bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of GABRG3 With Alcohol Dependence
Authors: Dick Danielle M. , Edenberg Howard J. , Xuei Xiaoling , Goate Alison , Kuperman Sam , Schuckit Marc , Crowe Raymond , Smith Tom L. , Porjesz Bernice , Begleiter Henri , Foroud Tatiana 
Published: January 2004

Abstract: Background: Evidence from human, animal, and in vitro cell models suggests that γ‐aminobutyric acid (GABA), the major inhibitory neurotransmitter in the human central nervous system, is involved in many of the neurochemical pathways that affect alcohol use, abuse, and dependence. Both linkage and association to the region on chromosome 15q that contains a cluster of GABAA receptor genes have previously been reported, but the role of these genes in alcoholism remains inconclusive.Methods: We conducted family‐based association analyses by using a large sample of multiplex alcoholic families collected as part of the Collaborative Study on the Genetics of Alcoholism, to test for an association between alcohol dependence and the GABAA receptor genes clustered on chromosome 15q. Multiple single‐nucleotide polymorphisms were tested in each of the three chromosome 15q GABAA receptor genes:GABRA5, GABRB3, and GABRG3.Results: Using both classic trio‐based analyses and extended‐family analyses, we found consistent evidence of association between alcohol dependence and GABRG3. Nearly all single‐nucleotide polymorphisms across the gene yielded evidence of association, and haplotype analyses were highly significant. No consistent evidence of association was observed with either GABRA5 or GABRB3, nor was there evidence for parent‐of‐origin effects with any of the genes.Conclusions: These analyses suggest that GABRG3 may be involved in the risk for alcohol dependence. These findings support the theory that the predisposition to alcoholism may be inherited as a general state of central nervous system disinhibition/hyperexcitability that results from an altered responsiveness to GABA.
Solvent–amino acid interaction energies in three‐dimensional‐lattice Monte Carlo simulations of a model 27‐mer protein: Folding thermodynamics and kinetics
Authors: Leonhard Kai , Prausnitz John M. , Radke Clayton J. 
Published: January 2004

AbstractAmino acid residue–solvent interactions are required for lattice Monte Carlo simulations of model proteins in water. In this study, we propose an interaction‐energy scale that is based on the interaction scale by Miyazawa and Jernigan. It permits systematic variation of the amino acid–solvent interactions by introducing a contrast parameter for the hydrophobicity, Cs, and a mean attraction parameter for the amino acids, ω. Changes in the interaction energies strongly affect many protein properties. We present an optimized energy parameter set for best representing realistic behavior typical for many proteins (fast folding and high cooperativity for single chains). Our optimal parameters feature a much weaker hydrophobicity contrast and mean attraction than does the original interaction scale. The proposed interaction scale is designed for calculating the behavior of proteins in bulk and at interfaces as a function of solvent characteristics, as well as protein size and sequence.
High‐temperature solution NMR structure of TmCsp
Authors: Jung Astrid , Bamann Christian , Kremer Werner , Kalbitzer Hans Robert , Brunner Eike 
Published: January 2004

AbstractCold shock proteins (Csps) are assumed to play a central role in the regulation of gene expression under cold shock conditions. Acting as single‐stranded nucleic acid‐binding proteins, they trigger the translation process and are therefore involved in the compensation of the influence of low temperatures (cold shock) upon the cell metabolism. However, it is unknown so far how Csps are switched on and off as a function of temperature. The aim of the present study is the study of possible structural changes responsible for this switching process. 1H‐15N HSQC spectra recorded at different temperatures and chemical‐shift analysis have indicated subtle conformational changes for the cold‐shock protein from the hyperthermophilic bacterium Thermotoga maritima (TmCsp) when the temperature is elevated from 303 K to its physiological temperature (343 K). The three‐dimensional structure of TmCsp was determined by nuclear magnetic resonance (NMR) spectroscopy at 343 K to obtain quantitative information concerning these structural changes. By use of residual dipolar couplings, the loss of NOE information at high temperature could be compensated successfully. Most pronounced conformational changes compared with room‐temperature conditions are observed for amino acid residues closely neighbored to two characteristic β‐bulges and a well‐defined loop region of the protein. Because the residues shown to be responsible for the interaction of TmCsp with single‐stranded nucleic acids can almost exclusively be found within these regions, nucleic acid‐binding activity might be down‐regulated with increasing temperature by the described conformational changes.
An automated in vitro protein folding screen applied to a human dynactin subunit
Authors: Scheich Christoph , Niesen Frank H. , Seckler Robert , Büssow Konrad 
Published: January 2004

