bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Variation at the Chromosome 16 Chemokine Gene Cluster: Development of a Strategy for Association Studies in Complex Disease
Authors: Fisher S. A. , Moody A. , Mirza M. M. , Cuthbert A. P. , Hampe J. , Macpherson A. , Sanderson J. , Forbes A. , Mansfield J. , Schreiber S. , Lewis C. M. , Mathew C. G. 
Published: August 2003

SummaryThe chemokine gene cluster [CCL22, CX3CL1, CCL17] (previously known as [SCYA22, SCYD1, SCYA17]) is a candidate locus for one of the susceptibility genes for inflammatory bowel disease that are located in the peri‐centromeric region of chromosome 16. Screening for sequence variation at this locus led to the detection of 14 single nucleotide polymorphisms (SNPs). An efficient experimental and computational approach was developed to estimate allele frequencies and pairwise linkage disequilibrium relationships between SNPs at this locus, and to test them for association with inflammatory bowel disease. The 12 common SNPs were assigned to 5 distinct linkage disequilibrium groups. Genotyping of one SNP from each linkage disequilibrium group in a large cohort of families with inflammatory bowel disease did not provide convincing evidence of association with either Crohn's disease or ulcerative colitis. We describe an efficient experimental design from SNP screening to association testing. This strategy can be used to test candidate genes for involvement in susceptibility to complex disease.
Statistical Analysis of Direct Identity‐by‐descent Mapping
Authors: Siegmund D. , Yakir B. 
Published: August 2003

SummaryGenetic mismatch scanning has been suggested as a method for using affected pairs of ostensibly unrelated but putatively distantly related affecteds in isolated populations to map disease genes. We model the regions of identity‐by‐descent of these affected pairs as a continuous time two state process with unknown parameters that depend on the (unknown) relationships, and we estimate the unknown parameters from the observed data. Simulated data involving pairs of first to fourth cousins show that the procedure thus obtained has properties similar, albeit slightly inferior, to the case where the relationships of the affected pairs, hence the parameters governing the processes, are known.
Structural characterization of transglutaminase‐catalyzed cross‐linking between glyceraldehyde 3‐phosphate dehydrogenase and polyglutamine repeats
Authors: Ruoppolo Margherita , Orrù Stefania , Francese Simona , Caputo Ivana , Esposito Carla 
Published: August 2003

AbstractThe accumulation of abnormal polyglutamine‐containing protein aggregates within the cytosol and nuclei of affected neurons is a hallmark of the progressive neurodegenerative disorders caused by an elongated (CAG)nrepeat in the genome. The polyglutamine domains are excellent substrates for the enzyme transglutaminase type 2 (tissue), resulting in the formation of cross‐links with polypeptides containing lysyl groups. Enzymatic activity toward the Qndomains increases greatly upon lengthening of such Qnstretches (n > 40). Among the possible amine donors, the glycolytic enzyme glyceraldehyde‐3‐phosphate‐dehydrogenase was shown to tightly bind several proteins involved in polyglutamine expansion diseases. Recently, the authors have shown that K191, K268, and K331, out of the 26 lysines present in glyceraldehyde‐3‐phosphate‐dehydrogenase, are the reactive amine‐donor sites forming cross‐links with substance P, which bears the simplest Qndomain (n = 2). The present study reports that synthetic peptides of both pathological and nonpathological length (n = 43 and 17, respectively) form cross‐links with the same K residues located in the C‐terminal region of glyceraldehyde‐3‐phosphate‐dehydrogenase. In addition, it is shown that extra K residues present in the C termini of glyceraldehyde‐3‐phosphate‐dehydrogenase are susceptible to cross‐linking in the presence of transglutaminase. The present results indicate a possible modulating effect of Qnstretches on tissue transglutaminase substrate specificity and mechanism of recognition.
The topomer search model: A simple, quantitative theory of two‐state protein folding kinetics
Authors: Makarov Dmitrii E. , Plaxco Kevin W. 
Published: August 2003

