenesis using, for example: (i) the Amersham technique (Amersham mutagenesis kit, Amersham, Inc., Cleveland, Ohio) based on the methods of Taylor, J. W. et al. (Dec. 20, 1985). “The Use of Phosphorothioate-Modified DNA in Restriction Enzyme Reactions to Prepare Nicked DNA,” Nucleic Acids Res. 13(24):8749-8764; Taylor, J. W. et al. (Dec. 20, 1985). “The Rapid Generation of Oligonucleotide-Directed Mutations at High Frequency Using Phosphorothioate-Modified DNA,” Nucleic Acids Res. 13(24):8765-8785; Nakamaye, K. L. et al. (Dec. 22, 1986). “Inhibition of Restriction Endonuclease Nci I Cleavage by Phosphorothioate Groups and its Application to Oligonucleotide-Directed Mutagenesis,” Nucleic Acids Res. 14(24):9679-9698; and Dente et al. (1985). in DNA Cloning, Glover, Ed., IRL Press, pages 791-802, (ii) the Promega kit (Promega Inc., Madison, Wis.), or (iii) the Biorad kit (Biorad Inc., Richmond, Calif.), based on the methods of Kunkel, T. A. (January 1985). “Rapid And Efficient Site-Specific Mutagenesis Without Phenotypic Selection,” Proc. Natl. Acad. Sci. USA 82(2):488-492; Kunkel, T. A. (1987). “Rapid And Efficient Site-Specific Mutagenesis Without Phenotypic, Selection,” Methods Enzymol. 154:367-382; Kunkel, U.S. Pat. No. 4,873,192, which are each hereby incorporated by reference in their entireties, particularly with respect to the mutagenesis of proteins. Mutagenesis can also be accomplished by other commercially available or non-commercial means, such as those that utilize site-directed mutagenesis with mutant oligonucleotides.
Site-directed mutagenesis can also be accomplished using PCR-based mutagenesis such as that described in Zhengbin et al. (1992). pages 205-207 in PCR Methods and Applications, Cold Spring Harbor Laboratory Press, New York; Jones, D. H. et al. (February 1990). “A Rapid Method For Site-Specific Mutagenesis And Directional Subcloning by Using the Polymerase Chain Reaction to Generate Recombinant Circles,” Biotechniques 8(2):178-183; Jones, D. H. et al. (January 1991). “A Rapid Method For Recombination And Site-Specific Mutagenesis by Placing Homologous Ends on DNA Using Polymerase Chain Reaction,” Biotechniques 10(1):62-66, which are each hereby incorporated by reference in their entireties, particularly with respect to the mutagenesis of proteins. Site-directed mutagenesis can also be accomplished using cassette mutagenesis with techniques that are known to those of skill in the art.
A mutant H-NOX nucleic acid can be incorporated into a vector, such as an expression vector, using standard techniques. For example, restriction enzymes can be used to cleave the mutant H-NOX nucleic acid and the vector. Then, the compatible ends of the cleaved mutant H-NOX nucleic acid and the cleaved vector can be ligated. The resulting vector can be inserted into a cell (e.g., an insect cell, a plant cell, a yeast cell, or a bacterial cell) using standard techniques (e.g., electroporation) for expression of the encoded H-NOX protein.
In particular, heterologous proteins have been expressed in a number of biological expression systems, such as insect cells, plant cells, yeast cells, and bacterial cells. Thus, any suitable biological protein expression system can be utilized to produce large quantities of recombinant H-NOX protein. In some embodiments, the H-NOX protein (e.g., a mutant or wild-type H-NOX protein) is an isolated protein. As used herein, an “isolated protein” means a protein separated from one or more components with which the protein is naturally associated in nature, including, for example, nucleic acids, lipids, and other proteins. An isolated protein also does not occur in a library of proteins, such as a library of 2, 5, 10, 20, 50 or more different proteins. An isolated protein can be obtained, for example, by expression of a recombinant nucleic acid encoding the protein or by chemical synthesis of the protein.