AbstractThe preparation of proteins for structural and functional analysis using the Escherichia coli expression system is often hampered by the formation of insoluble intracellular protein aggregates (inclusion bodies). Transferring those proteins into their native states by in vitro protein folding requires screening for the best buffer conditions and suitable additives. However, it is difficult to assess the success of such a screen if no biological assay is available. We established a fully automated folding screen and a system to detect folded protein that is based on analytical hydrophobic interaction chromatography and tryptophan fluorescence spectroscopy. The system was evaluated with two model enzymes (carbonic anhydrase II and malate dehydrogenase), and was successfully applied to the folding of the p22 subunit of human dynactin, which is expressed in inclusion bodies in E. coli. The described screen allows for high‐throughput folding analysis of inclusion body proteins for structural and functional analyses.
A simple formalism on dynamics of proteins on potential energy landscapes
Authors: Murugan Rajamanickam , Mazumdar Shymalava 
Published: January 2004

AbstractWe present a simple formalism for the dynamics of proteins on a potential energy landscape, using connectedness of configurational domains as an order parameter. This formalism clearly shows that the energy bias required to form a unit correct contact toward the native configuration of a two‐state folder, to overcome Levinthal's paradox, is Ebias ≅ RT ln 2. This result agrees well with earlier studies and indicates that the bias is mainly due to hydrophobic interaction. Further investigations have shown that the landscape funnel could be experimentally mapped onto a two‐dimensional space formed by denaturant concentration and the connectedness of configurational domains. The theoretical value of the depth‐of‐folding funnel in terms of denaturant concentration has been calculated for a model protein (P450cam), which agrees well with the experimental value. Using our model, it is also possible to explain the turnover nature of heat‐capacity change upon unfolding of proteins and the existence of enthalpy and entropy convergence temperatures during unfolding without any strict assumptions as proposed in earlier studies.
An accurate, residue‐level, pair potential of mean force for folding and binding based on the distance‐scaled, ideal‐gas reference state
Authors: Zhang Chi , Liu Song , Zhou Hongyi , Zhou Yaoqi 
Published: January 2004

AbstractStructure prediction on a genomic scale requires a simplified energy function that can efficiently sample the conformational space of polypeptide chains. A good energy function at minimum should discriminate native structures against decoys. Here, we show that a recently developed, residue‐specific, all‐atom knowledge‐based potential (167 atomic types) based on distance‐scaled, finite ideal‐gas reference state (DFIRE‐all‐atom) can be substantially simplified to 20 residue types located at side‐chain center of mass (DFIRE‐SCM) without a significant change in its capability of structure discrimination. Using 96 standard multiple decoy sets, we show that there is only a small reduction (from 80% to 78%) in success rate of ranking native structures as the top 1. The success rate is higher than two previously developed, all‐atom distance‐dependent statistical pair potentials. Applied to structure selections of 21 docking decoys without modification, the DFIRE‐SCM potential is 29% more successful in recognizing native complex structures than an all‐atom statistical potential trained by a database of dimeric interfaces. The potential also achieves 92% accuracy in distinguishing true dimeric interfaces from artificial crystal interfaces. In addition, the DFIRE potential with the Cα positions as the interaction centers recognizes 123 native structures out of a comprehensive 125‐protein TOUCHSTONE decoy set in which each protein has 24,000 decoys with only Cα positions. Furthermore, the performance by DFIRE‐SCM on newly established 25 monomeric and 31 docking Rosetta‐decoy sets is comparable to (or better than in the case of monomeric decoy sets) that of a recently developed, all‐atom Rosetta energy function enhanced with an orientation‐dependent hydrogen bonding potential.
The interface of a membrane‐spanning leucine zipper mapped by asparagine‐scanning mutagenesis
Authors: Ruan Weiming , Lindner Eric , Langosch Dieter 
Published: January 2004

