bluuebunny/crossref_metadata_2025 huggingface dataset:
High-resolution mapping of the HyHEL-10 epitope of chicken lysozyme by site-directed mutagenesis.
Authors: Kam-Morgan L N , Smith-Gill S J , Taylor M G , Zhang L , Wilson A C , Kirsch J F
Published: May 2006

The complex formed between hen egg white lysozyme (HEL) and the monoclonal antibody HyHEL-10 Fab fragment has an interface composed of van der Waals interactions, hydrogen bonds, and a single ion pair. The antibody overlaps part of the active site cleft. Putative critical residues within the epitope region of HEL, identified from the x-ray crystallographic structure of the complex, were replaced by site-directed mutagenesis to probe their relative importance in determining affinity of the antibody for HEL. Twenty single mutations of HEL at three contact residues (Arg-21HEL, Asp-101HEL, and Gly-102HEL) and at a partially buried residue (Asn-19HEL) in the epitope were made, and the effects on the free energies of dissociation were measured. A correlation between increased amino acid side-chain volume and reduced affinity for HELs with mutations at position 101 was observed. The D101GHEL mutant is bound to HyHEL-10 as tightly as wild-type enzyme, but the delta delta Gdissoc is increased by about 2.2 kcal (9.2 kJ)/mol for the larger residues in this position. HEL variants with lysine or histidine replacements for arginine at position 21 are bound 1.4-2.7 times more tightly than those with neutral or negatively charged amino acids in this position. These exhibit 1/40 the affinity for HyHEL-10 Fab compared with wild type. There is no side-chain volume correlation with delta delta Gdissoc at position 21. Although Gly-102HEL and Asn-19HEL are in the epitope, replacements at these positions have no effect on the affinity of HEL for the antibody.
Loss of function of the Drosophila zfh-1 gene results in abnormal development of mesodermally derived tissues.
Authors: Lai Z C , Rushton E , Bate M , Rubin G M
Published: May 2006

The Drosophila zfh-1 gene encodes an unusual protein with nine Cys2His2 type zinc-finger motifs and one homeodomain that shows a complex pattern of expression in the embryonic mesoderm and nervous system. To study the function of zfh-1, we generated loss-of-function zfh-1 mutations. Phenotypic analysis of zfh-1 mutant embryos reveals that the gene is not required for the initial segregation of the mesoderm or for the differentiation of mesodermally derived tissues. Rather, loss of zfh-1 function results in various degrees of local errors in cell fate or positioning.
Crystal structure of a ubiquitin-dependent degradation substrate: a three-disulfide form of lysozyme.
Authors: Hill C P , Johnston N L , Cohen R E
Published: May 2006

Covalent attachment of ubiquitin marks substrates for proteolysis, but features that identify ubiquitination targets such as chicken egg white lysozyme are poorly understood. Recognition of lysozyme first requires reduction of Cys-6 Cys-127, one of its four native disulfide bonds, and Cys-6,Cys-127-carboxymethylated (6,127-rcm) lysozyme can mimic this three-disulfide intermediate. The 6,127-rcm form of lysozyme is known to retain a substantially native-like conformation in solution, and we demonstrate that it is this folded structure that is recognized for ubiquitination. Because native lysozyme is not a substrate, differences between the native and three-disulfide structures must include features responsible for selective ubiquitination. The 1.9-A resolution crystal structure of 6,127-rcm-lysozyme, reported here, affords a view of this ubiquitin-dependent degradation substrate. Two conformers of 6,127-rcm-lysozyme were obtained in the crystal. These differ uniquely from crystal forms of native lysozyme by displacement of the C-terminal residues. The structures suggest that localized unfolding at the C terminus of three-disulfide lysozyme allows the complex of E3 alpha (ubiquitin-protein ligase) and E2 (ubiquitin-carrier protein) to bind to a surface that includes Lys-1 and the putative ubiquitination site Lys-13. From this we infer that the N-terminal and internal substrate recognition sites on the E3 alpha.E2 complex are separated by approximately 20 A.
Identification of a colon mucosa gene that is down-regulated in colon adenomas and adenocarcinomas.
Authors: Schweinfest C W , Henderson K W , Suster S , Kondoh N , Papas T S
Published: May 2006

A cDNA, which we call DRA (for down-regulated in adenoma) has been isolated. Its mRNA is expressed exclusively in normal colon tissue, probably only in the mucosal epithelia. Expression of the DRA gene is significantly decreased in adenomas (polyps) and adenocarcinomas of the colon. The DRA gene appears to be a single-copy gene present on chromosome 7, a chromosome associated with colorectal tumorigenesis. The predicted DRA polypeptide is an 84,500-Da protein that contains charged clusters of amino acids, primarily at the NH2 and COOH termini. Together with potential nuclear targeting motifs, an acidic transcriptional activation domain, and a homeobox domain, these elements suggest a transcription factor or a protein that may interact with transcription factors. Such a function may be consistent with a role in tissue-specific gene expression and/or as a candidate tumor-suppressor gene.
Images of evolution: origin of spontaneous RNA replication waves.
Authors: McCaskill J S , Bauer G J
Published: May 2006