If desired, H-NOX proteins can be purified using standard techniques. As used herein, a “purified protein” means a protein (e.g., a mutant or wild-type H-NOX protein) that has been separated from one or more components that are present when the protein is produced. In some embodiments, the protein is at least about 60%, by weight, free from other components that are present when the protein is produced. In various embodiments, the protein is at least about 75%, 90%, or 99%, by weight, pure. A purified protein can be obtained, for example, by purification (e.g., extraction) from a natural source, a recombinant expression system, or a reaction mixture for chemical synthesis. Exemplary methods of purification include immunoprecipitation, column chromatography such as immunoaffinity chromatography, magnetic bead immunoaffinity purification, and panning with a plate-bound antibody, as well as other techniques known to the skilled artisan. Purity can be assayed by any appropriate method, e.g., by column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis. In some embodiments, the purified protein is incorporated into a pharmaceutical composition of the invention or used in a method of the invention. The pharmaceutical composition of the invention may have additives, carriers, or other components in addition to the purified protein.
EXAMPLES
The examples, which are intended to be purely exemplary of the invention and should therefore not be considered to limit the invention in any way, also describe and detail aspects and embodiments of the invention discussed above. The examples are not intended to represent that the experiments below are all or the only experiments performed. Unless indicated otherwise, temperature is in degrees Centigrade and pressure is at or near atmospheric.
Example 1
Production of Wild-Type and Mutant H-NOX Proteins
Wild-type and mutant H-NOX proteins were produced, expressed, and purified using standard methods, essentially as described by Boon, E. M. et al. (2005). “Molecular Basis For NO Selectivity in Soluble Guanylate Cyclase,” Nature Chemical Biology 1:53-59 and Karow, D. S. et al. (Aug. 10, 2004). “Spectroscopic Characterization of The Soluble Guanylate Cyclase-Like Herne Domains From Vibrio Cholerae And Thermoanaerobacter Tengcongensis,” Biochemistry 43(31):10203-10211, which are both hereby incorporated by reference in their entireties, particularly with respect to the mutagenesis, expression, and purification of H-NOX proteins. Mutagenesis was performed using the QuickChange® protocol from Strategene (La Jolla, Calif.). Expression of the proteins in cell culture and subsequent purification of the proteins was performed as described by Karow, D. S. et al. (Aug. 10, 2004). “Spectroscopic Characterization of The Soluble Guanylate Cyclase-Like Heme Domains From Vibrio Cholerae And Thermoanaerobacter Tengcongensis,” Biochemistry 43(31):10203-10211.
Example 2
Characterization of Mutant H-NOX Proteins as Oxygen Delivery Vehicles
Kinetic KD:: Ratio of koff to kon 
The kinetic KD value was determined for wild-type and mutant H-NOX proteins essentially as described by Boon, E. M. et al. (2005). “Molecular Basis For NO Selectivity in Soluble Guanylate Cyclase,” Nature Chemical Biology 1:53-59, which is hereby incorporated by reference in its entirety, particularly with respect to the measurement of O2 association rates, O2 dissociation rates, dissociation constants for O2 binding, autoxidation rates, and NO dissociation rates.
kon (O2 Association Rate)
