bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ancient latitudinal gradients of C3/C4 grasses interpreted from stable isotopes of New World Pleistocene horse (Equus) teeth
Authors: Macfadden Bruce J , Cerling Thure E , Harris John M , Prado José 
Published: February 2004

ABSTRACTCarbon and oxygen isotopic data are reported from 116 Pleistocene Equus teeth from sixty‐six localities in the New World ranging from 68°N (Alaska, Canada) to 35°S (Argentina). Equus species have been predominantly grazers, and as such, carbon isotopic values of their tooth enamel provide evidence of the Pleistocene distribution of C3 and C4 grasses. The carbon data presented here indicate a gradient (δ13C range of 10 parts/mil) in the relative proportion of C3 and C4 grasses between high latitude and equatorial Equus samples. The largest amount of change from C3 to C4 grasses during the Pleistocene occurred in the mid‐latitudes between about 30 to 40°. The oxygen data, which vary proportionately with temperature, indicate a latitudinal gradient (δ18O range of 20 parts/mil) between high‐latitude and equatorial Equus samples. The basic pattern of latitudinal gradients of C3/C4 grass distribution and temperature as interpreted from these Pleistocene data is similar to the modern‐day. The use of stable isotopes of fossil herbivore teeth represents a new means to interpret Pleistocene climates and terrestrial ecology.
A life course approach to diet, nutrition and the prevention of chronic diseases
Authors: Darnton-Hill I , Nishida C , James WPT 
Published: February 2004

AbstractObjective:To briefly review the current understanding of the aetiology and prevention of chronic diseases using a life course approach, demonstrating the life-long influences on the development of disease.Design:A computer search of the relevant literature was done using Medline-‘life cycle’ and ‘nutrition’ and reviewing the articles for relevance in addressing the above objective. Articles from references dated before 1990 were followed up separately. A subsequent search using Clio updated the search and extended it by using ‘life cycle’, ‘nutrition’ and ‘noncommunicable disease’ (NCD), and ‘life course’. Several published and unpublished WHO reports were key in developing the background and arguments.Setting:International and national public health and nutrition policy development in light of the global epidemic in chronic diseases, and the continuing nutrition, demographic and epidemiological transitions happening in an increasingly globalized world.Results of review:There is a global epidemic of increasing obesity, diabetes and other chronic NCDs, especially in developing and transitional economies, and in the less affluent within these, and in the developed countries. At the same time, there has been an increase in communities and households that have coincident under- and over-nutrition.Conclusions:The epidemic will continue to increase and is due to a lifetime of exposures and influences. Genetic predisposition plays an unspecified role, and with programming during fetal life for adult disease contributing to an unknown degree. A global rise in obesity levels is contributing to a particular epidemic of type 2 diabetes as well as other NCDs. Prevention will be the most cost-effective and feasible approach for many countries and should involve three mutually reinforcing strategies throughout life, starting in the antenatal period.
Heroin users in Australia: population trends
Authors: KAYA C. YALÇIN , TUGAI YULIYA , FILAR JERZY A. , AGRAWAL MANJU R. , ALI ROBERT L. , GOWING LINDA R. , COOKE RICHARD 
Published: February 2004

AbstractThe aim of this paper is to identify certain important population trends among heroin users in Australia for the period 1971 – 97, such as: population growth, initiation, i.e. the number who were initiated to heroin in a given year, and quitting, i.e. the number that quit using heroin. For this purpose, we summarize and extract relevant characteristics from data from National Drug Strategy Household Survey (NDSHS 1998) conducted in Australia in 1998. We devise a systematic procedure to estimate historical trends from questions concerning past events. It is observed from our findings that the size of the heroin user population in Australia is in a sharp increase, especially from the early 1980s onwards. The general trend obtained for the period 1971 – 97 is strikingly similar to that obtained by Hall et al. (2000) for the dependent heroin user population in Australia, even though their study was based on different datasets and a different methodology. In our reconstruction of the time history we also detect a levelling‐off prior to 1990. Initiation is also observed to be on a sharp increase. The latter trend is accompanied by a similar trend of quitting, perhaps indicating a relatively short heroin use career. A sharp decrease in both initiation and quitting is observed after 1990. In conclusion, in the case of the trend in the population of heroin users a high rate of growth has been identified that is consistent with the existing literature. In the process, we demonstrated that even a static survey such as NDSHS 1998 can, sometimes, be used to extract historical (dynamic) trends of certain important variables.
Improved side‐chain prediction accuracy using an ab initio potential energy function and a very large rotamer library
Authors: Peterson Ronald W. , Dutton P. Leslie , Wand A. Joshua 
Published: February 2004