Self-replicating molecules set up traveling concentration waves that propagate in an aqueous enzyme solution. The velocity of each wave provides an accurate (+/- 0.1%) noninvasive measure of fitness for the RNA species currently growing in its front. Evolution may be followed from changes in the front velocity, and these differ from wave to wave. Thousands of controlled evolution reactions in traveling waves have been monitored in parallel to obtain quantitative images of the stochastic process of natural selection. An RNA polymerase (RNA-dependent RNA nucleotidyltransferase, EC 2.7.7.6), extracted from bacteria infected by the Q beta RNA virus, catalyzes the replication. The traveling waves that arise spontaneously without added RNA provide a model system for major evolutionary change.
PutA protein, a membrane-associated flavin dehydrogenase, acts as a redox-dependent transcriptional regulator.
Authors: Ostrovsky de Spicer P , Maloy S
Published: May 2006

The proline utilization (put) operon of Salmonella typhimurium is transcriptionally repressed by PutA protein in the absence of proline. PutA protein also carries out the enzymatic steps in proline catabolism. These two roles require different cellular localizations of PutA. Catabolism of proline requires PutA to associate with the membrane because reoxidation of the FAD cofactor in PutA needs the presence of an electron acceptor. Repression of the put operon requires PutA to bind to the put control-region DNA in the cytoplasm. The presence of proline, the inducer, is necessary but not sufficient for PutA to discriminate between its roles as an enzyme or as a repressor. Two conditions that prevent PutA protein binding to the put control region are (i) when proline and an electron acceptor or the cytoplasmic membrane are present or (ii) when PutA is reduced by dithionite. These two conditions increase the relative hydrophobicity of PutA protein, favoring membrane association and therefore enzymatic activity.
Detergent-enabled transport of proteins and nucleic acids through hydrophobic solvents.
Authors: Bromberg L E , Klibanov A M
Published: May 2006

It is demonstrated that proteins and nucleic acids can be transported through hydrophobic organic solvents (liquid membranes) via nonspecific complex formation with detergents, whereas no macromolecule transport is observed without the latter. A protein (or a nucleic acid) first interacts with an oppositely charged detergent due to hydrophobic ion pairing in the aqueous feed phase. The resultant hydrophobic complex readily partitions into an organic solvent and then into the aqueous receiver phase, where it dissociates. Experiments with (i) different detergent/protein molar ratios, (ii) a range of unrelated organic solvents as liquid membranes, and (iii) homologous detergents with hydrophobic tails of varying lengths indicate that the protein flux through the membrane directly correlates with the partitioning of the protein-detergent complexes from the aqueous feed into the organic phase. Very little protein transport was detected at detergent concentrations above the critical micelle concentration, suggesting that individual detergent molecules, rather than micelles, play the key role. The rate of the detergent-enabled protein transport is not a function of the protein molecular weight, provided that enough detergent molecules bind to make the complex sufficiently hydrophobic; e.g., bovine serum albumin can be transported faster than insulin, which is less than 1/10th of its size.
Attenuation of the induction of nitric oxide synthase by endogenous glucocorticoids accounts for endotoxin tolerance in vivo.
Authors: Szabó C , Thiemermann C , Wu C C , Perretti M , Vane J R
Published: May 2006

An enhanced formation of nitric oxide (NO) due to induction of a calcium-independent (inducible) NO synthase (iNOS) contributes importantly to the cardiovascular failure caused by bacterial endotoxin. Repeated challenges with small doses of endotoxin result in tolerance to both peripheral vascular failure and death caused by subsequent injection of a higher dose of endotoxin. Here we investigate whether tolerance to endotoxin is associated with a lack of induction of iNOS in vivo and whether endogenous glucocorticoids play a role in the development of endotoxin tolerance. In anesthetized rats, i.v. administration of Escherichia coli endotoxin [lipopolysaccharide (LPS); 2 mg.kg-1] resulted in a prolonged decrease in mean arterial blood pressure (MAP) and hyporeactivity to the contractile responses elicited by norepinephrine (NE; 10 nM) in aortic rings ex vivo. Hyporeactivity to NE was partially reversed by NG-nitro-L-arginine methyl ester (0.3 mM) in vitro, suggesting that an enhanced formation of NO contributes to this hyporeactivity. There was a substantial increase in the activity of iNOS in the lung 3 h after i.v. injection of LPS (0.2 +/- 0.1 to 6.6 +/- 0.6 pmol.mg-1.min-1; n = 5; P < 0.01). Rats injected i.p. with LPS (0.5 mg.kg-1) for 4 consecutive days became tolerant to an i.v. injection of LPS (2 mg.kg-1) in that both hypotension and vascular hyporeactivity to NE were significantly attenuated. Moreover, in these endotoxin-tolerant rats, the induction of iNOS by LPS in the lung was attenuated by 63% +/- 6%. Injection of LPS caused a 9-fold increase in plasma corticosterone (CCS) levels within 2 h and CCS levels remained significantly elevated 6 and 24 h after LPS. Animals rendered tolerant to endotoxin by administration of a low dose of LPS (0.5 mg.kg-1, i.p.) for 4 days still had a 6-fold increase in plasma CCS levels 24 h after the last injection of LPS. When endotoxin-tolerant rats were treated with the glucocorticoid receptor antagonist RU 486 (50 mg.kg-1, p.o. 3 h prior to LPS), there was a restoration of the effects of LPS (2 mg.kg-1, i.v.) in causing hypotension, vascular hyporeactivity to NE, and iNOS induction in the lung. However, in control rats RU 486 enhanced neither the decrease in MAP nor the induction of iNOS in response to LPS (2 mg.kg-1, i.v.). Thus, cardiovascular tolerance to endotoxin is accompanied and explained by reduced induction of iNOS in vivo due to the elevation of endogenous glucocorticoid levels.
Osmoprotective compounds in the Plumbaginaceae: a natural experiment in metabolic engineering of stress tolerance.
Authors: Hanson A D , Rathinasabapathi B , Rivoal J , Burnet M , Dillon M O , Gage D A
Published: May 2006