AbstractMost small, single‐domain proteins fold with the uncomplicated, single‐exponential kinetics expected for diffusion on a smooth energy landscape. Despite this energetic smoothness, the folding rates of these two‐state proteins span a remarkable million‐fold range. Here, we review the evidence in favor of a simple, mechanistic description, the topomer search model, which quantitatively accounts for the broad scope of observed two‐state folding rates. The model, which stipulates that the search for those unfolded conformations with a grossly correct topology is the rate‐limiting step in folding, fits observed rates with a correlation coefficient of ∼0.9 using just two free parameters. The fitted values of these parameters, the pre‐exponential attempt frequency and a measure of the difficulty of ordering an unfolded chain, are consistent with previously reported experimental constraints. These results suggest that the topomer search process may dominate the relative barrier heights of two‐state protein‐folding reactions.
Partial NMR assignments and secondary structure mapping of the isolated α subunit of Escherichia coli tryptophan synthase, a 29‐kD TIM barrel protein
Authors: Vadrevu Ramakrishna , Falzone Christopher J. , Matthews C. Robert 
Published: August 2003

AbstractThe α subunit of tryptophan synthase (αTS) from S. typhimurium belongs to the triosephosphate isomerase (TIM) or the (β/α)8 barrel fold, one of the most common structures in biology. To test the conservation of the global fold in the isolated Escherichia coli homolog, we have obtained a majority of the backbone assignments for the 29‐kD αTS by using standard heteronuclear multidimensional NMR methods on uniformly 15N‐ and 15N/13C‐labeled protein and on protein selectively 15N‐labeled at key hydrophobic residues. The secondary structure mapped by chemical shift index, nuclear Overhauser enhancements (NOEs), and hydrogen‐deuterium (H‐D) exchange, and several abnormal chemical shifts are consistent with the conservation of the global TIM barrel fold of the isolated E. coli αTS. Because most of the amide protons that are slow to exchange with solvent correspond to the β‐sheet residues, the β‐barrel is likely to play an important role in stabilizing the previously detected folding intermediates for E. coli αTS. A similar combination of uniform and selective labeling can be extended to other TIM barrel proteins to obtain insight into the role of the motif in stabilizing what appear to be common partially folded forms.
Pressure‐induced unfolding of the molten globule of all‐Ala α‐lactalbumin
Authors: Lassalle Michael W. , Li Hua , Yamada Hiroaki , Akasaka Kazuyuki , Redfield Christina 
Published: August 2003

AbstractPressure‐induced unfolding of a molten globule (MG) was studied in a residue‐specific manner with 1H‐15N two‐dimensional NMR spectroscopy using a variant of human α‐lactalbumin (α‐LA), in which all eight cysteines had been replaced with alanines (all‐Ala α‐LA). The NMR spectrum underwent a series of changes from 30 to 2000 bar at 20°C and from −18°C to 36°C at 2000 bar, showing a highly heterogeneous unfolding pattern according to the secondary structural elements of the native structure. Unfolding began in the loop part of the β‐domain, and then extended to the remainder of the β‐domain, after which the α‐domain began to unfold. Within the α‐domain, the pressure stability decreased in the order: D‐helix ∼ 310‐helix > C‐helix ∼ B‐helix > A‐helix. The D‐helix, C‐terminal 310‐helix and a large part of B‐ and C‐helices did not unfold at 2000 bar, even at 36°C or at −18°C. The results verify that the MG state consists of a mixture of variously unfolded conformers from the mostly folded to the nearly totally unfolded that differ in stability and partial molar volume. Not only heat but also cold denaturation was observed, supporting the view that the MG state is stabilized by hydrophobic interactions.
Structural energetics of protein–carbohydrate interactions: Insights derived from the study of lysozyme binding to its natural saccharide inhibitors
Authors: García‐Hernández Enrique , Zubillaga Rafael A. , Chavelas‐Adame Eneas A. , Vázquez‐Contreras Edgar , Rojo‐Domínguez Arturo , Costas Miguel 
Published: August 2003