AbstractAccurate prediction of the placement and comformations of protein side chains given only the backbone trace has a wide range of uses in protein design, structure prediction, and functional analysis. Prediction has most often relied on discrete rotamer libraries so that rapid fitness of side‐chain rotamers can be assessed against some scoring function. Scoring functions are generally based on experimental parameters from small‐molecule studies or empirical parameters based on determined protein structures. Here, we describe the NCN algorithm for predicting the placement of side chains. A predominantly first‐principles approach was taken to develop the potential energy function incorporating van der Waals and electrostatics based on the OPLS parameters, and a hydrogen bonding term. The only empirical knowledge used is the frequency of rotameric states from the PDB. The rotamer library includes nearly 50,000 rotamers, and is the most extensive discrete library used to date. Although the computational time tends to be longer than most other algorithms, the overall accuracy exceeds all algorithms in the literature when placing rotamers on an accurate backbone trace. Considering only the most buried residues, 80% of the total residues tested, the placement accuracy reaches 92% for χ1, and 83% for χ1 + 2, and an overall RMS deviation of 1 Å. Additionally, we show that if information is available to restrict χ1 to one rotamer well, then this algorithm can generate structures with an average RMS deviation of 1.0 Å for all heavy side‐chains atoms and a corresponding overall χ1 + 2 accuracy of 85.0%.
Rapid evolution in conformational space: A study of loop regions in a ubiquitous GTP binding domain
Authors: Blouin Christian , Butt Davin , Roger Andrew James 
Published: February 2004

AbstractThe rapidly evolving subsets of a protein are often evident in multiple sequence alignments as poorly defined, gap‐containing regions. We investigated the 3D context of these regions observed in 28 protein structures containing a GTP‐binding domain assumed to be homologous to the transforming factor p21‐RAS. The phylogenetic depth of this data set is such that it is possible to observe lineages sharing a common protein core that diverged early in the eukaryotic cell history. The sequence variability among these homolog proteins is directly linked to the structural variability of surface loops. We demonstrate that these regions are self‐contained and thus mostly free of the evolutionary constraints imposed by the conserved core of the domain. These intraloop interactions have the property to create stem‐like structures. Interestingly, these stem‐like structures can be observed in loops of varying size, up to the size of small protein domains. We propose a model under which the diversity of protein topologies observed in these loops can be the product of a stochastic sampling of sequence and conformational space in a near‐neutral fashion, while the proximity of the functional features of the domain core allows novel beneficial traits to be fixed. Our comparative observations, limited here to the proteins containing the RAS‐like GTP‐binding domain, suggest that a stochastic process of insertion/deletion analogous to “budding” of loops is a likely mechanism of structural innovation. Such a framework could be experimentally exploited to investigate the folding of increasingly complex model inserts.
Dimethyl sulfoxide at 2.5% (v/v) alters the structural cooperativity and unfolding mechanism of dimeric bacterial NAD+ synthetase
Authors: Yang Zhengrong W. , Tendian Susan W. , Carson W. Michael , Brouillette Wayne J. , Delucas Lawrence J. , Brouillette Christie G. 
Published: February 2004