In common with other zwitterionic quarternary ammonium compounds (QACs), glycine betaine acts as an osmoprotectant in plants, bacteria, and animals, with its accumulation in the cytoplasm reducing adverse effects of salinity and drought. For this reason, the glycine betaine biosynthesis pathway has become a target for genetic engineering of stress tolerance in crop plants. Besides glycine betaine, several other QAC osmoprotectants have been reported to accumulate among flowering plants, although little is known about their distribution, evolution, or adaptive value. We show here that various taxa of the highly stress-tolerant family Plumbaginaceae have evolved four QACs, which supplement or replace glycine betaine-namely, choline O-sulfate and the betaines of beta-alanine, proline, and hydroxyproline. Evidence from bacterial bioassays demonstrates that these QACs function no better than glycine betaine as osmoprotectants. However, the distribution of QACs among diverse members of the Plumbaginaceae adapted to different types of habitat indicates that different QACs could have selective advantages in particular stress environments. Specifically, choline O-sulfate can function in sulfate detoxification as well as in osmoprotection, beta-alanine betaine may be superior to glycine betaine in hypoxic saline conditions, and proline-derived betaines may be beneficial in chronically dry environments. We conclude that the evolution of osmoprotectant diversity within the Plumbaginaceae suggests additional possibilities to explore in the metabolic engineering of stress tolerance in crops.
Calcium oscillations in pituitary gonadotrophs: comparison of experiment and theory.
Authors: Li Y X , Rinzel J , Keizer J , Stojilković S S
Published: May 2006

We have developed a mathematical model that describes several aspects of agonist-induced Ca2+ signaling in single pituitary gonadotrophs. Our model is based on fast activation of the inositol 1,4,5-trisphosphate (InsP3) receptor Ca2+ channels at low free cytosolic Ca2+ concentration ([Ca2+]i) and slow inactivation at high [Ca2+]i. Previous work has shown that these gating properties, when combined with a Ca(2+)-ATPase, are sufficient to generate simulated Ca2+ oscillations. The Hodgkin-Huxley-like description we formulate here incorporates these different gating properties explicitly and renders their effects transparent and easy to modulate. We introduce regulatory mechanisms of channel opening which enable the model, both in the absence and in the presence of Ca2+ entry, to give responses to a wide range of agonist doses that are in good agreement with experimental findings, including subthreshold responses, superthreshold oscillations with frequency determined by [InsP3], and nonoscillatory "biphasic" responses followed occasionally by small-amplitude oscillations. A particular added feature of our model, enhanced channel opening by reduced concentration of Ca2+ in the lumen of the endoplasmic reticulum, allows oscillations to continue during pool depletion. The model predicts that ionomycin and thapsigargin can induce oscillations with basal [InsP3] and zero Ca2+ entry, while Ca2+ injection cannot. Responses to specific pairings of sub- or superthreshold stimuli of agonist, ionomycin, and thapsigargin are also correctly predicted. Since this model encompasses a wide range of observed dynamic behaviors within a single framework, based on well-established mechanisms, its relevance should not be restricted to gonadotrophs.
Cyclic peptides as proteases: a reevaluation.
Authors: Corey D R , Phillips M A
Published: May 2006

A recent report [Atassi, M. Z. and Manshouri, T. (1993) Proc. Natl. Acad. Sci. USA 90, 8282-8286] described the design and synthesis of two 29-amino acid cyclic peptides that were reported to hydrolyze both ester and amide bonds with chymotrypsin-like or trypsin-like specificity. We have synthesized the trypsin-mimic peptide (TrPepz) and detect no activity toward either ester or peptide substrates. The same result was independently obtained by Wells et al. [Wells, J. A., Fairbrother, W. J., Otlewski, J., Laskowski, M., Jr., & Burnier, J. (1994) Proc. Natl. Acad. Sci. USA 91, 4110-4114.] Additionally, we found that Atassi and Manshouri failed to obtain accurate kinetic constants for trypsin- and chymotrypsin-catalyzed ester hydrolysis because the high concentrations of trypsin and chymotrypsin that they report using would have prevented evaluation of initial rates. These findings are incompatible with the claims, reported by Atassi and Manshouri, that TrPepz has trypsin-like activity.
Identification of a binding site in the disintegrin domain of fertilin required for sperm-egg fusion.
Authors: Myles D G , Kimmel L H , Blobel C P , White J M , Primakoff P
Published: May 2006