AbstractAn oligo‐leucine sequence has previously been shown to function as an artificial transmembrane segment that efficiently self‐assembles in membranes and in detergent solution. Here, a novel technique, asparagine‐scanning mutagenesis, was applied to probe the interface of the self‐assembled oligo‐leucine domain. This novel approach identifies interfacial residues whose exchange to asparagine leads to enhanced self‐interaction of transmembrane helices by interhelical hydrogen bond formation. As analyzed by the ToxR system in membranes, the interface formed by the oligo‐leucine domain is based on a leucine‐zipper‐like heptad repeat pattern of amino acids. In general, the strongest impacts on self‐assembly were seen with asparagines located around the center of the sequence, indicating that interaction is be more efficient here than at the termini of the transmembrane domains.
The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV‐1 protease
Authors: Trylska Joanna , Grochowski Paweł , McCammon J. Andrew 
Published: January 2004

AbstractThe hydrogen‐bond network in various stages of the enzymatic reaction catalyzed by HIV‐1 protease was studied through quantum‐classical molecular dynamics simulations. The approximate valence bond method was applied to the active site atoms participating directly in the rearrangement of chemical bonds. The rest of the protein with explicit solvent was treated with a classical molecular mechanics model. Two possible mechanisms were studied, general‐acid/general‐base (GA/GB) with Asp 25 protonated at the inner oxygen, and a direct nucleophilic attack by Asp 25. Strong hydrogen bonds leading to spontaneous proton transfers were observed in both reaction paths. A single‐well hydrogen bond was formed between the peptide nitrogen and outer oxygen of Asp 125. The proton was diffusely distributed with an average central position and transferred back and forth on a picosecond scale. In both mechanisms, this interaction helped change the peptide‐bond hybridization, increased the partial charge on peptidyl carbon, and in the GA/GB mechanism, helped deprotonate the water molecule. The inner oxygens of the aspartic dyad formed a low‐barrier, but asymmetric hydrogen bond; the proton was not positioned midway and made a slightly elongated covalent bond, transferring from one to the other aspartate. In the GA/GB mechanism both aspartates may help deprotonate the water molecule. We observed the breakage of the peptide bond and found that the protonation of the peptidyl amine group was essential for the peptide‐bond cleavage. In studies of the direct nucleophilic mechanism, the peptide carbon of the substrate and oxygen of Asp 25 approached as close as 2.3 Å.
Disabling the folding catalyst is the last critical step in α‐lytic protease folding
Authors: Cunningham Erin L. , Agard David A. 
Published: January 2004

AbstractAlpha‐Lytic protease (αLP) is an extracellular bacterial pro‐protease marked by extraordinary conformational rigidity and a highly cooperative barrier to unfolding. Although these properties successfully limit its proteolytic destruction, thereby extending the functional lifetime of the protease, they come at the expense of foldability (t1/2 = 1800 yr) and thermodynamic stability (native αLP is less stable than the unfolded species). Efficient folding has required the coevolution of a large N‐terminal pro region (Pro) that rapidly catalyzes αLP folding (t1/2 = 23 sec) and shifts the thermodynamic equilibrium in favor of folded protease through tight native‐state binding. Release of active αLP from this stabilizing, but strongly inhibitory, complex requires the proteolytic destruction of Pro. αLP is capable of initiating Pro degradation via cleavage of a flexible loop within the Pro C‐terminal domain. This single cleavage event abolishes Pro catalysis while maintaining strong native‐state binding. Thus, the loop acts as an Achilles' heel by which the Pro foldase machinery can be safely dismantled, preventing Pro‐catalyzed unfolding, without compromising αLP native‐state stability. Once the loop is cleaved, Pro is rapidly degraded, releasing active αLP.
Crystal structure of a tetrameric GDP‐d‐mannose 4,6‐dehydratase from a bacterial GDP‐d‐rhamnose biosynthetic pathway
Authors: Webb Nicole A. , Mulichak Anne M. , Lam Joseph S. , Rocchetta Heather L. , Garavito R. Michael 
Published: January 2004