AbstractHigh‐sensitivity isothermal titration calorimetry was used to characterize the binding of the glycohydrolitic enzyme hen egg‐white lysozyme to its natural saccharide inhibitors, chitobiose and chitrotriose. Measurements were done at a pH of 4.7, in the 15°C −45°C temperature range. Using a structural‐energetic parameterization derived previously for lectin‐carbohydrate associations, both binding enthalpies and entropies for the present systems and for the complex of chitobiose with turkey egg‐white lysozyme from the literature were correctly accounted for. These observations suggest that both lysozymes and lectins follow the same structural‐energetic behavior in the binding to their ligands. From the analysis of lysozyme data in conjunction with other binding data reported in the literature, an ad hoc parameterization of ΔCp for protein–carbohydrate complexes was derived for the first time. The novel parameters for both polar and apolar surface areas differed significantly from correlations obtained previously from model compounds and protein‐folding data. As ΔCp is extremely sensitive to changes in solvent structure, this finding indicates that protein–carbohydrate complexes have distinctive hydration properties. According to our analysis, the dehydration of polar groups is the major cause for the observed decrease in ΔCp, which implies that these groups behave hydrophobically. The contribution of apolar surface areas was found of the expected sign, but their specific weight is much smaller than those obtained in other correlations. This small contribution to ΔCp is consistent with Lemieux's hypothesis of a low degree of hydration of apolar surfaces on carbohydrates.
Homology modeling and molecular dynamics simulations of the N‐terminal domain of wheat high molecular weight glutenin subunit 10
Authors: Cazalis Roland , Aussenac Thierry , Rhazi Larbi , Marin Antoine , Gibrat Jean‐François 
Published: August 2003

AbstractHigh molecular weight glutenin subunits (HMW‐GS) are of a particular interest because of their biomechanical properties, which are important in many food systems such as breadmaking. Using fold‐recognition techniques, we identified a fold compatible with the N‐terminal domain of HMW‐GS Dy10. This fold corresponds to the one adopted by proteins belonging to the cereal inhibitor family. Starting from three known protein structures of this family as templates, we built three models for the N‐terminal domain of HMW‐GS Dy10. We analyzed these models, and we propose a number of hypotheses regarding the N‐terminal domain properties that can be tested experimentally. In particular, we discuss two possible ways of interaction between the N‐terminal domains of the y‐type HMW glutenin subunits. The first way consists in the creation of interchain disulfide bridges. According to our models, we propose two plausible scenarios: (1) the existence of an intrachain disulfide bridge between cysteines 22 and 44, leaving the three other cysteines free of engaging in intermolecular bonds; and (2) the creation of two intrachain disulfide bridges (involving cysteines 22–44 and cysteines 10–55), leaving a single cysteine (45) for creating an intermolecular disulfide bridge. We discuss these scenarios in relation to contradictory experimental results. The second way, although less likely, is nevertheless worth considering. There might exist a possibility for the N‐terminal domain of Dy10, Nt‐Dy10, to create oligomers, because homologous cereal inhibitor proteins are known to exist as monomers, homodimers, and heterooligomers. We also discuss, in relation to the function of the cereal inhibitor proteins, the possibility that this N‐terminal domain has retained similar inhibitory functions.
Energy landscape and dynamics of the β‐hairpin G peptide and its isomers: Topology and sequences
Authors: Ma Buyong , Nussinov Ruth 
Published: August 2003