Fertilization and certain later stages in mammalian embryonic development require fusion between membranes of individual cells. The mechanism of eukaryotic cell-cell fusion is unknown, and no surface molecules required for this process have been unequivocally identified. The role of the sperm surface protein fertilin in sperm-egg fusion was tested by using peptide analogues of a potential integrin binding site in the fertilin beta subunit. Peptide analogues that include a TDE sequence from the disintegrin region of fertilin beta are able to bind to the egg plasma membrane and strongly inhibit sperm-egg fusion. These results show that the disintegrin domain of fertilin beta binds to the egg plasma membrane and that this binding is required for membrane fusion.
Targeted nuclear antisense RNA mimics natural antisense-induced degradation of polyoma virus early RNA.
Authors: Liu Z , Batt D B , Carmichael G G
Published: May 2006

We describe a general antisense strategy to inhibit target gene expression. The substitution of a cis-acting ribozyme for a polyadenylylation signal in an antisense expression vector results in the nuclear retention of RNAs and the efficient degradation of their targets. We demonstrate the utility of this system in polyoma virus, where early-strand RNA levels are downregulated in the nucleus by antisense late-strand counterparts. We show that mutations destabilizing these naturally occurring antisense transcripts lead to increased levels of early-strand RNAs. Furthermore, expression in trans of nuclear antisense transcripts lowers early-strand RNA levels and quantitatively mimics the natural regulation.
Codon reiteration and the evolution of proteins.
Authors: Green H , Wang N
Published: May 2006

Sequence data banks have been searched for proteins possessing uninterrupted reiterations of any amino acid. Hydrophilic amino acids, and particularly glutamine, account for a large proportion of the longer reiterants. In the genes for these proteins, the most common reiterants are those that contain poly(CAG), even out-of-frame or, to a lesser degree, those that contain repeated doublets of CA, AG, or GC. The preferential generation of such reiterants requires that DNA strand-specific signals predispose to reiteration and thus to the extension of coding regions.
Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization.
Authors: Wagner A
Published: May 2006

Networks of transcriptional regulators have key roles in metazoan development. Important forces in the evolution of these networks are gene duplications and gene deletions, events that may change the spatiotemporal expression pattern of network genes. A measure for the probability of such changes after gene-duplication events is proposed. This measure is based on a simple mathematical model that describes such networks as dynamical systems and on properties of ensembles of these dynamical systems. It is predicted that this probability depends only on the fraction of genes duplicated in a single event and that it is largest if approximately 40% of the genes in a network are duplicated. This property is robust with respect to variations in model parameters. On these grounds, it is argued that (i) evolution of gene networks should preferentially occur either by duplication of single genes or by duplication of all genes involved in a network, and that (ii) tight linkage ("clustering") or strong dispersal are the two evolutionarily most favorable forms of genomic organization of genes forming such networks.
Prevention of ischemia-induced ventricular fibrillation by omega 3 fatty acids.
Authors: Billman G E , Hallaq H , Leaf A
Published: May 2006

A specially prepared dog model of myocardial infarction was used to test the efficacy of the long-chain polyunsaturated fish oil omega 3 fatty acids eicosapentaenoic (20:5 n-3) and docosahexaenoic (22:6 n-3) acids to prevent ischemia-induced malignant cardiac arrhythmias. The dogs had sustained a prior experimental myocardial infarction from ligation of the left anterior descending coronary artery, and a hydraulic cuff was implanted around the left circumflex artery at that operation. After recovery from that procedure the animals were tested during a treadmill exercise test. With compression of the left circumflex artery sensitive animals will predictably develop ventricular fibrillation (VF). In such prepared dogs an emulsion of fish oil fatty acids was infused i.v. over a 50- to 60-min period just before the exercise-plus-ischemia test, and the effect on development of VF was recorded. The infusion was 100 ml of a 10% (vol/vol) emulsion of a fish oil concentrate containing 70% omega 3 fatty acids with free eicosapentaenoic acid and docosahexaenoic acid composing 33.9% and 25.0% of that total, respectively. Alternatively, some animals similarly received an emulsion containing 5 ml of the free fatty acid concentrate plus 5 ml of a triacylglyerol concentrate containing 65% omega 3 fatty acids with eicosapentaenoic acid and docosahexaenoic acid composing 34.0% and 23.6% of that total, respectively. In seven of eight animals the infusion of the fish oil emulsion completely prevented the acute occurrence of VF in the susceptible animals (P < 0.005). In five of five of these animals the subsequent exercise-plus-ischemia test after a similar infusion of an emulsion in which soy bean oil replaced the fish oil fatty acid concentrates resulted in prompt development of VF. Possible mechanisms for this protective effect of omega 3 fatty acids against exercise and ischemia-induced malignant arrhythmias are considered.
High-affinity binding of short peptides to major histocompatibility complex class II molecules by anchor combinations.
Authors: Hammer J , Belunis C , Bolin D , Papadopoulos J , Walsky R , Higelin J , Danho W , Sinigaglia F , Nagy Z A
Published: May 2006

