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B Ma

Publications and source records attributed to B Ma.

At least 37 records · Page 2Linked to original sources
PubMed2001

Combined modality treatment for locally advanced squamous-cell carcinoma of the oropharynx in a woman with Bloom's syndrome: a case report and review of the literature.

We describe a case of locally advanced unresectable squamous-cell carcinoma of the oropharynx in a young woman with Bloom's syndrome. She was treated with radical radiation therapy and concurrent chemotherapy (cisplatin and 5-flurouracil). She was unable to complete treatment due to the development of severe side effects: confluent mucositis, moist desquamating skin reaction, severe diarrhea and severe myelosupression with neutropenic sepsis. The limited relevant literature is presented. We conclude that chemotherapy should be used with extreme caution in Bloom's syndrome patients.

Adult↗
PubMed2001

Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop.

Tetraloops are very abundant structural elements of RNA that are formed by four nucleotides in a hairpin loop which is closed by a double stranded helical stem with some Watson-Crick base pairs. A tetraloop r(GCGAAGGC) was identified from the crystal structure of the central domain of 16S rRNA (727-730) in the Thermus thermophilus 30S ribosomal complex. The crystal structure of the 30S complex includes a total of 104 nucleotides from the central domain of the 16S rRNA and three ribosomal proteins S6, S15 and S18. Independent biochemical experiments have demonstrated that protein S15 plays the role in initiating the formation of the central domain of this complex. In the crystal, the tetraloop interacts with the protein S15 at two sites: one of them is associated with hydrogen bond interactions between residue His50 and nucleotide G730, and the other is associated with the occurrence of residue Arg53 beside A728. This paper uses molecular dynamics (MD) simulations to investigate the protein-dependent structural stability of the tetraloop and demonstrates the folding pathway of this tetraloop via melting denaturation and its subsequent refolding. Three important results are derived from these simulations: (i) The stability of nucleotide A728 appears to be protein dependent. Without the interaction with S15, A728 flips away from stacking with A729. (ii) The melting temperature demonstrated by the simulations is analogous to the results of thermodynamic experiments. In addition, the simulated folding of the tetraloop is stepwise: the native shape of the backbone is formed first; this is then followed by the formation of the Watson- Crick base pairs in the stem; and finally the hydrogen bonds and base stacking in the loop are formed. (iii) The tetraloop structure is similar to the crystal structure at salt concentrations of 0.1 M and 1.0 M used for the simulations, but the refolded structure at 0.1 M salt is more comparable to the crystal structure than at 1.0 M. The results from the simulations using both the Generalized Born continuum model and explicit solvent model (Particle Mesh Ewald) generate a similar pathway for unfolding/refolding of the tetraloop.

Arginine↗
PubMed2001

Protein folding: binding of conformationally fluctuating building blocks via population selection.

Here we review different aspects of the protein folding literature. We present a broad range of observations, showing them to be consistent with a general hierarchical protein folding model. In such a model, local relatively stable, conformationally fluctuating building blocks bind through population selection, to yield the native state. The model includes several components: (1) the fluctuating building blocks that constitute local minima along the polypeptide chain, which even if unstable still possess higher population times than all alternate conformations; (2) the landscape around the bottom of the funnels; (3) the consideration that protein folding involves intramolecular recognition; (4) similar landscapes are observed for folding and for binding, and that (5) the landscape is dynamic, changing with the conditions. The model considers protein folding to be guided by native interactions. The reviewed literature includes the effects of changing the conditions, intermediates and kinetic traps, mutations, similar topologies, fragment complementation experiments, fragments and pathways, focusing on one specific well-studied example, that of the dihydrofolate reductase, chaperones, and chaperonines, in vivo vs. in vitro folding, still using the dihydrofolate example, amyloid formation, and molecular "disorder". These are consistent with the view that binding and folding are similar events, with the differences stemming from different stabilities and hence population times.

Models, Molecular↗
PubMed2001

Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations.