O2 association to the heme was measured using flash photolysis at 20° C. It was not possible to flash off the FeII—O2 complex as a result of the very fast geminate recombination kinetics; thus, the FeII—CO complex was subjected to flash photolysis with laser light at 560 nm (Hewlett-Packard, Palo Alto, Calif.), producing the 5-coordinate FeII intermediate, to which the binding of molecular O2 was followed at various wavelengths. Protein samples were made by anaerobic reduction with 10 mM dithionite, followed by desalting on a PD-10 column (Millipore, Inc., Billerica, Mass.). The samples were then diluted to 20 μM heme in 50 mM TEA, 50 mM NaCl, pH 7.5 buffer in a controlled-atmosphere quartz cuvette, with a size of 100 μL to 1 mL and a path-length of 1-cm. CO gas was flowed over the headspace of this cuvette for 10 minutes to form the FeII—CO complex, the formation of which was verified by UV-visible spectroscopy (Soret maximum 423 nm). This sample was then either used to measure CO-rebinding kinetics after flash photolysis while still under 1 atmosphere of CO gas, or it was opened and stirred in air for 30 minutes to fully oxygenate the buffer before flash photolysis to watch O2-rebinding events. O2 association to the heme was monitored at multiple wavelengths versus time. These traces were fit with a single exponential using Igor Pro software (Wavemetrics, Inc., Oswego, Oreg.; latest 2005 version). This rate was independent of observation wavelength but dependent on O2 concentration. UV-visible spectroscopy was used throughout to confirm all the complexes and intermediates (Cary 3K, Varian, Inc. Palo Alto, Calif.). Transient absorption data were collected using instruments described in Dmochowski, I. J. et al. (Aug. 31, 2000). “Enantiomeric Discrimination of Ru-Substrates by Cytochrome P450cam,” Inorg Biochem. 81(3):221-228, which is hereby incorporated by reference in its entirety, particularly with respect to instrumentation. The instrument has a response time of 20 ns, and the data are digitized at 200 megasamples s−1.
koff (O2 Dissociation Rate)
To measure the koff, FeII—O2 complexes of protein (5 μM heme), diluted in anaerobic 50 mM TEA, 50 mM NaCl, pH 7.5 buffer, were rapidly mixed with an equal volume of the same buffer (anaerobic) containing various concentrations of dithionite and/or saturating CO gas. Data were acquired on a HI-TECH Scientific SF-61 stopped-flow spectrophotometer equipped with a Neslab RTE-100 constant-temperature bath set to 20° C. (TGK Scientific LTD., Bradford On Avon, United Kingdom). The dissociation of O2 from the heme was monitored as an increase in the absorbance at 437 nm, a maximum in the FeII—FeII—O2 difference spectrum, or 425 nm, a maximum in the FeII—FeII—CO difference spectrum. The final traces were fit to a single exponential using the software that is part of the instrument. Each experiment was done a minimum of six times, and the resulting rates were averaged. The dissociation rates measured are independent of dithionite concentration (100, 50, 25, 10, 5 and 2.5 mM dithionite were tested) and independent of saturating CO as a trap for the reduced species, both with and without 10 mM dithionite present.
Kinetic KD 
The kinetic KD is determined by calculating the ratio of koff to kon using the measurements of koff and kon described above.
Calculated KD 
To measure the calculated KD, the values for the koff and kinetic KD that were obtained as described above were graphed. A linear relationship between koff and kinetic KD was defined by the equation (y=mx+b). koff values were then interpolated along the line to derive the calculated KD using Excel: MAC 2004 (Microsoft, Redmond, Wash.). In the absence of a measured kon, this interpolation provides a way to relate koff to ICD.
Rate of Autoxidation
To measure the rate of autoxidation, the protein samples were anaerobically reduced, then diluted to 5 μM heme in aerobic 50 mM TEA, 50 mM NaCl, pH 7.5 buffer. These samples were then incubated in a Cary 3E spectrophotometer equipped with a Neslab RTE-100 constant-temperature bath set to 37° C. and scanned periodically (Cary 3E, Varian, Inc., Palo Alto, Calif.). The rate of autoxidation was determined from the difference between the maximum and minimum in the FeIII—FeII difference spectrum plotted versus time and fit with a single exponential using Excel: MAC 2004 (Microsoft, Redmond, Wash.).