We have previously identified four anchor positions in HLA-DRB1*0101-binding peptides, and three anchors involved in peptide binding to DRB1*0401 and DRB1*1101 molecules, by screening of an M13 peptide display library (approximately 20 million independent nonapeptides) for DR-binding activity. In this study, high stringency screening of the M13 library for DRB1*0401 binding has resulted in identification of three further anchor positions. Taken together, a peptide-binding motif has been obtained, in which six of seven positions show enrichment of certain residues. We have demonstrated an additive effect of anchors in two different ways: (i) the addition of more anchors is shown to compensate for progressive truncation of designer peptides; (ii) the incorporation of an increasing number of anchors into 6- or 7-residue-long designer peptides is shown to result in a gradual increase of binding affinity to the level of 13-residue-long high-affinity epitopes. The anchor at relative position 1 seems to be obligatory, in that its substitution abrogates binding completely, whereas the elimination of other anchors results only in partial loss of binding affinity. The spacing between anchors is critical, since their effect is lost by shifting them one position toward the N or C terminus. The information born out of this study has been successfully used to identify DR-binding sequences from natural proteins.
Inhibition of human immunodeficiency virus infection by agents that interfere with thiol-disulfide interchange upon virus-receptor interaction.
Authors: Ryser H J , Levy E M , Mandel R , DiSciullo G J
Published: May 2006

The cell surface of mammalian cells is capable of reductively cleaving disulfide bonds of exogenous membrane-bound macromolecules (for instance, the interchain disulfide of diphtheria toxin), and inhibiting this process with membrane-impermeant sulfhydryl reagents prevents diphtheria toxin cytotoxicity. More recently it was found that the same membrane function can be inhibited by bacitracin, an inhibitor of protein disulfide-isomerase (PDI), and by monoclonal antibodies against PDI, suggesting that PDI catalyzes a thiol-disulfide interchange between its thiols and the disulfides of membrane-bound macromolecules. We provide evidence that the same reductive process plays a role in the penetration of membrane-bound human immunodeficiency virus (HIV) and show that HIV infection of human lymphoid cells is markedly inhibited by the membrane-impermeant sulfhydryl blocker 5,5'-dithiobis(2-nitrobenzoic acid), by bacitracin, and by anti-PDI antibodies. The results imply that HIV and its target cell engage in a thiol-disulfide interchange mediated by PDI and that the reduction of critical disulfides in viral envelope glycoproteins may be the initial event that triggers conformational changes required for HIV entry and cell infection. These findings suggest additional approaches to impede cell infection by HIV.
Herpes simplex virus DNA replication: a spacer sequence directs the ATP-dependent formation of a nucleoprotein complex at oriS.
Authors: Gustafsson C M , Hammarsten O , Falkenberg M , Elias P
Published: May 2006

The origin-binding protein (OBP) from herpes simplex virus 1 is a member of the SF2 helicase superfamily and is required for the initiation of DNA synthesis from a viral origin of DNA replication (oriS). The high-affinity binding sites for OBP in oriS, boxes I and II, are separated by an A+T-rich spacer. We used the gel retardation technique to examine the influence of this spacer sequence on the formation of a specific complex, referred to as complex II, between OBP and oriS. The formation of this OBP-oriS complex was greatly promoted by adenosine 5'-[gamma-thio]triphosphate and other nucleotide cofactors. Surprisingly, oriS constructs where the spacer sequence had been altered with approximately half of a helical turn (+4 or -6 base pairs) supported the formation of a more stable complex II than the wild-type origin. DNase I footprinting experiments showed that the cooperative binding of OBP to boxes I and II was affected by the length of the spacer sequence in the same way. In contrast, the ability of oriS-containing plasmids to replicate was most efficient with wild-type oriS. This paradox can be resolved if it is assumed that an ATP-dependent cooperative binding of OBP to properly spaced recognition sequences in oriS is required to induce a conformational change of DNA, thereby facilitating initiation of DNA replication.
Persistent increase of hippocampal presynaptic axon excitability after repetitive electrical stimulation: dependence on N-methyl-D-aspartate receptor activity, nitric-oxide synthase, and temperature.
Authors: McNaughton B L , Shen J , Rao G , Foster T C , Barnes C A
Published: May 2006

The electrical excitability of Schaffer collateral axons and/or terminals was studied in hippocampal slices by monitoring single, CA3 pyramidal neurons activated antidromically from CA1 stratum radiatum. At 22 degrees C, weak, repetitive stimulation with as few as 10 impulses at 2 Hz led to a robust lowering of the antidromic activation threshold that lasted > 30 min. The effect was completely absent at 32 degrees C and was blocked by both the N-methyl-D-aspartate receptor antagonist, 2-amino-5-phosphonovalerate and the inhibitor of nitric-oxide synthase, L-nitro-arginine methyl ester. Such threshold lowering would alter the variance of synaptic responses from axons stimulated in the variable excitation region of their input-output functions. These results thus raise important doubts about the interpretation of experiments in which the so-called minimal-stimulation method has been used at reduced temperature to infer changes in quantal transmission during hippocampal long-term potentiation. In the present experiments, no changes were observed in the estimate of excitatory postsynaptic potential quantal content in long-term potentiation experiments at either temperature, which could not be accounted for by an artificial, temperature-dependent change in the responsiveness of presynaptic axons.
cGMP binding sites on photoreceptor phosphodiesterase: role in feedback regulation of visual transduction.
Authors: Cote R H , Bownds M D , Arshavsky V Y
Published: May 2006