AbstractDimethyl sulfoxide (DMSO) is commonly used as a cosolvent to improve the aqueous solubility of small organic compounds. Its use in a screen to identify novel inhibitors of the enzyme NAD+ synthetase led to this investigation of its potential effects on the structure and stability of this 60‐kD homodimeric enzyme. Although no effects are observed on the enzyme's catalytic activity, as low as 2.5% (v/v) DMSO led to demonstrable changes in the stability of the dimer and its unfolding mechanism. In the absence of DMSO, the dimer behaves hydrodynamically as a single ideal species, as determined by equilibrium analytical ultracentrifugation, and thermally unfolds according to a two‐state dissociative mechanism, based on analysis by differential scanning calorimetry (DSC). In the presence of 2.5% (v/v) DMSO, an equilibrium between the dimer and monomer is now detectable with a measured dimer association constant, Ka, equal to 5.6 × 106/M. DSC curve analysis is consistent with this finding. The data are best fit to a three‐state sequential unfolding mechanism, most likely representing folded dimer ⇆ folded monomer ⇆ unfolded monomer. The unusually large change in the relative stabilities of dimer and monomer, e.g., the association equilibrium shifts from an infinitely large Ka down to ∼106/M, in the presence of relatively low cosolvent concentration is surprising in view of the significant buried surface area at the dimer interface, roughly 20% of the surface area of each monomer is buried. A hypothetical structural mechanism to explain this effect is presented.
Oligomerization of hydrophobin SC3 in solution: From soluble state to self‐assembly
Authors: Wang Xiaoqin , Graveland‐Bikker Johanna F. , De Kruif Cornelis G. , Robillard George T. 
Published: February 2004

AbstractHydrophobin SC3 is a protein with special self‐association properties that differ depending on whether it is in solution, on an air/water interface or on a solid surface. Its self‐association on an air/water interface and solid surface have been extensively characterized. The current study focuses on its self‐association in water because this is the starting point for the other two association processes. Size‐exclusion chromatography was used to fractionate soluble‐state SC3. Real‐time multiangular light scattering detection of the eluate indicated that SC3 mainly exists as a dimer in buffer, accompanied with a small amount of monomer, tetramer, and larger aggregates. Dimeric SC3 has very likely an elongated shape, as indicated by the hydrodynamic radius determined by using dynamic light scattering (DLS) and fluorescence anisotropy measurements on dansyl‐labeled SC3. Size‐exclusion chromatography experiments also indicated that the protein oligomerizes very slowly at low temperature (4°C) but rather rapidly at room temperature. Ionic strength plays an important role in the oligomerization; a short‐lived monomeric SC3 species could be observed in pure water. Oligomerization was not affected by low pH but was accelerated by high pH. Fluorescence resonance energy transfer showed that dissociation occurred when the protein concentration was lowered; a large population of oligomers, presumably dimers, dissociate when the protein concentration is <4.5 μg/mL. This value is similar to the critical concentration for SC3 self‐assembly. Therefore, dimeric SC3 is indicated to be the building block for both aggregation in solution and self‐assembly at hydrophobic/hydrophilic interfaces.
Analysis and prediction of affinity of TAP binding peptides using cascade SVM
Authors: Bhasin Manoj , Raghava G.P.S. 
Published: February 2004

AbstractThe generation of cytotoxic T lymphocyte (CTL) epitopes from an antigenic sequence involves number of intracellular processes, including production of peptide fragments by proteasome and transport of peptides to endoplasmic reticulum through transporter associated with antigen processing (TAP). In this study, 409 peptides that bind to human TAP transporter with varying affinity were analyzed to explore the selectivity and specificity of TAP transporter. The abundance of each amino acid from P1 to P9 positions in high‐, intermediate‐, and low‐affinity TAP binders were examined. The rules for predicting TAP binding regions in an antigenic sequence were derived from the above analysis. The quantitative matrix was generated on the basis of contribution of each position and residue in binding affinity. The correlation of r = 0.65 was obtained between experimentally determined and predicted binding affinity by using a quantitative matrix. Further a support vector machine (SVM)‐based method has been developed to model the TAP binding affinity of peptides. The correlation (r = 0.80) was obtained between the predicted and experimental measured values by using sequence‐based SVM. The reliability of prediction was further improved by cascade SVM that uses features of amino acids along with sequence. An extremely good correlation (r = 0.88) was obtained between measured and predicted values, when the cascade SVM‐based method was evaluated through jackknife testing. A Web service, TAPPred (http://www.imtech.res.in/raghava/tappred/ or http://bioinformatics.uams.edu/mirror/tappred/), has been developed based on this approach.
Cooperativity in two‐state protein folding kinetics
Authors: Weikl Thomas R. , Palassini Matteo , Dill Ken A. 
Published: February 2004