We have carried out molecular dynamics simulations of the native dihydrofolate reductase from Escherichia coli and several of its folded protein fragments at standard temperature. The simulations have shown fragments 1--36, 37--88, and 89--159 to be unstable, with a C(alpha)RMSD (C(alpha) root mean squared deviation) >5 A after 3.0 nsec of simulation. The unfolding of fragment 1--36 was immediate, whereas fragments 37--88 and 89--159 gradually unfolded because of the presence of the beta-sheet core structure. In the absence of residues 1--36, the two distinct domains comprising fragment 39--159 associated with each other, resulting in a stable conformation. This conformation retained most of its native structural elements. We have further simulated fragments derived from computational protein cutting. These were also found to be unstable, with the exception of fragment 104--159. In the absence of alpha(4), the loose loop region of residues 120--127 exhibited a beta-strand-like behavior, associating itself with the beta-sheet core of the protein fragment. The current study suggests that the folding of dihydrofolate reductase involves cooperative folding of distinct domains which otherwise would have been unstable as independent folded units in solution. Finally, the critical role of residues 1--36 in allowing the two distinct domains of fragment 104--159 to fold into the final native conformation is discussed.

Computer Simulation↗
PubMed2001

The green fluorescent protein gene functions as a reporter of gene expression in Phanerochaete chrysosporium.

The enhanced green fluorescent protein (GFP) gene (egfp) was used as a reporter of gene expression driven by the glyceraldehyde-p-dehydrogenase (gpd) gene promoter and the manganese peroxidase isozyme 1 (mnp1) gene promoter in Phanerochaete chrysosporium. Four different constructs were prepared. pUGGM3' and pUGiGM3' contain the P. chrysosporium gpd promoter fused upstream of the egfp coding region, and pUMGM3' and pUMiGM3' contain the P. chrysosporium mnp1 promoter fused upstream of the egfp gene. In all constructs, the egfp gene was followed by the mnp1 gene 3' untranslated region. In pUGGM3' and pUMGM3', the promoters were fused directly with egfp, whereas in pUGiGM3' and pUMiGM3', following the promoters, the first exon (6 bp), the first intron (55 bp), and part of the second exon (9 bp) of the gpd gene were inserted at the 5' end of the egfp gene. All constructs were ligated into a plasmid containing the ura1 gene of Schizophyllum commune as a selectable marker and were used to transform a Ural1 auxotrophic strain of P. chrysosporium to prototrophy. Crude cell extracts were examined for GFP fluorescence, and where appropriate, the extracellular fluid was examined for MnP activity. The transformants containing a construct with an intron 5' of the egfp gene (pUGiGM3' and pUMiGM3') exhibited maximal fluorescence under the appropriate conditions. The transformants containing constructs with no introns exhibited minimal or no fluorescence. Northern (RNA) blots indicated that the insertion of a 5' intron resulted in more egfp RNA than was found in transformants carrying an intronless egfp. These results suggest that the presence of a 5' intron affects the expression of the egfp gene in P. chrysosporium. The expression of GFP in the transformants carrying pUMiGM3' paralled the expression of endogenous mnp with respect to nitrogen and Mn levels, suggesting that this construct will be useful in studying cis-acting elements in the mnp1 gene promoter.

Base Sequence↗
PubMed2001

[Sequencing and comparative analysis of the complete glycoprotein gene of three Crimean-Congo hemorrhagic fever virus Chinese isolates].

OBJECTIVE: To determine the complete sequences of glycoprotein (M) gene of Crimean-Congo hemorrhagic fever virus (CCHFV) Chinese isolates (Xinjiang hemorrhagic fever virus, XHFV) BA66019, BA8402 BA88166 and to compare and analyze the relationships among the viruses. METHODS: Based on the conserved reverse complementarity of the CCHFV genomic termini, a primer PCM-Tag was designed and used together with random hexmers to initiate reverse transcription of viral RNA to synthesize cDNA. The latter was amplified with single primer PCM-Tag using the proof-reading DNA polymerase to produce the complete M gene. The PCR products were gel-purified and the whole M segment was sequenced and the comparison and analysis were performed aided by computer for the phylogenesis and coding strategy. RESULTS: Comparison of the whole M gene sequences of XHFV reference strain BA66019 with international prototype CCHFV IbAr10200 showed an excess of 5 base pairs in length, resulting in 5,365 bp; while BA8402 and BA8816 are 5,365 bp long, 4 more base pairs than IbAr10200. The first start codons of long ORFs were located at the 78th base pair in M gene of BA66019, BA8402 and BA88166, which were 15 base pairs prior to that of IbAr10200. The precursors encoded by these M genes were totaled 1,689 amino acids (AA), 6 AAs more than that of IbAr10200. The similaries between CCHFV M genes in nucleotide level were: 80.9% (IbAr10200-BA66019), 80.2% (IbAr10200-BA8402), 80.2% (IbAr10200-BA88166), 83.7% (BA8402-BA66019), 83.6% (BA88166-BA66019), and 99.0% (BA8402-BA88166), respectively. The corresponding similarities in amino acid level were 85.1%, 86.3%, 86.6%, 87.8%, 88.0%, and 98.8%, respectively. The similarities of M genes of CCHFVs and Dugbe virus in both nucleotide and amino acid levels were around 55% and 37%, which were much lower than those among CCHFVs. CONCLUSION: The M genes of XHFVs and IbAr10200 formed respective independent phylogenetic branches genetically and the human-origin isolate BA88166 might be a variant of tick-borne BA8402, suggesting that there was only one kind virus prevailing in Xinjiang epidemic areas in 1980s.