A central step in vertebrate visual transduction is the rapid drop in cGMP levels that causes cGMP-gated ion channels in the photoreceptor cell membrane to close. It has long been a puzzle that the cGMP phosphodiesterase (PDE) whose activation causes this decrease contains not only catalytic sites for cGMP hydrolysis but also noncatalytic cGMP binding sites. Recent work has shown that occupancy of these noncatalytic sites slows the rate of PDE inactivation. We report here that PDE activation induced by activated transduction lowers the cGMP binding affinity for noncatalytic sites on PDE and accelerates the dissociation of cGMP from these sites. These sites can exist in three states: high affinity (Kd = 60 nM) for the nonactivated PDE, intermediate affinity (Kd approximately 180 nM) when the enzyme is activated in a complex with transducin, and low affinity (Kd > 1 microM) when transducin physically removes the inhibitory subunits of PDE from the PDE catalytic subunits. Activation of PDE by transducin causes a 10-fold increase in the rate of cGMP dissociation from one of the two noncatalytic sites; physical removal of the inhibitory subunits from the PDE catalytic subunits further accelerates the cGMP dissociation rate from both sites > 50-fold. Because PDE molecules lacking bound cGMP inactivate more rapidly, this suggests that a prolonged cGMP decrease may act as a negative feedback regulator to generate the faster, smaller photoresponses characteristic of light-adapted photoreceptors.
Nuclear and mitochondrial gene genealogies and allozyme polymorphism across a major phylogeographic break in the copepod Tigriopus californicus.
Authors: Burton R S , Lee B N
Published: May 2006

The genetic structure of natural populations is frequently inferred from geographic distributions of alleles at multiple gene loci. Surveys of allozyme polymorphisms in the tidepool copepod Tigriopus californicus have revealed sharp genetic differentiation of populations, indicating that gene flow among populations is highly restricted. Analysis of population structure in this species has now been extended to include nuclear and mitochondrial gene genealogies. DNA sequences of the mtDNA-encoded cytochrome-c oxidase subunit I gene from 21 isofemale lines derived from seven populations reveal a phylogeographic break between populations north and south of Point Conception, California, with sequence divergence across the break exceeding 18%, the highest level of mtDNA divergence yet reported among conspecific populations. Divergence between populations based on 22 sequences of the nuclear histone H1 gene is geographically concordant with the mitochondrial sequences. In contrast with previously studied nuclear genes in other sexually reproducing metazoans, the H1 gene genealogy from T. californicus shows no evidence of recombination. The apparent absence of intragenic recombinants probably results from the persistent lack of gene flow among geographically separated populations, a conclusion strongly supported by allozyme data and the mitochondrial gene genealogy. Despite strong population differentiation at allozyme loci, the phylogeographic break identified by the DNA sequences was not evident in the allozyme data.
Genetic instability of plant tissue cultures: breakdown of normal controls.
Authors: Phillips R L , Kaeppler S M , Olhoft P
Published: May 2006

Plants regenerated from relatively undifferentiated callus cultures possess a vast array of genetic changes. Such variations can result in useful agricultural and horticultural products. For other purposes, however, variations in traits other than those of interest may be undesirable--for example, using cultured cells for genetic engineering. Any steps made toward understanding the basis of tissue culture-induced genetic variation should be helpful in developing a more stable and manipulatable somatic cell system. This review provides a glimpse at the specific kinds of genetic changes encountered among regenerated plants and their progeny. Included among these variations are cytosine methylation alterations of the genome. The repeat-induced point mutation (RIP) phenomenon, reported for filamentous fungi, is invoked to provide a framework to consider the origin of variation in plant tissue cultures.
A role for destabilizing amino acid replacements in light-chain amyloidosis.
Authors: Hurle M R , Helms L R , Li L , Chan W , Wetzel R
Published: May 2006

Light-chain (L-chain) amyloidosis is characterized by deposition of fibrillar aggregates composed of the N-terminal L-chain variable region (VL) domain of an immunoglobulin, generally in individuals overproducing a monoclonal L chain. In addition to proteolytic fragmentation and high protein concentration, particular amino acid substitutions may also contribute to the tendency of an L chain to aggregate in L-chain amyloidosis, although evidence in support of this has been limited and difficult to interpret. In this paper we identify particular amino acid replacements at specific positions in the VL domain that are occupied at frequencies significantly higher in those L chains associated with amyloidosis. Analysis of the structural model for the VL domain of the Bence-Jones protein REI suggests that these positions play important roles in maintaining domain structure and stability. Using an Escherichia coli expression system, we prepared single-point mutants of REI VL incorporating amyloid-associated amino acid replacements that are both rare and located at structurally important positions. These mutants support ordered aggregate formation in an in vitro L-chain fibril formation model in which wild-type REI VL remains soluble. Moreover, the ability of these sequences to aggregate in vitro correlates well with the extent to which domain stability is decreased in denaturant-induced unfolding. The results are consistent with a mechanism for the disease process in which the VL domain, either before or after proteolytic cleavage from the L-chain constant region domain, unfolds by virtue of one or more destabilizing amino acid replacements to generate an aggregation-prone nonnative state.
Spectrophotometric assay for enzyme-mediated unwinding of double-stranded DNA.
Authors: Houston P , Kodadek T
Published: May 2006

