bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of an optimal Chebyshev‐expanded discrimination function for globular proteins
Authors: Fain Boris , Xia Yu , Levitt Michael 
Published: October 2002

AbstractWe describe the construction of a scoring function designed to model the free energy of protein folding. An optimization technique is used to determine the best functional forms of the hydrophobic, residue‐residue and hydrogen‐bonding components of the potential. The scoring function is expanded by use of Chebyshev polynomials, the coefficients of which are determined by minimizing the score, in units of standard deviation, of native structures in the ensembles of alternate decoy conformations. The derived effective potential is then tested on decoy sets used conventionally in such studies. Using our scoring function, we achieve a high level of discrimination between correct and incorrect folds. In addition, our method is able to represent functions of arbitrary shape with fewer parameters than the usual histogram potentials of similar resolution. Finally, our representation can be combined easily with many optimization methods, because the total energy is a linear function of the parameters. Our results show that the techniques of Z‐score optimization and Chebyshev expansion work well.
Thermal denaturation of Bungarus fasciatus acetylcholinesterase: Is aggregation a driving force in protein unfolding?
Authors: Shin I. , Wachtel E. , Roth E. , Bon C. , Silman I. , Weiner L. 
Published: October 2002

AbstractA monomeric form of acetylcholinesterase from the venom of Bungarus fasciatus is converted to a partially unfolded molten globule species by thermal inactivation, and subsequently aggregates rapidly. To separate the kinetics of unfolding from those of aggregation, single molecules of the monomeric enzyme were encapsulated in reverse micelles of Brij 30 in 2,2,4‐trimethylpentane, or in large unilamellar vesicles of egg lecithin/cholesterol at various protein/micelle (vesicle) ratios. The first‐order rate constant for thermal inactivation at 45°C, of single molecules entrapped within the reverse micelles (0.031 min−1), was higher than in aqueous solution (0.007 min−1) or in the presence of normal micelles (0.020 min−1). This clearly shows that aggregation does not provide the driving force for thermal inactivation of BfAChE. Within the large unilamellar vesicles, at average protein/vesicle ratios of 1:1 and 10:1, the first‐order rate constants for thermal inactivation of the encapsulated monomeric acetylcholinesterase, at 53°C, were 0.317 and 0.342 min−1, respectively. A crosslinking technique, utilizing the photosensitive probe, hypericin, showed that thermal denaturation produces a distribution of species ranging from dimers through to large aggregates. Consequently, at a protein/vesicle ratio of 10:1, aggregation can occur upon thermal denaturation. Thus, these experiments also demonstrate that aggregation does not drive the thermal unfolding of Bungarus fasciatus acetylcholinesterase. Our experimental approach also permitted monitoring of recovery of enzymic activity after thermal denaturation in the absence of a competing aggregation process. Whereas no detectable recovery of enzymic activity could be observed in aqueous solution, up to 23% activity could be obtained for enzyme sequestered in the reverse micelles.
Active site geometry of oxalate decarboxylase from Flammulina velutipes: Role of histidine‐coordinated manganese in substrate recognition
Authors: Chakraborty Subhra , Chakraborty Niranjan , Jain Deepti , Salunke Dinakar M. , Datta Asis 
Published: October 2002

AbstractOxalate decarboxylase (OXDC) from the wood‐rotting fungus Flammulina velutipes, which catalyzes the conversion of oxalate to formic acid and CO2 in a single‐step reaction, is a duplicated double‐domain germin family enzyme. It has agricultural as well as therapeutic importance. We reported earlier the purification and molecular cloning of OXDC. Knowledge‐based modeling of the enzyme reveals a β‐barrel core in each of the two domains organized in the hexameric state. A cluster of three histidines suitably juxtaposed to coordinate a divalent metal ion exists in both the domains. Involvement of the two histidine clusters in the catalytic mechanism of the enzyme, possibly through coordination of a metal cofactor, has been hypothesized because all histidine knockout mutants showed total loss of decarboxylase activity. The atomic absorption spectroscopy analysis showed that OXDC contains Mn2+ at up to 2.5 atoms per subunit. Docking of the oxalate in the active site indicates a similar electrostatic environment around the substrate‐binding site in the two domains. We suggest that the histidine coordinated manganese is critical for substrate recognition and is directly involved in the catalysis of the enzyme.
α1‐Proteinase inhibitor mutants with specificity for plasma kallikrein and C1s but not C1
Authors: Sulikowski Thomas , Bauer Bryan A. , Patston Philip A. 
Published: October 2002