Rate of Reaction with NO
NO reactivity was measured using purified proteins (Tt WT HNOX, Tt Y140H HNOX, and Homo sapiens hemoglobin (Hs Hb)) prepared at 2 μM in buffer A and NO prepared at 200 μM in Buffer A (Buffer A: 50 mM Hepes, pH 7.5, 50 mM NaCl). Data were acquired on a HI-TECH Scientific SF-61 stopped-flow spectrophotometer equipped with a Neslab RTE-100 constant-temperature bath set to 20° C. (TGK Scientific LTD., Bradford On Avon, United Kingdom). The protein was rapidly mixed with NO in a 1:1 ratio with an integration time of 0.00125 sec. The wavelengths of maximum change were fit to a single exponential using the software that is part of the spectrometer, essentially measuring the rate-limiting step of oxidation by NO. The end products of the reaction were ferric-NO for the HNOX proteins and ferric-aquo for Hs Hb.
p50 Measurements
If desired, the p50 value for mutant or wild-type H-NOX proteins can be measured as described by Guarnone, R. et al. (September/October 1995). “Performance Characteristics of Hemox-Analyzer For Assessment of The Hemoglobin Dissociation Curve,” Haematologica 80(5):426-430, which is hereby incorporated by reference in its entirety, particularly with respect to the measurement of p50 values. The p50 value is determined using a HemOx analyzer. The measurement chamber starts at 0% oxygen and slowly is raised, incrementally, towards 100% oxygen. An oxygen probe in the chamber measures the oxygen saturation %. A second probe (UV-V is light) measures two wavelengths of absorption, tuned to the alpha and beta peaks of the hemoprotein's (e.g., a protein such as H-NOX complexed with heme) UV-V is spectra. These absorption peaks increase linearly as hemoprotein binds oxygen. The percent change from unbound to 100% bound is then plotted against the % oxygen values to generate a curve. The p50 is the point on the curve where 50% of the hemoprotein is bound to oxygen.
Specifically, the Hemox-Analyzer (TCS Scientific Corporation, New Hope, Pa.) determines the oxyhemoprotein dissociation curve (ODC) by exposing 50 μL of blood or hemoprotein to an increasing partial pressure of oxygen and deoxygenating it with nitrogen gas. A Clark oxygen electrode detects the change in oxygen tension, which is recorded on the x-axis of an x-y recorder. The resulting increase in oxyhemoprotein fraction is simultaneously monitored by dual-wavelength spectrophotometry at 560 nm and 576 nm and displayed on the y-axis. Blood samples are taken from the antemedial vein, anticoagulated with heparin, and kept at 4° C. on wet ice until the assay. Fifty μL of whole blood are diluted in 5 μL of Hemox-solution, a manufacturer-provided buffer that keeps the pH of the solution at a value of 7.4±0.01. The sample-buffer is drawn into a cuvette that is part of the Hemox-Analyzer and the temperature of the mixture is equilibrated and brought to 37° C.; the sample is then oxygenated to 100% with air. After adjustment of the pO2 value the sample is deoxygenated with nitrogen; during the deoxygenation process the curve is recorded on graph paper. The P50 value is extrapolated on the x-axis as the point at which O2 saturation is 50% using the software that is part of the Hemox-Analyzer. The time required for a complete recording is approximately 30 minutes.
The p50 values for any of the H-NOX proteins can be compared to that of hemoglobin as an indication of the relative affinity of the H-NOX protein for O2 compared to that of hemoglobin. Table 13 lists previously reported p50 values for hemoglobin.