Amino Acid Sequence↗
PubMed2001

Characterization of a thrombin-like serine protease, Kangshuanmei, isolated from the venom of a Chinese snake, Agkistrodon halys brevicaudus stejneger.

An enzyme, referred to as Kangshuanmei, was isolated from the venom of the Chinese snake Agkistrodon halys brevicaudus stejneger by gel filtration chromatography followed by affinity chromatography. Kangshuanmei is composed of a single polypeptide chain with a molecular weight of approximately 34,000, estimated by SDS-PAGE. The enzyme hydrolyzed both benzoyl-arginine ethyl ester and H-D-Phe-Pip-Arg-p-nitroanilide, specific substrates for thrombin. The protease activity of Kangshuanmei was inhibited by 4-(2-aminoethyl)-benzensulfonyl fluoride, but was not affected by EDTA. The enzyme acted on human fibrinogen to form a fibrin clot and released three fragments. These fragments were shown to be fibrinopeptide A, fibrinopeptide B, and the Bbeta1-42 peptide of fibrinogen, respectively. These results indicate that Kangshuanmei is a thrombin-like serine protease with coagulant activity. However, the enzyme did not induce activation of blood coagulation factor XIII, unlike thrombin. Moreover, antithrombin-III, the specific thrombin inhibitor in plasma, had no inhibitory effect on the thrombin-like amidolytic activity of Kangshuanmei. The N-terminal amino acid sequence of the enzyme up to 50 residues was determined by a peptide sequencer. The N-terminal sequence of Kangshuanmei was highly homologous to most thrombin-like serine proteases from the venom of the snakes of the crotalidae family.

Agkistrodon↗
PubMed2001

beta-Oxidation of simvastatin in mouse liver preparations.

All current 3-hydroxy-3-methylglutaryl-CoA reductase inhibitors [simvastatin (SV), lovastatin (LV), atorvastatin, pravastatin, fluvastatin, and cerivastatin] are believed to undergo an atypical beta-oxidation of the dihydroxy heptanoic or heptanoic acid side chain. Metabolites, which are shortened by two- and/or four-carbon units consistent with beta-oxidation products, have been reported exclusively in rodents following LV and SV administration and across species (rodents, dogs, and humans) following the other statins. In this study, in vitro formation of a beta-oxidation product of simvastatin hydroxy acid (SVA) and its intermediates in mouse livers is described. Incubation of SVA with mouse liver preparations fortified with CoASH and ATP led to formation of SV and two major products (P1 and P2). Based on mass spectrometry (MS), tandem mass spectrometry, and/or NMR spectral characteristics, P1 was an alpha,beta-unsaturated metabolite, formed by dehydration of the D,D-dihydroxy heptanoic acid side chain, whereas P2 was probably the L,D-dihydroxy acid isomer of SVA, formed by stereospecific hydration of P1. When NAD(+) was also included in the incubation mixture, there were two additional metabolites with the MS and/or NMR characteristics consistent with a two-carbon shortened product (P3) and its dehydrated derivative (P4). In a complete incubation system with all cofactors (ATP, CoASH, NAD(+), and NADPH) present, there was an additional product with MS spectra and liquid chromatography retention time identical to the beta-oxidized, unsubstituted pentanoic acid metabolite (P5) detected in rats and mice following simvastatin administration. The involvement of CoASH and NAD(+) and the presence of the four metabolic intermediates suggest that SVA (and presumably the other statins) is a substrate for the beta-oxidation enzyme complex in mice. Additionally, the present finding of CoASH-dependent formation of SV substantiates a mechanism proposed previously for the in vivo lactonization of statin hydroxy acids.