AbstractCoagulation and complement proteinases are activated in sepsis, and one approach to therapy is to develop proteinase inhibitors that will specifically inhibit these proteinases without inhibiting activated protein C, a proteinase that is beneficial to survival. In this study, we made mutants of the serpin α1‐PI, designed to mimic the specificity of C1‐inhibitor. The P3‐P2‐P1 residues of α1‐PI were changed from IPM to LGR and PFR, sequences preferred by C1s and kallikrein, respectively. Inhibition of C1s, kallikrein, factor XIIa, and activated protein C was assessed by SDS‐PAGE, and by determination of the kapp and SI. α1‐PI‐LGR inhibited C1s with a rate of 7790 M−1s−1, but only minimal inhibition of C1 in a hemolytic assay was observed. Kallikrein, factor XIIa, and activated protein C were inhibited with rates of 382,180 M−1s−1, 10,400 M−1s−1, and 3500 M−1s−1, respectively. α1‐PI‐PFR was a poor inhibitor of C1s, factor XIIa, and activated protein C, but had enhanced reactivity with kallikrein. Changing the P4′ residue of α1‐PI‐LGR Pro to Glu reduced the activity with C1s, consistent with the idea that C1s requires hydrophobic residues in this region of the serpin for optimal interaction. The data provide insight into the requirements for kallikrein and C1s inhibition necessary for designing inhibitors with appropriate properties for further investigation as therapeutic agents.
Surface adhesion of fusion proteins containing the hydrophobins HFBI and HFBII from Trichoderma reesei
Authors: Linder Markus , Szilvay Geza R. , Nakari‐Setälä Tiina , Söderlund Hans , Penttilä Merja 
Published: October 2002

AbstractHydrophobins are surface‐active proteins produced by filamentous fungi, where they seem to be ubiquitous. They have a variety of roles in fungal physiology related to surface phenomena, such as adhesion, formation of surface layers, and lowering of surface tension. Hydrophobins can be divided into two classes based on the hydropathy profile of their primary sequence. We have studied the adhesion behavior of two Trichoderma reesei class II hydrophobins, HFBI and HFBII, as isolated proteins and as fusion proteins. Both hydrophobins were produced as C‐terminal fusions to the core of the hydrolytic enzyme endoglucanase I from the same organism. It was shown that as a fusion partner, HFBI causes the fusion protein to efficiently immobilize to hydrophobic surfaces, such as silanized glass and Teflon. The properties of the surface‐bound protein were analyzed by the enzymatic activity of the endoglucanase domain, by surface plasmon resonance (Biacore), and by a quartz crystal microbalance. We found that the HFBI fusion forms a tightly bound, rigid surface layer on a hydrophobic support. The HFBI domain also causes the fusion protein to polymerize in solution, possibly to a decamer. Although isolated HFBII binds efficiently to surfaces, it does not cause immobilization as a fusion partner, nor does it cause polymerization of the fusion protein in solution. The findings give new information on how hydrophobins function and how they can be used to immobilize fusion proteins.
Impact of domain interchange on conformational stability and equilibrium folding of chimeric class μ glutathione transferases
Authors: Luo Jiann‐Kae , Hornby Judith A.T. , Wallace Louise A. , Chen Jihong , Armstrong Richard N. , Dirr Heini W. 
Published: October 2002

AbstractRat μ class glutathione transferases M1‐1 and M2‐2 are homodimers that share a 78% sequence identity but display differences in stability. M1‐1 is more stable at the secondary and tertiary structural levels, whereas its quaternary structure is less stable. Each subunit in these proteins consists of two structurally distinct domains with intersubunit contacts occurring between domain 1 of one subunit and domain 2 of the other subunit. The chimeric subunit variants M(12), which has domain 1 of M1 and domain 2 of M2, and its complement M(21), were used to investigate the conformational stability of the chimeric homodimers M(12)‐(12) and M(21)‐(21) to determine the contribution of each domain toward stability. Exchanging entire domains between class μ GSTs is accommodated by the GST fold. Urea‐induced equilibrium unfolding data indicate that whereas the class μ equilibrium unfolding mechanism (i.e., N2 ↔ 2I ↔ 2U) is not altered, domain exchanges impact significantly on the conformational stability of the native dimers and monomeric folding intermediates. Data for the wild‐type and chimeric proteins indicate that the order of stability for the native dimer (N2) is M2‐2 > M(12)‐(12) M1‐1 ∼ M(21)‐(21), and that the order of stability of the monomeric intermediate (I) is M1 > M2 ∼ M(12) > M(21). Interactions involving Arg 77, which is topologically conserved in GSTs, appear to play an important role in the stability of both the native dimeric and folding monomeric structures.
The role of irregular unit, GAAS, on the secondary structure of Bombyx mori silk fibroin studied with 13C CP/MAS NMR and wide‐angle X‐ray scattering
Authors: Asakura Tetsuo , Sugino Rena , Okumura Tatsushi , Nakazawa Yasumoto 
Published: October 2002