Abstractd‐Rhamnose is a rare 6‐deoxy monosaccharide primarily found in the lipopolysaccharide of pathogenic bacteria, where it is involved in host–bacterium interactions and the establishment of infection. The biosynthesis of d‐rhamnose proceeds through the conversion of GDP‐d‐mannose by GDP‐d‐mannose 4,6‐dehydratase (GMD) to GDP‐4‐keto‐6‐deoxymannose, which is subsequently reduced to GDP‐d‐rhamnose by a reductase. We have determined the crystal structure of GMD from Pseudomonas aeruginosa in complex with NADPH and GDP. GMD belongs to the NDP‐sugar modifying subfamily of the short‐chain dehydrogenase/reductase (SDR) enzymes, all of which exhibit bidomain structures and a conserved catalytic triad (Tyr‐XXX‐Lys and Ser/Thr). Although most members of this enzyme subfamily display homodimeric structures, this bacterial GMD forms a tetramer in the same fashion as the plant MUR1 from Arabidopsis thaliana. The cofactor binding sites are adjoined across the tetramer interface, which brings the adenosyl phosphate moieties of the adjacent NADPH molecules to within 7 Å of each other. A short peptide segment (Arg35–Arg43) stretches into the neighboring monomer, making not only protein–protein interactions but also hydrogen bonding interactions with the neighboring cofactor. The interface hydrogen bonds made by the Arg35–Arg43 segment are generally conserved in GMD and MUR1, and the interacting residues are highly conserved among the sequences of bacterial and eukaryotic GMDs. Outside of the Arg35–Arg43 segment, residues involved in tetrameric contacts are also quite conserved across different species. These observations suggest that a tetramer is the preferred, and perhaps functionally relevant, oligomeric state for most bacterial and eukaryotic GMDs.
Zymogenic and enzymatic properties of the 70–80 loop mutants of factor X/Xa
Authors: Chen Lin , Manithody Chandrashekhara , Yang Likui , Rezaie Alireza R. 
Published: January 2004

AbstractThe Ca2+ binding 70–80 loop of factor X (fX) contains one basic (Arg71) and three acidic (Glu74, Glu76, and Glu77) residues whose contributions to the zymogenic and enzymatic properties of the protein have not been evaluated. We prepared four Ala substitution mutants of fX (R71A, E74A, E76A, and E77A) and characterized their activation kinetics by the factor VIIa and factor IXa in both the absence and presence of cofactors. Factor VIIa exhibited normal activity toward E74A and E76A and less than a twofold impaired activity toward R71A and E77A in both the absence and presence of tissue factor. Similarly, factor IXa in the absence of factor VIIIa exhibited normal activity toward both E74A and E76A; however, its activity toward R71A and E77A was impaired approximately two‐ to threefold. In the presence of factor VIIIa, factor IX activated all mutants with approximately two‐ to fivefold impaired catalytic efficiency. In contrast to changes in their zymogenic properties, all mutant enzymes exhibited normal affinities for factor Va, and catalyzed the conversion of prothrombin to thrombin with normal catalytic efficiencies. However, further studies revealed that the affinity of mutant enzymes for interaction with metal ions Na+ and Ca2+ was impaired. These results suggest that although charged residues of the 70–80 loop play an insignificant role in fX recognition by the factor VIIa‐tissue factor complex, they are critical for the substrate recognition by factor IXa in the intrinsic Xase complex. The results further suggest that mutant residues do not play a specific role in the catalytic function of fXa in the prothrombinase complex.
Accurate and efficient loop selections by the DFIRE‐based all‐atom statistical potential
Authors: Zhang Chi , Liu Song , Zhou Yaoqi 
Published: January 2004