AbstractWe have investigated free energy landscape [MM/PBSA + normal modes entropy] of permutations in the G peptide (41–56) from the protein G B1 domain by studying six isomers corresponding to moving the hydrophobic cluster along the β‐strands (toward the turn: T1, AGEWTYDDKTFTVTET; T2, GEDTWDYATFTVTKTE; T3, GEDDWTYATFTVTKTE; toward the end: E1, WTYDDAGETKTFTVT; E2, WEYTGDDATKTETFTV; E3, WTYEGDDATKTETFTV). The free energy terms include molecular mechanics energy, Poisson‐Boltzmann electrostatic solvation energy, surface area solvation energy, and conformational entropy estimated by using normal mode analysis. From the wild type to T1, then T3, and finally T2, we see a progressively changing energy landscape, toward a less stable β‐hairpin structure. Moving the hydrophobic cluster outside toward the end region causes a greater change in the energy landscape. α‐Helical instead of a β‐hairpin structure was the most stable form for the E2 isomer. However, no matter how much the sequence changes, for all variants studied, ideal “native” β‐hairpin topologies remain as minima (regardless of whether global or local) in the energy landscape. In general, we find that the energy landscape is dependent on the hydrophobic cluster topology and on the sequence. Our present study indicates that the key is the relative conformational energies of the different conformations. Changes in the sequence strongly modulate the relative stabilities of topologically similar regions in the energy landscape, rather than redefine the topology space. This finding is consistent with a population redistribution in the process of protein folding. The limited variation of topological space, compared with the number of possible sequence changes, may relate to the observation that the number of known protein folds are far less than the sequential allowance.
Asymmetric mutation rates at enzyme–inhibitor interfaces: Implications for the protein–protein docking problem
Authors: Bradford James R. , Westhead David R. 
Published: August 2003

AbstractWe have carried out a thorough and systematic sequence‐structure study on how the pattern of conservation at the interface differs from the noninteracting surface in seven proteases and their inhibitors. As expected, the interface of a protease could be easily distinguished from the noninteracting surface by a concentrated area of conservation. In contrast, there was less distinction to be made between the interface and the noninteracting surface of inhibitors, and in five of the seven cases, a higher proportion of the interface area was variable compared to the rest of the surface. This is likely to cause a problem for binding‐site prediction methods that assume the largest cluster of highly conserved residues on the surface of a protein corresponds to the interface. We conclude that such methods would succeed when applied to our protease test cases, but complications could arise with the inhibitors. These results also impact on methods to solve the protein–protein docking problem that use conservation at the interface to provide the location of the two protein binding sites prior to application of the docking algorithm.
Calculating pKa values in enzyme active sites
Authors: Nielsen Jens Erik , McCammon J. Andrew 
Published: August 2003

AbstractThe ionization properties of the active‐site residues in enzymes are of considerable interest in the study of the catalytic mechanisms of enzymes. Knowledge of these ionization constants (pKa values) often allows the researcher to identify the proton donor and the catalytic nucleophile in the reaction mechanism of the enzyme. Estimates of protein residue pKa values can be obtained by applying pKa calculation algorithms to protein X‐ray structures. We show that pKa values accurate enough for identifying the proton donor in an enzyme active site can be calculated by considering in detail only the active‐site residues and their immediate electrostatic interaction partners, thus allowing for a large decrease in calculation time. More specifically we omit the calculation of site‐site interaction energies, and the calculation of desolvation and background interaction energies for a large number of pairs of titratable groups. The method presented here is well suited to be applied on a genomic scale, and can be implemented in most pKa calculation algorithms to give significant reductions in calculation time with little or no impact on the accuracy of the results. The work presented here has implications for the understanding of enzymes in general and for the design of novel biocatalysts.
Archaeal signal peptides—A comparative survey at the genome level
Authors: Bardy Sonia L. , Eichler Jerry , Jarrell Ken F. 
Published: August 2003

AbstractThe correct delivery of noncytoplasmic proteins to locations both within and outside the cell depends on the appropriate targeting signals. Protein translocation across the bacterial plasma membrane and the eukaryal endoplasmic reticulum membrane relies on cleavable N‐terminal signal peptides. Although the signal peptides of secreted proteins in Bacteria and Eukarya have been extensively studied at the sequence, structure, and functional levels, little is known of the nature of archaeal signal peptides. In this report, genome‐based analysis was performed in an attempt to define the amino acid composition, length, and cleavage sites of various signal peptide classes in a wide range of archaeal species. The results serve to present a picture of the archaeal signal peptide, revealing the incorporation of bacterial, eukaryal, and archaeal traits.
A graph‐theory algorithm for rapid protein side‐chain prediction
Authors: Canutescu Adrian A. , Shelenkov Andrew A. , Dunbrack Roland L. 
Published: August 2003