A method is described for monitoring the enzyme-mediated unwinding of duplex DNA spectrophotometrically. The assay employs a partially duplex oligonucleotide substrate modified at the complementary end with coumarin and fluorescein moieties. When in close proximity the fluorescein quenches the fluorescence of coumarin. However, when the strands are separated by the action of a DNA helicase, the coumarin fluorescence increases greatly. Therefore, the progress of enzyme-mediated DNA unwinding can be measured in real time by fluorescence spectroscopy. This assay provides a simple method to screen for helicase inhibitors, which are of growing interest as potential anticancer agents. The application of this technique to kinetic analyses of the mechanism of action of DNA helicases is also discussed.
The bat gene of Halobacterium halobium encodes a trans-acting oxygen inducibility factor.
Authors: Gropp F , Betlach M C
Published: May 2006

Oxygen and light affect the expression of the bacterioopsin gene (bop), which encodes a light-driven proton pump in the purple membrane of Halobacterium halobium. This response is thought to be mediated by a set of genes located adjacent to the bop gene. DNA fragments containing either the bop gene or the entire bop gene cluster reversed the phenotype of purple membrane-deficient strains with mutations in the bop gene. Purple membrane synthesis was constitutive in one of these strains transformed with the bop gene alone. The same strain transformed with the bop gene cluster was inducible by low oxygen tension. Moreover, another strain that constitutively expresses purple membrane remained constitutive when transformed with the bop gene alone but the phenotype of the strain changed to inducible when transformed with the bop gene cluster. Additional experiments have confirmed that one of the genes of the bop gene cluster, the bat gene, encodes a trans-acting factor that is necessary and sufficient to confer inducibility of purple membrane synthesis by low oxygen tension.
Molecular mapping of the heparin-binding exosite of thrombin.
Authors: Sheehan J P , Sadler J E
Published: May 2006

Thrombin contains electropositive patches at opposite poles of the molecule which represent potential exosites for the binding of macromolecular ligands. The function of anion-binding exosite I, the fibrin(ogen) recognition site, has been well described. Anion-binding exosite II, located near the carboxyl terminus of the molecule, has been proposed to bind heparin on the basis of chemical modification studies. To define the functional heparin-binding site on thrombin, purified recombinant alpha-thrombins were prepared with glutamic acid substitution for selected basic amino acid residues in exosite II or exosite I. Heparin affinity was assessed by NaCl gradient elution from heparin-agarose, and second-order rate constants for inhibition by antithrombin III were determined in the absence and presence of heparin. Affinity for heparin-agarose was reduced markedly by selected mutations in exosite II (R89E, R245E, K248E, and K252E, numbered from the amino terminus of the B chain) but not by other mutations in exosite II (K174E, K247E) or by mutations in exosite I (R68E, K154E). All recombinant thrombins had similar rate constants for inhibition by antithrombin III without heparin. However, affinity for heparin-agarose correlated directly with the rate of inhibition by antithrombin III with heparin. These results demonstrate that selected mutations in anion-binding exosite II define a functional heparin-binding site and support the template mechanism of heparin action.
Selective inactivation of viruses in the presence of human platelets: UV sensitization with psoralen derivatives.
Authors: Goodrich R P , Yerram N R , Tay-Goodrich B H , Forster P , Platz M S , Kasturi C , Park S C , Aebischer N J , Rai S , Kulaga L
Published: May 2006

Inactivation of viruses in blood products requires that the method employed display selectivity in its action for viral elements while not affecting the biological entity of interest. Several methods have been developed for the treatment of human plasma or products derived from human plasma. An effective technique for the treatment of the cellular components of blood has been lacking, in part due to the inability to develop agents capable of selectively targeting viral agents in the milieu of cellular material. In this paper, we examine the behavior of a group of viral sensitizers designed to be added to cellular samples and be activated upon exposure to UVA light. Upon activation, these agents are capable of disrupting nucleic acids of the virus in a manner that renders them inactive for proliferation. The selectivity observed in this inactivation is determined by the chemical structure of the sensitizer, which can be varied to increase viral killing capacity while diminishing collateral damage to cellular and protein constituents.
Finding a needle in a haystack: detection of a small protein (the 12-kDa VP26) in a large complex (the 200-MDa capsid of herpes simplex virus).
Authors: Booy F P , Trus B L , Newcomb W W , Brown J C , Conway J F , Steven A C
Published: May 2006

Macromolecular complexes that consist of homopolymeric protein frameworks with additional proteins attached at strategic sites for a variety of structural and functional purposes are widespread in subcellular biology. One such complex is the capsid of herpes simplex virus type 1 whose basic framework consists of 960 copies of the viral protein, VP5 (149 kDa), arranged in an icosahedrally symmetric shell. This shell also contains major amounts of three other proteins, including VP26 (12 kDa), a small protein that is approximately equimolar with VP5 and accounts for approximately 6% of the capsid mass. With a view to inferring the role of VP26 in capsid assembly, we have localized it by quantitative difference imaging based on three-dimensional reconstructions calculated from cryo-electron micrographs. Purified capsids from which VP26 had been removed in vitro by treatment with guanidine hydrochloride were compared with preparations of the same depleted capsids to which purified VP26 had been rebound and with native (undepleted) capsids. The resulting three-dimensional density maps indicate that six VP26 subunits are distributed symmetrically around the outer tip of each hexon protrusion on VP26-containing capsids. Because VP26 may be readily dissociated from and reattached to the capsid, it does not appear to contribute significantly to structural stabilization. Rather, its exposed location suggests that VP26 may be involved in linking the capsid to the surrounding tegument and envelope at a later stage of viral assembly.
D-MEF2: a MADS box transcription factor expressed in differentiating mesoderm and muscle cell lineages during Drosophila embryogenesis.
Authors: Lilly B , Galewsky S , Firulli A B , Schulz R A , Olson E N
Published: May 2006