TABLE 13







Hemoglobin variants and their reported oxygen affinities













KD

Reference/


Name
Modification
(nM)
p50 (mmHg)
Manufacturer





Hemoglobin

~400
14



(stroma-free)


Hemoglobin


27


(RBC's)


Hemopure (HBOC-
Bovine

36
Biopure


201)
polymerized


Oxyglobin (HBOC-
Bovine

54
Biopure


301
polymerized


Hemospan (MP4)
Maleimide-

 5
Sangart



PEG


Polyheme
Pyridoxal

28-30
Northfield Labs


Hemolink
0-raffinose

40
Hemosol


Hemassist
Diaspirin

32
Baxter









Viscosity Measurements

If desired, the viscosity of the H-NOX solutions can be measured using a cone/plate rheometer (model DV-III, Brookfield; Middleboro, Mass.) with the CPE-40 cone spindle at a shear rate of 200/s. Solutions with viscosities between 1 and 4 centipoise (cP) administered in hemodilution oxygen delivery experiments are reported as safe (Winslow, R. M. et al. (October 2004). “Comparison of PEG-Modified Albumin And Hemoglobin in Extreme Hemodilution in the Rat,” J Appl Physiol. 97(4):1527-1534, U.S. Pat. Nos. 6,974,795, and 6,432,918, which are each hereby incorporated by reference in their entireties, particularly with respect to the measurement of viscosity). Accordingly, in some embodiments, the viscosity of the H-NOX protein solution is between 1 and 4 cP.
Colloid Oncotic Pressure Measurements
If desired, the colloid oncotic pressure can be measured using a colloid osmometer according to the manufacturer's instructions (model 4420, Wescor; Logan, Utah). Exemplary methods to measure colloid oncotic pressure are described in Vandegriff, K. D. et al. (November 1997). “Colloid Osmotic Properties of Modified Hemoglobins: Chemically Cross-Linked Versus Polyethylene Glycol Surface-Conjugated,” Biophys. Chem. 69(1):23-30, in the world-wide web at “anaesthesiamcq.com/FluidBook/f12_4.php;” U.S. Pat. Nos. 6,974,795, and 6,432,918, which are each hereby incorporated by reference in their entireties, particularly with respect to measuring colloid oncotic pressure. Solutions with colloid oncotic pressure between 20 and 50 mm Hg administered in hemodilution oxygen delivery experiments are reported as safe (Winslow, R. M. et al. (October 2004). “Comparison of PEG-Modified Albumin And Hemoglobin in Extreme Hemodilution in the Rat,” J. Appl. Physiol. 97(4):1527-1534). Accordingly, in some embodiments, the colloid oncotic pressure of the H-NOX protein solution is between 20 and 50 mm Hg.
Example 3
Surgery Model for O2 Carrier H-NOX Mutants: Comparison of a Panel of O2 Carrier H-NOX Mutants and H-NOX in Extreme Hemodilution in the Rat
To evaluate the ability of H-NOX mutants to transport O2 in a surgery model, an adaptation of an established protocol (Winslow, R. M. et al. (October 2004). “Comparison of PEG-Modified Albumin And Hemoglobin in Extreme Hemodilution in the Rat,” J. Appl. Physiol. 97(4):1527-1534, which is hereby incorporated by reference in its entirety, particularly with respect to surgery models) can be performed using continuous exchange transfusion in the rat.
Acclimated male Sprague-Dawley rats are anesthetized by intramuscular injection of a rodent cocktail containing a mixture of ketamine (40 mg/kg), acepromazine (0.75 mg/kg), and xylazine (3 mg/kg). Catheters made of polyetheylene tubing (Clay Adams PE-50 and PE-10) are implanted into both femoral arteries and one femoral vein. The catheters are externalized at the base of the tail and covered by a tail sheath for protection and future access. After closure of the surgical wounds, animals are returned to their cages and allowed to wake up and recover for 24 h before initiation of the experiment. Animals are given free access to food and water during recovery. For the hemodynamic measurements, the femoral artery catheter is connected through a stopcock and a 23-gauge needle to a pressure transducer, and the arterial pressure is sampled continuously at 100 Hz.
Arterial pH, PCO2, and PO2 are measured in a Bayer model 248 blood-gas analyzer using 100-μl heparinized samples of blood. Lactic acid is measured in femoral artery blood using a YSI lactate analyzer (Yellow Springs Institute, Yellow Springs, Ohio). Total CO2, standard bicarbonate (HCO), and base excess (BE) are calculated from PCO2, pH, and Hb concentration.