AbstractFast and accurate side‐chain conformation prediction is important for homology modeling, ab initio protein structure prediction, and protein design applications. Many methods have been presented, although only a few computer programs are publicly available. The SCWRL program is one such method and is widely used because of its speed, accuracy, and ease of use. A new algorithm for SCWRL is presented that uses results from graph theory to solve the combinatorial problem encountered in the side‐chain prediction problem. In this method, side chains are represented as vertices in an undirected graph. Any two residues that have rotamers with nonzero interaction energies are considered to have an edge in the graph. The resulting graph can be partitioned into connected subgraphs with no edges between them. These subgraphs can in turn be broken into biconnected components, which are graphs that cannot be disconnected by removal of a single vertex. The combinatorial problem is reduced to finding the minimum energy of these small biconnected components and combining the results to identify the global minimum energy conformation. This algorithm is able to complete predictions on a set of 180 proteins with 34,342 side chains in <7 min of computer time. The total χ1 and χ1 + 2 dihedral angle accuracies are 82.6% and 73.7% using a simple energy function based on the backbone‐dependent rotamer library and a linear repulsive steric energy. The new algorithm will allow for use of SCWRL in more demanding applications such as sequence design and ab initio structure prediction, as well addition of a more complex energy function and conformational flexibility, leading to increased accuracy.
Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein–nucleic acid complex crystals
Authors: Kantardjieff Katherine A. , Rupp Bernhard 
Published: August 2003

AbstractEstimating the number of molecules in the crystallographic asymmetric unit is one of the first steps in a macromolecular structure determination. Based on a survey of 15,641 crystallographic Protein Data Bank (PDB) entries the distribution of VM, the crystal volume per unit of protein molecular weight, known as Matthews coefficient, has been reanalyzed. The range of values and frequencies has changed in the 30 years since Matthews first analysis of protein crystal solvent content. In the statistical analysis, complexes of proteins and nucleic acids have been treated as a separate group. In addition, the VM distribution for nucleic acid crystals has been examined for the first time. Observing that resolution is a significant discriminator of VM, an improved estimator for the probabilities of the number of molecules in the crystallographic asymmetric unit has been implemented, using resolution as additional information.
Prospects and limitations of the rational engineering of fibrillar collagens
Authors: Majsterek Ireneusz , McAdams Erin , Adachi Eijiro , Dhume Shirish T. , Fertala Andrzej 
Published: August 2003

AbstractRecombinant collagens are attractive proteins for a number of biomedical applications. To date, significant progress was made in the large‐scale production of nonmodified recombinant collagens; however, engineering of novel collagen‐like proteins according to customized specifications has not been addressed. Herein we investigated the possibility of rational engineering of collagen‐like proteins with specifically assigned characteristics. We have genetically engineered two DNA constructs encoding multi‐D4 collagens defined as collagen‐like proteins, consisting primarily of a tandem of the collagen II D4 periods that correspond to the biologically active region. We have also attempted to decrease enzymatic degradation of novel collagen by mutating a matrix metalloproteinase 1 cleavage site present in the D4 period. We demonstrated that the recombinant collagen α‐chains consisting predominantly of the D4 period but lacking most of the other D periods found in native collagen fold into a typical collagen triple helix, and the novel procollagens are correctly processed by procollagen N‐proteinase and procollagen C‐proteinase. The nonmutated multi‐D4 collagen had a normal melting point of 41°C and a similar carbohydrate content as that of control. In contrast, the mutant multi‐D4 collagen had a markedly lower thermostability of 36°C and a significantly higher carbohydrate content. Both collagens were cleaved at multiple sites by matrix metalloproteinase 1, but the rate of hydrolysis of the mutant multi‐D4 collagen was lower. These results provide a basis for the rational engineering of collagenous proteins and identifying any undesirable consequences of altering the collagenous amino acid sequences.