AbstractWe present a solvable model that predicts the folding kinetics of two‐state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small‐loop closure events that can be inferred from native structures. For CI2, the src SH3 domain, TNfn3, and protein L, the model reproduces two‐state kinetics, and it predicts well the average Φ‐values for secondary structures. The barrier to folding is the formation of predominantly local structures such as helices and hairpins, which are needed to bring nonlocal pairs of amino acids into contact.
Lead optimization of antifungal peptides with 3D NMR structures analysis
Authors: Landon Céline , Barbault Florent , Legrain Michèle , Menin Laure , Guenneugues Marc , Schott Valérie , Vovelle Françoise , Dimarcq Jean‐Luc 
Published: February 2004

AbstractAntimicrobial peptides are key components of the innate immune response in most multicellular organisms. These molecules are considered as one of the most innovative class of anti‐infective agents that have been discovered over the last two decades, and therefore, as a source of inspiration for novel drug design. Insect cystein‐rich antimicrobial peptides with the CSαβ scaffold (an α‐helix linked to a β‐sheet by two disulfide bridges) represent particularly attractive templates for the development of systemic agents owing to their remarkable resistance to protease degradation. We have selected heliomicin, a broad spectrum antifungal CSαβ peptide from Lepidoptera as the starting point of a lead optimization program based on phylogenic exploration and fine tuned mutagenesis. We report here the characterization, biological activity, and 3D structure of heliomicin improved analogs, namely the peptides ARD1, ETD‐135, and ETD‐151. The ARD1 peptide was initially purified from the immune hemolymph of the caterpillars of Archeoprepona demophoon. Although it differs from heliomicin by only two residues, it was found to be more active against the human pathogens Aspergillus fumigatus and Candida albicans. The peptides ETD‐135 and ETD‐151 were engineered by site‐directed mutagenesis of ARD1 in either cationic or hydrophobic regions. ETD‐135 and ETD‐151 demonstrated an improved antifungal activity over the native peptides, heliomicin and ARD1. A comparative analysis of the 3D structure of the four molecules highlighted the direct impact of the modification of the amphipathic properties on the molecule potency. In addition, it allowed to characterize an optimal organization of cationic and hydrophobic regions to achieve best antifungal activity.
Laser light‐scattering evidence for an altered association of βB1‐crystallin deamidated in the connecting peptide
Authors: Harms Michael J. , Wilmarth Philip A. , Kapfer Deborah M. , Steel Eric A. , David Larry L. , Bächinger Hans Peter , Lampi Kirsten J. 
Published: February 2004

AbstractDeamidation is a prevalent modification of crystallin proteins in the vertebrate lens. The effect of specific sites of deamidation on crystallin stability in vivo is not known. Using mass spectrometry, a previously unreported deamidation in βB1‐crystallin was identified at Gln146. Another deamidation was investigated at Asn157. It was determined that whole soluble βB1 contained 13%–17% deamidation at Gln146 and Asn157. Static and quasi‐elastic laser light scattering, circular dichroism, and heat aggregation studies were used to explore the structure and associative properties of recombinantly expressed wild‐type (wt) βB1 and the deamidated βB1 mutants, Q146E and N157D. Dimer formation occurred for wt βB1, Q146E, and N157D in a concentration‐dependent manner, but only Q146E showed formation of higher ordered oligomers at the concentrations studied. Deamidation at Gln146, but not Asn157, led to an increased tendency of βB1 to aggregate upon heating. We conclude that deamidation creates unique effects depending upon where the deamidation is introduced in the crystallin structure.
The role of phosphagen specificity loops in arginine kinase
Authors: Azzi Arezki , Clark Shawn A. , Ellington W. Ross , Chapman Michael S. 
Published: February 2004