Fully conscious animals (n=5 for each treatment group) are placed in Plexiglas restrainers. The arterial and venous cannulae are flushed with 200 and 100 respectively, of heparinized saline (100 U/ml). The arterial and venous catheters are connected to an infusion pump (Labconco model 4262000, Kansas City, Mo.), and exchange-transfusion carried out at a rate of 0.5 ml/min for 100 minutes. Thus the total volume of solution exchanged is 50 ml or 2.5 blood volumes. The peristaltic pump is operated so that blood is removed at exactly the same rate as test material is infused. Test solutions are warmed to 37° C. in a water bath before infusion and kept warm during infusion by a heating pad. At the end of the 100-minute exchange period, animals that survive are monitored for an additional 70 minutes before euthanasia. Blood samples (0.3 ml) are taken every 10 minutes for hematologic and blood-gas analysis.
The treatment groups include animals that are administered one or more H-NOX proteins that have been previously tested for NO or O2 dissociation constants, NO-reactivity, stability, physio-compatibility, or combinations of two or more of the foregoing. Red blood cell H-NOX and pentastarch treated groups provide positive and negative controls, respectively.
Objective end points include survival and the onset of anaerobic metabolism, signaled by acid-base derangement and accumulation of lactic acid. H-NOX proteins that increase the survival rate (such as producing a statistically significant increase in survival rate) compared to that of the control group are useful for oxygenating tissues in extreme hemodilution. Such H-NOX proteins are expected to also be useful to treat other indications for which delivery of O2 is beneficial.
Example 4
Trauma Model for O2 Carrier H-NOX Mutants: Comparing the Effects of O2 Carrier H-NOX Mutants and Recombinant-Hemoglobin Solutions on Blood Pressure, Intestinal Blood Flow, and Gut Oxygenation in a Rat Model of Hemorrhagic Shock
To evaluate the ability of H-NOX proteins to transport O2 in a trauma model, an adaptation of an established protocol (Raat, N. J. et al. (January 2005). “Effects of Recombinant-Hemoglobin Solutions rHb2.0 and rHb1.1 on Blood Pressure, Intestinal Blood Flow, And Gut Oxygenation in a Rat Model of Hemorrhagic Shock,” J Lab Clin Med. 145(1):21-32, which is hereby incorporated by reference in its entirety, particularly with respect to animal models of trauma) can be performed in a fixed-pressure (40 mm Hg) rat model of hemorrhagic shock and resuscitation.
Wistar rats are anesthetized with an intraperitoneal injection of a mixture of 90 mg/kg ketamine, O_5 mg/kg medetomidine, and 0.005 mg/kg atropine sulfate. The body temperature of each rat is kept between 36.5° C. and 37.5° C. with the use of a heating pad thermocontrolled by a temperature probe placed in the rat's rectum. In addition, heat loss is compensated for with the use of a ceramic heating lamp positioned 40 to 50 cm above the rat. For mechanical ventilation, a tracheotomy is performed and a 3.5-cm length of 6F polyvinyl chloride tubing placed 0.5 cm into the trachea and secured with a suture. A modified infant ventilator is used to ventilate the animal. To minimize ventilatory fluid loss, a humidity filter is placed before the ventilation tube. A side port of this filter is used to monitor end-tidal CO2 with the use of a capnograph. Ventilation parameters such as inspiratory phase (0.25-0.35) and respiration rate (50-75 breaths/min) are adjusted to keep arterial PCO2 values between 35 and 45 mm Hg during surgery as checked by taking a baseline blood sample. No further adjustments are made till the end of the experiment.
Vessels are cannulated using 0.5×0.9-mm polyethylene vein catheter. The catheters are filled with 0.9% NaCl solution with 25 IU of heparin. The right carotid artery catheter is shortened to 20 cm and fitted to a pressure transducer for continuous monitoring of mean arterial pressure (MAP) and heart rate. MAP is calculated with the use of this formula: (Systolic blood pressure−Diastolic blood pressure)/3+Diastolic blood pressure. In addition, the jugular vein is cannulated for fluid support with 15 mL/kg/hr Ringer's lactate and 5 mL/kg/hr maintenance anesthesia (ketamine 50 mg/kg/hr in Ringer's lactate). The femoral artery is cannulated for blood withdrawal and arterial blood-gas sampling. The femoral vein is cannulated for infusion of the resuscitation fluids and venous blood-gas sampling.
A midline laparotomy is performed on each rat: the abdomen is covered with Saran wrap to prevent evaporation of body fluids. A small hole is pierced in the Saran wrap to permit access of the optical fiber for microcirculatory PO2 measurements. An ileocecal vein is also cannulated with a 0.8-mm polyethylene catheter for mesenteric venous blood sampling.