Animals↗
PubMed2001

[Analysis of immunophenotype of hematopoietic stem/progenitor cells in human umbilical cord blood with flow cytometry and its significance].

OBJECTIVE: To study the difference of immunophenotype of hematopoietic stem/progenitor cells (HSPCs) between human umbilical cord blood(UCB) and bone marrow(BM). METHODS: The expression of CD antigens and cell adhesion molecules on HSPCs in 38 UCB and 10 cases BM were investigated with monoclonal antibodies and double immunofluorescence using flow cytometry. RESULTS: 1. The CD34+ cell population in nucleated cells of UCB was similar to that of BM, being about 0.5%; 2. The frequencies of CD34+CD38-, CD34+HLA-DR- and CD34+H-CAM+ (CD44+) cells in UCB CD34+ cells were higher, while the frequencies of CD34+CD13+ and CD34+CD19+ cells in UCB were lower than that in BM. CONCLUSION: The total number of CD34+ cells in UCB and BM was very similar. However, there was a higher proportion of more primary HSPCs in UCB, which was able to reconstitute hematopoiesis as an potential source of HSPCs, the proportion of relatively mature HSPCs (CD34+ CD19+ and CD34+CD13+) were less in UCB than in BM, which probably accounted for the relatively slow haematopoietic reconstitution following UCB transplantation.

Antigens, CD34↗
PubMed2001

[Transcatheter arterial embolization in intractable postpartum hemorrhage].

OBJECTIVE: To asses the value of transcatheter arterial embolization treatment in intractable postpartum hemorrhage. METHODS: Fourteen patients of postpartum hemorrhage failed to the drugs treatment were performed transcatheter arterial embolization (TAE). Superselective catheterization to the bilateral uterial arteries or anterior branches of internal iliac arteries was carried out after intubation to single-side femoral artery by Seldinger's technique. When the catheter tip was proved in right place by digital substraction angiography (DSA) techniques, antibiotic solution was poured into arteries and then the arterial embolization with gelfoam particles was followed. RESULTS: All the patients were performed TAE successfully. The duration of TAE was 30-50 minutes [mean (41.8 +/- 6.4) minutes]. Bleeding was found in DSA mostly as diffuse intrauterine flow outward sign from one side or both side of uterial artery branches. After one time of TAE, the vaginal bleeding of all patients was stopped in 3-10 minutes [mean (6.1 +/- 3.6) minutes]. The follow-up showed that all patients had normal menstrual periods in 2-60 months and no serious complications were found. CONCLUSION: With the characteristic of fast homeostasis and less complications, TAE was proved to be an effective method for intractable postpartum hemorrhage.

Adult↗
PubMed2001

Induced mandibular condylar growth in a sheep model after functional appliance treatment.

This paper reports on changes in mandibular condylar growth in sheep fitted with experimental functional appliances. The paper also addresses the similarities of mandibular condylar growth in sheep and humans. Experimental functional appliances were developed, constructed and applied to four, four-month old, male sheep. Another four sheep served as matched controls. All animals received fluorochrome bone labels during the study and their weight gain also was recorded. Fifteen weeks later, all animals were sacrificed and each temporo-mandibular joint and left metacarpus were removed. Undecalcified mid-sagittal sections of the joint and metacarpus were prepared for fluorescence microscopy. The mandibular condylar growth vector in sheep was found to be in a postero-superior direction. Condylar growth in the control sheep during the experimental period varied from 8.8 to 11.9 mm, with the mean being 10.6 mm, which is quantitatively similar to two years of condylar growth in human adolescents. In the experimental sheep, the condylar growth varied from 8.5 to 13.3 mm, with the mean being 11.4 mm. When metacarpal growth and weight gain were taken into consideration using multivariant analysis, the coefficients for growth in the postero-superior and posterior direction were found to be high, with adjusted r2 as 0.84 and 0.82 respectively. The induced condylar growth was estimated to be largest in the posterior direction (2.30 mm), which is also similar to previous reports in humans. These findings suggest the appropriateness of using sheep as a model for quantitative histological analysis when investigating the mechanisms of functional appliance treatment.

Analysis of Variance↗
PubMed2000

A map of protein-protein contacts within the small nuclear RNA-activating protein complex SNAPc.