The myocyte enhancer factor (MEF) 2 family of transcription factors has been implicated in the regulation of muscle transcription in vertebrates. We have cloned a protein from Drosophila, termed D-MEF2, that shares extensive amino acid homology with the MADS (MCM1, Agamous, Deficiens, and serum-response factor) domains of the vertebrate MEF2 proteins. D-mef2 gene expression is first detected during Drosophila embryogenesis within mesodermal precursor cells prior to specification of the somatic and visceral muscle lineages. Expression of D-mef2 is dependent on the mesodermal determinants twist and snail but independent of the homeobox-containing gene tinman, which is required for visceral muscle and heart development. D-mef2 expression precedes that of the MyoD homologue, nautilus, and, in contrast to nautilus, D-mef2 appears to be expressed in all somatic and visceral muscle cell precursors. Its temporal and spatial expression patterns suggest that D-mef2 may play an important role in commitment of mesoderm to myogenic lineages.
A trigonometric sum relevant to the nonrelativistic theory of atoms.
Authors: Córdoba A , Fefferman C , Seco L
Published: May 2006

We extend Van der Corput's method for exponential sums to study an oscillatory term appearing in the quantum theory of large atoms. We obtain an interpretation in terms of classical dynamics and we produce sharp asymptotic upper and lower bounds for the oscillations.
Radiation inactivation of human gamma-interferon: cellular activation requires two dimers.
Authors: Langer J A , Rashidbaigi A , Garotta G , Kempner E
Published: May 2006

gamma-Interferon (IFN-gamma) is a 17-kDa broad-spectrum cytokine which exerts its effects on a variety of target cells through its interaction with the IFN-gamma receptor. Although physicochemical studies of Escherichia coli-derived IFN-gamma, as well as its crystal structure, demonstrate that it is a homodimer in solution (M(r) 34,000), previous radiation inactivation studies yielded a functional size for IFN-gamma of 63-73 kDa in an antiviral assay. To understand the relationship between the solution form of IFN-gamma and the moiety that actually binds to the cellular receptor and activates cells, we examined irradiated nonradioactive and 32P-labeled IFN-gamma for its migration in SDS/polyacrylamide gels (to determine its physical integrity), its binding to cells, its reactivity in an ELISA, and its antiviral activity. The functional size of IFN-gamma differed in the assays, being 22 +/- 2 kDa for the physical destruction of IFN-gamma, 56 +/- 2 kDa for the cellular binding assay, 45-50 kDa for reactivity in the ELISA, and 72 +/- 6 kDa for antiviral activity. The results from the binding assays constitute direct evidence that IFN-gamma binds to its cellular receptor as a dimer. However, for antiviral activity, the functional mass is equivalent to a tetramer. This is consistent with models involving ligand-induced receptor dimerization, whereby two dimers acting in concert (equivalent to the target size of a tetramer) are required to activate cells in the antiviral assay.
Disulfide linkages in the in vitro refolded intermediates of recombinant human macrophage-colony-stimulating factor: analysis of the sulfhydryl alkylation of free cysteine residues by fast-atom bombardment mass spectrometry.
Authors: Glocker M O , Arbogast B , Milley R , Cowgill C , Deinzer M L
Published: May 2006

Fast-atom bombardment mass spectrometry was used to follow the time course of disulfide bond formation during in vitro refolding of recombinant human macrophage-colony-stimulating factor. The content of iodoacetamide-alkylated half-cystines in proteolytic peptides of trapped refolding intermediates collected at 0, 6, 17, 24, and 72 hr was determined under reducing conditions. Size-exclusion high-performance liquid chromatography analyses of the collected alkylated samples indicate that aggregated monomer proceeded through a nonaggregated monomer to an intermediate dimer and finally to the fully folded and active dimer. Underalkylation was first detected by fast-atom bombardment mass spectrometry in 17-hr samples at Cys157 and Cys159 and this corresponded to the first sample containing dimer. Analyses of intermediates from subsequent time points indicated a decrease in alkylated sulfhydryls, and at 72 hr no alkylated peptide was detected. Early samples containing only monomer showed no evidence of disulfide bonds, and the occurrence of disulfide shuffling at the monomer stage could be ruled out under the highly reducing conditions used for refolding. Biological activity was not detectable in early samples but increased to 3.6% after 24 hr of refolding and to 86% of maximum at the 72-hr time point.
Antibody catalysis of peptide bond formation.
Authors: Jacobsen J R , Schultz P G
Published: May 2006

An antibody generated against a neutral phosphonate diester transition-state (TS not equal to) analog catalyzes the formation of an amide bond between a phenylalanyl amino group and an acyl azide derived from L-alanine. The antibody is selective for L- vs. D-alanine and does not catalyze the hydrolysis of the acyl azide to an appreciable degree. A rate acceleration of 10,000-fold relative to the uncatalyzed reaction is observed. The antibody may achieve its catalytic efficiency both by acting as an entropy trap and by stabilizing the deprotonated form of the amine nucleophile. These experiments constitute a first step toward a general strategy for the generation of sequence-specific peptide ligases.