Intestinal microvascular PO2 is measured using the previously described technique of oxygen-dependent quenching of palladium-porphyrin phosphorence. After 2.5 to 3 hours of surgery, palladium (II) meso-tetra(4-carboxy-phenyl) porphine coupled to HSA solution (50 mg in 10 mL of 4% albumin solution, 4 mmol/L palladium-porphyrin solution, pH adjusted to 7.4 with HCl) is infused at a dose of 12 mg/kg body wt at a rate of 9.6 mL/kg/hr for 15 minutes.
Excitation of palladium-porphyrin with a pulse of light causes emission of phosphorescence with a decay in time, which is quantitatively related to the oxygen concentration (Vanderkooi, J. M. et al. (Apr. 25, 1987). “An Optical Method for Measurement of Dioxygen Concentration Based Upon Quenching of Phosphorescence,” J. Biol. Chem. 262(12):5476-5482). Microvascular PO2 measurements are made with an optical fiber positioned above the proximal part of the ileum. The flash lamp is recorded before infusing the palladium-porphyrin and a deconvolution algorithm is used to calculate oxygen concentrations. After the infusion of palladium-porphyrin solution and 45 minutes' stabilization, baseline blood samples (0.2 mL/sample) are taken from the femoral artery, femoral vein, and mesenteric vein for blood-gas determination. Blood samples are analyzed in a blood-gas analyzer and a hemoximeter.
Hemorrhagic shock is induced by withdrawing blood from the femoral artery in 3-mL syringes with heparin (25 IU/mL blood) at a rate of approximately 1 mL/min for several minutes until the MAP is approximately 40 mm Hg. MAP is maintained at this level with the use of further blood withdrawals or blood infusions for 45 minutes. Just before resuscitation, blood samples (0.2 mL/sample) are withdrawn from the femoral artery, femoral vein, and mesenteric vein for blood-gas determination, and a similar amount of rat blood (collected during hemorrhagic shock) is reinfused. After this shock period, animals are randomly assigned to 1 of 8 different resuscitation groups. Resuscitation is carried out with wild-type or mutant H-NOX proteins or with another O2 carrier, such as recombinant hemoglobin solution rHb1.1 (Baxter), rHb2.0 (Baxter), serum free hemoglobin (standard solution), MP4 (Sangart), hemopure (Biopure), or polyheme (Northfield Labs) (Raat, N. J. et ed. (January 2005). J Lab Clin Med. 145(1):21-32; stock concentration 100 mg/mL), all at a dose of 20 mL/kg (2 g/kg) infused at a rate of 60 mL/kg/hr. HSA (13.4% albumin solution) infused at the same dosage (20 mL/kg) and rate is used as a control for the volume effect on pressure and flow during resuscitation. When resuscitation is complete, 0.2-mL blood samples are taken from the femoral artery, femoral vein, and mesenteric vein after 30, 60, 90, and 120 minutes, and a similar amount of rat blood is given back each time.
H-NOX that cause the same or less (such as substantially or significantly less) systemic vasoconstriction, the same or less of an increase in MAP, or the same or less of an increase in mesenteric vascular resistance (MVR) after resuscitation compared with that caused by another O2 carrier (such as rHb1.1, rHb2.0, serum free hemoglobin, MP4, hemospan, or polyheme) or by oncotically matched HAS are useful to treat hemorrhagic shock. Such H-NOX proteins are expected to also be useful to treat other indications for which delivery of O2 is beneficial.
The foregoing examples and detailed description are offered by way of illustration and not by way of limitation. All publications, patent applications, and patents cited in this specification are herein incorporated by reference as if each individual publication, patent application, or patent were specifically and individually indicated to be incorporated by reference. Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.
Unless defined otherwise, the meanings of all technical and scientific terms used herein are those commonly understood by one of skill in the art to which this invention belongs. One of skill in the art will also appreciate that any methods and materials similar or equivalent to those described herein can also be used to practice or test the invention.
For use herein, unless clearly indicated otherwise, use of the terms “a”, “an,” and the like refers to one or more.
Reference to “about” a value or parameter herein includes (and describes) embodiments that are directed to that value or parameter per se. For example, description referring to “about X” includes description of “X.”
It is understood that aspect and embodiments of the invention described herein include “comprising,” “consisting,” and “consisting essentially of” aspects and embodiments.