The nucleation of RNA polymerases I-III transcription complexes is usually directed by distinct multisubunit factors. In the case of the human RNA polymerase II and III small nuclear RNA (snRNA) genes, whose core promoters consist of a proximal sequence element (PSE) and a PSE combined with a TATA box, respectively, the same multisubunit complex is involved in the establishment of RNA polymerase II and III initiation complexes. This factor, the snRNA-activating protein complex or SNAP(c), binds to the PSE of both types of promoters and contains five types of subunits, SNAP190, SNAP50, SNAP45, SNAP43, and SNAP19. SNAP(c) binds cooperatively with both Oct-1, an activator of snRNA promoters, and in the RNA polymerase III snRNA promoters, with TATA-binding protein, which binds to the TATA box located downstream of the PSE. Here we have defined subunit domains required for SNAP(c) subunit-subunit association, and we show that complexes containing little more than the domains mapped here as required for subunit-subunit contacts bind specifically to the PSE. These data provide a detailed map of the subunit-subunit interactions within a multifunctional basal transcription complex.

Amino Acid Sequence↗
PubMed2000

High-yield formation of giant bis(bicyclic) and crypt-tris(bicyclic) molecules under normal reaction conditions

We report the unexpected result of the reaction of 1, 3-bis[(9-anthrylmethoxy)methyl]benzene (1a) or 1,3, 5-tris[(9-anthrylmethoxy)methyl]benzene (1b) with tris(2-maleimidoethyl)amine (2) in homogeneous solution leading to giant bis(bicyclic) and crypt-tris(bicyclic) molecules. The anticipated, intractable solids are obtained in a condensed state reaction using an oscillating mill.

Journal Article↗
PubMed2000

Conservation of polar residues as hot spots at protein interfaces.

A number of studies have addressed the question of which are the critical residues at protein-binding sites. These studies examined either a single or a few protein-protein interfaces. The most extensive study to date has been an analysis of alanine-scanning mutagenesis. However, although the total number of mutations was large, the number of protein interfaces was small, with some of the interfaces closely related. Here we show that although overall binding sites are hydrophobic, they are studded with specific, conserved polar residues at specific locations, possibly serving as energy "hot spots." Our results confirm and generalize the alanine-scanning data analysis, despite its limited size. Previously Trp, Arg, and Tyr were shown to constitute energetic hot spots. These were rationalized by their polar interactions and by their surrounding rings of hydrophobic residues. However, there was no compelling reason as to why specifically these residues were conserved. Here we show that other polar residues are similarly conserved. These conserved residues have been detected consistently in all interface families that we have examined. Our results are based on an extensive examination of residues which are in contact across protein interfaces. We utilize all clustered interface families with at least five members and with sequence similarity between the members in the range of 20-90%. There are 11 such clustered interface families, comprising a total of 97 crystal structures. Our three-dimensional superpositioning analysis of the occurrences of matched residues in each of the families identifies conserved residues at spatially similar environments. Additionally, in enzyme inhibitors, we observe that residues are more conserved at the interfaces than at other locations. On the other hand, antibody-protein interfaces have similar surface conservation as compared to their corresponding linear sequence alignment, consistent with the suggestion that evolution has optimized protein interfaces for function.

Amino Acid Sequence↗
PubMed2000

Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity?

Proteins are not rigid structures; they are dynamic entities, with numerous conformational isomers (substates). The dynamic nature of protein structures amplifies the structural variation of the transition state for chemical reactions performed by proteins. This suggests that utilizing a transition state ensemble to describe chemical reactions involving proteins may be a useful representation. Here we re-examine the nature of the transition state of protein chemical reactions (enzyme catalysis), considering both recent developments in chemical reaction theory (Marcus theory for SN2 reactions), and protein dynamics effects. The classical theory of chemical reactions relies on the assumption that a reaction must pass through an obligatory transition-state structure. The widely accepted view of enzymatic catalysis holds that there is tight binding of the substrate to the transition-state structure, lowering the activation energy. This picture, may, however, be oversimplified. The real meaning of a transition state is a surface, not a single saddle point on the potential energy surface. In a reaction with a "loose" transition-state structure, the entire transition-state region, rather than a single saddle point, contributes to reaction kinetics. Consequently, here we explore the validity of such a model, namely, the enzymatic modulation of the transition-state surface. We examine its utility in explaining enzyme catalysis. We analyse the possibility that instead of optimizing binding to a well-defined transition-state structure, enzymes are optimized by evolution to bind efficiently with a transition-state ensemble, with a broad range of activated conformations. For enzyme catalysis, the key issue is still transition state (ensemble) stabilization. The source of the catalytic power is the modulation of the transition state. However, our definition of the transition state is the entire transition-state surface rather just than a single well-defined structure. This view of the transition-state ensemble is consistent with the nature of the protein molecule, as embodied and depicted in the protein energy landscape of folding, and binding, funnels.