AbstractThe conformations of loops are determined by the water‐mediated interactions between amino acid residues. Energy functions that describe the interactions can be derived either from physical principles (physical‐based energy function) or statistical analysis of known protein structures (knowledge‐based statistical potentials). It is commonly believed that statistical potentials are appropriate for coarse‐grained representation of proteins but are not as accurate as physical‐based potentials when atomic resolution is required. Several recent applications of physical‐based energy functions to loop selections appear to support this view. In this article, we apply a recently developed DFIRE‐based statistical potential to three different loop decoy sets (RAPPER, Jacobson, and Forrest‐Woolf sets). Together with a rotamer library for side‐chain optimization, the performance of DFIRE‐based potential in the RAPPER decoy set (385 loop targets) is comparable to that of AMBER/GBSA for short loops (two to eight residues). The DFIRE is more accurate for longer loops (9 to 12 residues). Similar trend is observed when comparing DFIRE with another physical‐based OPLS/SGB‐NP energy function in the large Jacobson decoy set (788 loop targets). In the Forrest‐Woolf decoy set for the loops of membrane proteins, the DFIRE potential performs substantially better than the combination of the CHARMM force field with several solvation models. The results suggest that a single‐term DFIRE‐statistical energy function can provide an accurate loop prediction at a fraction of computing cost required for more complicate physical‐based energy functions. A Web server for academic users is established for loop selection at the softwares/services section of the Web site http://theory.med.buffalo.edu/.
Blinded by the Enlightenment: Günter Grass in Calcutta
Authors: Reynolds Daniel 
Published: January 2004

AbstractGünter Grass's 1988 Zunge zeigen has been criticised as an example of Eurocentricism, an especially harsh charge against this author known for his critique of globalisation. The claim that Grass writes about India as a colonising Westerner overlooks the ways in which he undermines the sovereignty of the Western subject through his polyphonic, self‐reflexive account. The result is a sincere attempt to destabilise the oppressive subject he has been accused of promoting. This attempt notwithstanding, Grass's critique does falter for two reasons that critics of Zunge zeigen have not addressed. The first concerns his use of Theodor Fontane both as a bridge to the history of colonialism and as a model for engaged literature. Fontane proves tenuous on both counts, and diverts Grass's attention both from India's colonial history and literary present. Second, Grass's prescription for overcoming the misery he documents in India and Bangladesh – the Enlightenment – ultimately reinscribes a discourse of domination that favours Europe. By choosing Kali, the Hindu goddess of destruction, to represent India, Grass reinforces the notion that rationality is a European invention that is alien to the mystical, chaotic East. Ultimately, Grass fails to account for the Enlightenment's own historical complicity in colonialism.
‘Phantomspuren’: Zu W.G. Sebalds Poetik der Erinnerung in Austerlitz
Authors: Fuchs Anne 
Published: January 2004

AbstractDie vorliegende Lektüre von Sebalds Roman Austerlitz beschäftigt sich mit dem Entwurf eben jenes ethisch motivierten Erinnerungskonzepts, das für die Prosa Sebalds insgesamt konstitutiv ist. Es geht damit im Folgenden um die Frage, wie der Anspruch auf eine Platzhalterschaft für die Opfer der Geschichte erzählerisch umgesetzt wird, oder in Austerlitzens eigenen Worten, um die ‘Schmerzensspuren, die sich in unzähligen feinen Linien durch die Geschichte ziehen’. Hierbei zeigt die Analyse des Sebaldschen Umgangs mit den Themen Archiv, Historiographie, Namen, Intertextualität, bricolage und Film, dass Sebald Erinnerung grundsätzlich als eine von der Imagination geleitete Spurensuche in Szene setzt, die mit einem Benjaminschen Verfahren der ästhetischen Analogiebildung arbeitet. Sebalds oft diskutierter Enzyklopädismus resultiert daher auch in Austerlitz niemals in der rationalen Erledigung der Vergangenheit, sondern umgekehrt in der hyperbolischen Verrätselung der Geschichtserfahrung. Erinnern in der Sebaldschen Prosa wird damit beschreibbar als eine Phantomjagd, welche nicht‐rationale und halluzinatorische Korrespondenzen zwischen den Gegenständen freilegt, um so die epistemologische Unbegreiflichkeit eines katastrophalen Geschichtsverlaufs zum Vorschein zu bringen.