## Claims

1. An isolated H-NOX protein comprising at least one distal pocket mutation that alters the O2 dissociation constant or NO reactivity compared to that of a corresponding wild-type H-NOX protein, wherein the O2 dissociation constant of the mutant H-NOX protein is within 2 orders of magnitude of that of hemoglobin, wherein the NO reactivity of the mutant H-NOX protein is at least 10-fold lower than that of hemoglobin, wherein the H-NOX protein does not comprise a guanylyl cyclase catalytic domain, wherein the distal pocket mutation comprises a substitution at a residue that corresponds to at least one of Thr4, Ile5, Thr8, Trp9, Trp67, Asn74, Ile75, Phe78, Phe82, Tyr140, and Leu144 of a T. tengcongensis H-NOX of SEQ ID NO: 54, and wherein the mutant H-NOX protein is not T. tengcongensis H-NOX Y140L, T. tengcongensis H-NOX F78Y/Y140L, T. tengcongensis H-NOX W9F, T. tengcongensis H-NOX W9F/Y140L, H. sapiens β1 H-NOX (1-385) I145Y, or L. pneumophilia 2 H-NOX F142Y.

2. The isolated H-NOX protein of claim 1, wherein the O2 dissociation constant of the mutant H-NOX protein is between 1 nM and 1 mM at 20° C., and the NO reactivity of the mutant H-NOX protein is less than 700 s−1 at 20° C.

3. The isolated H-NOX protein of claim 1, wherein the O2 dissociation constant of the H-NOX protein is between 2 nM and 50 μM at 20° C.

4. The isolated H-NOX protein of claim 1, wherein the NO reactivity of the H-NOX protein is less than 1 s−1 at 20° C.

5. The isolated H-NOX protein of claim 1, wherein the NO reactivity of the H-NOX protein is at least 100-fold lower than that of human hemoglobin alpha.

6. The isolated H-NOX protein of claim 1, wherein the koff for oxygen of the H-NOX protein is between 0.01 s−1 and 200 s−1 at 20° C.

7. The isolated H-NOX protein of claim 1, wherein the rate of heme autoxidation of the H-NOX protein is less than 1 h−1 at 37° C.

8. The isolated H-NOX protein of claim 1, wherein the distal pocket mutation is a L144F mutation.

9. The isolated H-NOX protein of claim 1, wherein the H-NOX protein is a T. tengcongensis H-NOX protein comprising a L144F mutation in SEQ ID NO: 54.

10. The isolated H-NOX protein of claim 1, wherein the H-NOX protein is a fusion protein that includes an H-NOX domain and part or all of another protein.

11. The isolated H-NOX protein of claim 1, wherein the H-NOX protein is covalently bound to polyethylene glycol.

12. An isolated H-NOX protein comprising a distal pocket mutation wherein the O2 dissociation constant of the H-NOX protein is within 2 orders of magnitude of that of hemoglobin, wherein the NO reactivity of the mutant H-NOX protein is at least 10-fold lower than that of hemoglobin, and wherein the distal pocket mutation is at an amino acid position corresponding to position L144 of T. tengcongensis H-NOX of SEQ ID NO: 54, wherein the H-NOX protein does not comprise a guanylyl cyclase catalytic domain.

13. The isolated H-NOX protein of claim 12, wherein the H-NOX protein is a fusion protein that includes an H-NOX domain and part or all of another protein.

14. The isolated H-HOX protein of claim 12, wherein the H-NOX protein is covalently bound to polyethylene glycol.

15. The isolated H-NOX protein of claim 13, wherein the H-NOX protein is covalently bound to polyethylene glycol.

16. An isolated H-NOX protein comprising a distal pocket mutation, wherein the O2 dissociation constant of the mutant H-NOX protein is within 2 orders of magnitude of that of hemoglobin, wherein the NO reactivity of the mutant H-NOX protein is at least 10-fold lower than that of hemoglobin, wherein the H-NOX protein is a T. tengcongensis H-NOX protein comprising a L144F mutation in SEQ ID NO: 54 and does not comprise a guanylyl cyclase catalytic domain, wherein the H-NOX protein is a fusion protein that includes an H-NOX domain and part or all of another protein, and wherein the H-NOX protein is covalently bound to polyethylene glycol.