AbstractBombyx mori silk fibroin is a fibrous protein whose fiber is extremely strong and tough, although it is produced by the silkworm at room temperature and from an aqueous solution. The primary structure is mainly Ala‐Gly alternative copolypeptide, but Gly‐Ala‐Ala‐Ser units appear frequently and periodically. Thus, this study aims at elucidating the role of such Gly‐Ala‐Ala‐Ser units on the secondary structure. The sequential model peptides containing Gly‐Ala‐Ala‐Ser units selected from the primary structure of B. mori silk fibroin were synthesized, and their secondary structure was studied with 13C CP/MAS NMR and wide‐angle X‐ray scattering. The 13C isotope labeling of the peptides and the 13C conformation‐dependent chemical shifts were used for the purpose. The Ala‐Ala units take antiparallel β‐sheet structure locally, and the introduction of one Ala‐Ala unit in (Ala‐Gly)15 chain promotes dramatical structural changes from silk I (repeated β‐turn type II structure) to silk II (antiparallel β‐sheet structure). Thus, the presence of Ala‐Ala units in B. mori silk fibroin chain will be one of the inducing factors of the structural transition for silk fiber formation. The role of Tyr residue in the peptide chain was also studied and clarified to induce “locally nonordered structure.”
The β‐barrel finder (BBF) program, allowing identification of outer membrane β‐barrel proteins encoded within prokaryotic genomes
Authors: Zhai Yufeng , Saier Milton H. 
Published: October 2002

AbstractMany outer membrane proteins (OMPs) in Gram‐negative bacteria possess known β‐barrel three‐dimensional (3D) structures. These proteins, including channel‐forming transmembrane porins, are diverse in sequence but exhibit common structural features. We here report computational analyses of six outer membrane proteins of known 3D structures with respect to (1) secondary structure, (2) hydropathy, and (3) amphipathicity. Using these characteristics, as well as the presence of an N‐terminal targeting sequence, a program was developed allowing prediction of integral membrane β‐barrel proteins encoded within any completely sequenced prokaryotic genome. This program, termed the β‐barrel finder (BBF) program, was used to analyze the proteins encoded within the Escherichia coli genome. Out of 4290 sequences examined, 118 (2.8%) were retrieved. Of these, almost all known outer membrane proteins with established β‐barrel structures as well as many probable outer membrane proteins were identified. This program should be useful for predicting the occurrence of outer membrane proteins in bacteria with completely sequenced genomes.
Interdomain engineered disulfide bond permitting elucidation of mechanisms of inactivation of coagulation factor Va by activated protein C
Authors: Gale Andrew J. , Xu Xiao , Pellequer Jean‐Luc , Getzoff Elizabeth D. , Griffin John H. 
Published: October 2002

AbstractProcoagulant factor Va (FVa) is inactivated via limited proteolysis at three Arg residues in the A2 domain by the anticoagulant serine protease, activated protein C (APC). Cleavage by APC at Arg306 in FVa causes dissociation of the A2 domain from the heterotrimeric A1:A2:A3 structure and complete loss of procoagulant activity. To help distinguish inactivation mechanisms involving A2 domain dissociation from inactivation mechanisms involving unfavorable changes in factor Xa (FXa) affinity, we used our FVa homology model to engineer recombinant FVa mutants containing an interdomain disulfide bond (Cys609‐Cys1691) between the A2 and A3 domains (A2‐SS‐A3 mutants) in addition to cleavage site mutations, Arg506Gln and Arg679Gln. SDS‐PAGE analysis showed that the disulfide bond in A2‐SS‐A3 mutants prevented dissociation of the A2 domain. In the absence of A2 domain dissociation from the A1:A2:A3 trimer, APC cleavage at Arg306 alone caused a sevenfold decrease in affinity for FXa, whereas APC cleavages at Arg306, Arg506, and Arg679 caused a 70‐fold decrease in affinity for FXa and a 10‐fold decrease in the kcat of the prothrombinase complex for prothrombin without any effect on the apparent Km for prothrombin. Therefore, for FVa inactivation by APC, dissociation of the A2 domain may provide only a modest final step, whereas the critical events are the cleavages at Arg506 and Arg306, which effectively inactivate FVa before A2 dissociation can take place. Nonetheless, for FVa Leiden (Gln506‐FVa) inactivation by APC, A2 domain dissociation may become mechanistically important, depending on the ambient FXa concentration.
Majorations Uniformes de Normes D'Inverses Dans Les Algèbres de Beurling
Authors: El-Fallah O. , Ezzaaraoui A. 
Published: October 2002