Animals↗
PubMed2000

Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces.

How is the native structure encoded in the amino acid sequence? For the traditional backbone centric view, the dominant forces are hydrogen bonds (backbone) and phi-psi propensity. The role of hydrophobicity is non-specific. For the side-chain centric view, the dominant force of protein folding is hydrophobicity. In order to understand the balance between backbone and side-chain forces, we have studied the contributions of three components of a beta-hairpin peptide: turn, backbone hydrogen bonding and side-chain interactions, of a 16-residue fragment of protein G. The peptide folds rapidly and cooperatively to a conformation with a defined secondary structure and a packed hydrophobic cluster of aromatic side-chains. Our strategy is to observe the structural stability of the beta-hairpin under systematic perturbations of the turn region, backbone hydrogen bonds and the hydrophobic core formed by the side-chains, respectively. In our molecular dynamics simulations, the peptides are solvated. with explicit water molecules, and an all-atom force field (CFF91) is used. Starting from the original peptide (G41EWTYDDATKTFTVTE56), we carried out the following MD simulations. (1) unfolding at 350 K; (2) forcing the distance between the C(alpha) atoms of ASP47 and LYS50 to be 8 A; (3) deleting two turn residues (Ala48 and Thr49) to form a beta-sheet complex of two short peptides, GEWTYDD and KTFTVTE; (4) four hydrophobic residues (W43, Y45, F52 and T53) are replaced by a glycine residue step-by-step; and (5) most importantly, four amide hydrogen atoms (T44, D46, T53, and T55, which are crucial for backbone hydrogen bonding), are substituted by fluorine atoms. The fluorination not only makes it impossible to form attractive hydrogen bonding between the two beta-hairpin strands, but also introduces a repulsive force between the two strands due to the negative charges on the fluorine and oxygen atoms. Throughout all simulations, we observe that backbone hydrogen bonds are very sensitive to the perturbations and are easily broken. In contrast, the hydrophobic core survives most perturbations. In the decisive test of fluorination, the fluorinated peptide remains folded under our simulation conditions (5 ns, 278 K). Hydrophobic interactions keep the peptide folded, even with a repulsive force between the beta-strands. Thus, our results strongly support a side-chain centric view for protein folding.

Amino Acid Sequence↗
PubMed2000

Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers.

Here we seek to understand the higher frequency of occurrence of salt bridges in proteins from thermophiles as compared to their mesophile homologs. We focus on glutamate dehydrogenase, owing to the availability of high resolution thermophilic (from Pyrococcus furiosus) and mesophilic (from Clostridium symbiosum) protein structures, the large protein size and the large difference in melting temperatures. We investigate the location, statistics and electrostatic strengths of salt bridges and of their networks within corresponding monomers of the thermophilic and mesophilic enzymes. We find that many of the extra salt bridges which are present in the thermophilic glutamate dehydrogenase monomer but absent in the mesophilic enzyme, form around the active site of the protein. Furthermore, salt bridges in the thermostable glutamate dehydrogenase cluster within the hydrophobic folding units of the monomer, rather than between them. Computation of the electrostatic contribution of salt bridge energies by solving the Poisson equation in a continuum solvent medium, shows that the salt bridges in Pyrococcus furiosus glutamate dehydrogenase are highly stabilizing. In contrast, the salt bridges in the mesophilic Clostridium symbiosum glutamate dehydrogenase are only marginally stabilizing. This is largely the outcome of the difference in the protein environment around the salt bridges in the two proteins. The presence of a larger number of charges, and hence, of salt bridges contributes to an electrostatically more favorable protein energy term. Our results indicate that salt bridges and their networks may have an important role in resisting deformation/unfolding of the protein structure at high temperatures, particularly in critical regions such as around the active site.

Clostridium↗