The Beurling algebras l1(D,ω)(D=N,Z) that are semi‐simple, with compact Gelfand transform, are considered. The paper gives a necessary and sufficient condition (on ω) such that l1(D,ω) possesses a uniform quantitative version of Wiener's theorem in the sense that there exists a function ϕ:]0,+∞[→]0,+∞ such that, for every invertible element x in the unit ball of l1(D,ω), we have‖x−1‖⩽ϕ(r(x−1)) r(x−1) is the spectral radius of x−1.
Tangential Lusternik–Schnirelmann Category of Foliations
Authors: Colman Hellen , Macias-Virgós Enrique 
Published: October 2002

A new invariant of (integrable) homotopy type for foliations is introduced: the tangential category of a foliated manifold.The classical Lusternik–Schnirelmann theory is generalized to foliations and the relations of the tangential category with other known invariants such as the fibrewise and the equivariant category are studied. Cohomological lower bounds are provided in terms of foliated cohomology.If the foliation is a product, the tangential category coincides with the ordinary category of the leaves. In general it is just bounded below. Estimates are given of the tangential category for compact‐Hausdorff foliations and suspensions. Examples show that the lower and upper bounds are realized.
A New Method for Predicting the Opening Angle for Soft Tissues
Authors: Van Dyke Timothy J. , Hoger Anne 
Published: October 2002

Abstract
The purpose of this paper is to present a simple new method for calculating the opening angle produced by a given residual stress field in a soft biological tissue. The method uses minimization of potential energy, and is therefore named the MPE method. The accuracy of the MPE method is evaluated by comparing the opening angle it predicts to results from a finite element model of the opening angle experiment. We show that the MPE method provides good predictions of the opening angle, and that it is significantly more accurate than two other methods previously used in the literature.
Genetic and Biochemical Characterization of CGB-1, an Ambler Class B Carbapenem-Hydrolyzing β-Lactamase from
Chryseobacterium gleum
Authors: Bellais Samuel , Naas Thierry , Nordmann Patrice 
Published: October 2002

ABSTRACT

Chryseobacterium gleum
(previously included in the
Flavobacterium
IIb species) is a gram-negative aerobe that is a source of nosocomial infections. An Ambler class B β-lactamase gene was cloned and expressed in
Escherichia coli
from reference strain
C. gleum
CIP 103039 that had reduced susceptibility to expanded-spectrum cephalosporins and carbapenems. The purified β-lactamase, CGB-1, with a pI value of 8.6 and a determined relative molecular mass of ca. 26 kDa, hydrolyzed penicillins; narrow- and expanded-spectrum cephalosporins; and carbapenems. CGB-1 was a novel member of the molecular subclass B1 of metallo-enzymes. It had 83 and 42% amino acid identity with IND-1 from
Chryseobacterium indologenes
and BlaB from
C. meningosepticum
, respectively. Thus, in addition to the previously characterized clavulanic acid-inhibited extended-spectrum β-lactamase CGA-1 of Ambler class A,
C. gleum
produces a very likely chromosome-borne class B β-lactamase.
Isoniazid-Induced Transient High-Level Resistance in
Mycobacterium tuberculosis
Authors: Viveiros Miguel , Portugal Isabel , Bettencourt Rosário , Victor Thomas C. , Jordaan Annemarie M. , Leandro Clara , Ordway Diane , Amaral Leonard 
Published: October 2002

ABSTRACT

An American Type Culture Collection reference strain and eight clinical strains of
Mycobacterium tuberculosis
, all of which were susceptible to isoniazid (INH) (mean MIC, 0.06 mg/liter) and negative for the Ser315Thr
katG
mutation, were left in their BACTEC 12B vials (for use with the BACTEC 460-TB method) containing 0.1 mg of INH per liter for periods of up to 28 days after the completion of the antibiotic susceptibility test. Each eventually grew to levels compatible with those of INH-resistant strains. Successive passages in INH-containing BACTEC 12B vials and onto solid media showed that the resistance noted above was maintained. Successive passages of these
M. tuberculosis
strains in which INH resistance had been induced into BACTEC 12B vials or solid media containing stepwise increases in INH concentrations eventually yielded organisms resistant to 20 mg of INH per liter. Transfer of cells in which INH resistance had been induced to drug-free medium followed by repeated passages in that medium eventually yielded organisms whose susceptibility to INH was identical to that of the original parent strains. The cycle of induced INH resistance could be repeated with these now INH-susceptible cells. The use of
M. tuberculosis
identification probes and IS
6110
-based restriction fragment length polymorphism analyses of cultures throughout the induction of INH resistance and the reversal of resistance in drug-free medium eliminated the possibility that the culture was contaminated or that the initial specimen had a mixed type of infection. Induced high-level resistance to INH (20 mg/liter) could be reduced 100-fold with a subinhibitory concentration of reserpine but not with verapamil. These results collectively suggest that high-level resistance to INH can be induced in INH-susceptible
M. tuberculosis
strains by the induction of a reserpine-sensitive efflux mechanism.
Samarangenin B from
Limonium sinense
Suppresses Herpes Simplex Virus Type 1 Replication in Vero Cells by Regulation of Viral Macromolecular Synthesis
Authors: Kuo Yuh-Chi , Lin Lie-Chwen , Tsai Wei-Jern , Chou Cheng-Jen , Kung Szu-Hao , Ho Yen-Hui 
Published: October 2002

ABSTRACT

Inhibitory effects of ethanolic extracts from 10 Chinese herbs on herpes simplex virus type 1 (HSV-1) replication were investigated. By a bioassay-guided fractionation procedure, samarangenin B (Sam B) was isolated from
Limonium sinense
; Sam B significantly suppressed HSV-1 multiplication in Vero cells without apparent cytotoxicity. Time-of-addition experiments suggested that the inhibitory action of Sam B on HSV-1 replication was not due to the blocking of virus adsorption. In an attempt to further localize the point in the HSV-1 replication cycle where arrest occurred, a set of key regulatory events leading to viral multiplication was examined, including viral immediate-early (α), early (β), and late (γ) gene expression and DNA replication. Results indicated that levels of glycoprotein B (gB), gC, gD, gG, and infected-cell protein 5 (ICP5) expression and gB mRNA expression in Vero cells were impeded by Sam B. Data from PCR showed that replication of HSV-1 DNA in Vero cells was arrested by Sam B. Furthermore, Sam B decreased DNA polymerase, ICP0, and ICP4 gene expression in Vero cells. Results of an electrophoretic mobility shift assay demonstrated that Sam B interrupted the formation of an α-
trans
-induction factor/C1/Oct-1/GARAT multiprotein complex. The mechanisms of antiviral action of Sam B seem to be mediated, at least in part, by inhibiting HSV-1 α gene expression, including expression of the ICP0 and ICP4 genes, by blocking β transcripts such as DNA polymerase mRNA, and by arresting HSV-1 DNA synthesis and structural protein expression in Vero cells. These results show that Sam B is an antiviral agent against HSV-1 replication.
In Vitro and In Vivo Synergy of Fosmidomycin, a Novel Antimalarial Drug, with Clindamycin
Authors: Wiesner Jochen , Henschker Dajana , Hutchinson David B. , Beck Ewald , Jomaa Hassan 
Published: October 2002

ABSTRACT

Fosmidomycin acts through inhibition of 1-deoxy-
d
-xylulose 5-phosphate (DOXP) reductoisomerase, a key enzyme of the nonmevalonate pathway of isoprenoid biosynthesis. It possesses potent antimalarial activity in vitro and in murine malaria. In a recent clinical study, fosmidomycin was effective and well tolerated in the treatment of patients with acute uncomplicated
Plasmodium falciparum
malaria but resulted in an unacceptably high rate of recrudescence. In order to identify a potential combination partner, the interaction of fosmidomycin with a number of antimalarial drugs in current use was investigated in a series of in vitro experiments. Synergy was observed between fosmidomycin and the lincosamides, lincomycin and clindamycin. The efficacy of a combination of fosmidomycin and clindamycin was subsequently demonstrated in the
Plasmodium vinckei
mouse model.