AbstractPhosphagen kinases catalyze the reversible transfer of a phosphate between ATP and guanidino substrates, a reaction that is central to cellular energy homeostasis. Members of this conserved family include creatine and arginine kinases and have similar reaction mechanisms, but they have distinct specificities for different guanidino substrates. There has not been a full structural rationalization of specificity, but two loops have been implicated repeatedly. A small domain loop is of length that complements the size of the guanidino substrate, and is located where it could mediate a lock‐and‐key mechanism. The second loop contacts the substrate with a valine in the methyl‐substituted guanidinium of creatine, and with a glutamate in the unsubstituted arginine substrate, leading to the proposal of a discriminating hydrophobic/hydrophilic minipocket. In the present work, chimeric mutants were constructed with creatine kinase loop elements inserted into arginine kinase. Contrary to the prior rationalizations of specificity, most had measurable arginine kinase activity but no creatine kinase activity or enhanced phosphocreatine binding. Guided by structure, additional mutations were introduced in each loop, recovering arginine kinase activities as high as 15% and 64% of wild type, respectively, even though little activity would be expected in the constructs if the implicated sites had dominant roles in specificity. An atomic structure of the mismatched complex of arginine kinase with creatine and ADP indicates that specificity can also be mediated by an active site that allows substrate prealignment that is optimal for reactivity only with cognate substrates and not with close homologs that bind but do not react.
The PRESAT‐vector: Asymmetric T‐vector for high‐throughput screening of soluble protein domains for structural proteomics
Authors: Goda Natsuko , Tenno Takeshi , Takasu Hirotoshi , Hiroaki Hidekazu , Shirakawa Masahiro 
Published: February 2004

AbstractA rapid unidirectional method for cloning PCR‐amplified cDNA fragments into virtually any fusion protein expression vector is described. The method, termed PRESAT‐vector cloning, is based on a T‐vector technique that does not require restriction endonuclease digestion of the PCR product. Subsequently, we applied a novel ORF selection method of the ligated plasmid products. This second step involves restriction endonuclease treatment that eliminates the plasmids containing an ORF in the wrong orientation prior to transformation into the bacterial host for further protein expression studies. To achieve this selection, we customized the 5′‐sequence of the “rear” PCR primer corresponding to the C terminus of the protein to be expressed. The colonies harbored only the ligated products of the desired orientation at >90% efficiency. This method is applied to a GST fusion expression system, and an HTS system for soluble proteins from an expression library was tested.
Defining the minimum size of a hydrophobic cluster in two‐stranded α‐helical coiled‐coils: Effects on protein stability
Authors: Lu Stephen M. , Hodges Robert S. 
Published: February 2004

AbstractThe α‐helical coiled‐coil motif is characterized by a heptad repeat pattern (abcdefg)n in which residues a and d form the hydrophobic core. Long coiled‐coils (e.g., tropomyosin, 284 residues per polypeptide chain) typically do not have a continuous hydrophobic core of stabilizing residues, but rather one that consists of alternating clusters of stabilizing and destabilizing residues. We have arbitrarily defined a cluster as a minimum of three consecutive stabilizing or destabilizing residues in the hydrophobic core. We report here on a series of two‐stranded, disulfide‐bridged parallel α‐helical coiled‐coils that contain a central cassette of three consecutive hydrophobic core positions (d, a, and d) with a destabilizing cluster of three consecutive Ala residues in the hydrophobic core on each side of the cassette. The effect of adding one to three stabilizing hydrophobes in these positions (Leu or Ile; denoted as •) was investigated. Alanine residues (denoted as ○) are used to represent destabilizing residues. The peptide with three Ala residues in the d a d cassette positions (○○○) was among the least stable coiled‐coil (Tm = 39.3°C and Urea1/2 = 1.9 M). Surprisingly, the addition of one stabilizing hydrophobe (Leu) to the cassette or two stabilizing hydrophobes (Leu), still interspersed by an Ala in the cassette (•○•), also did not lead to any gain in stability. However, peptides with two adjacent hydrophobes in the cassette (••○)(○••) did show a gain in stability of 0.9 kcal/mole over the peptide with two interspersed hydrophobes (•○•). Because the latter three peptides have the same inherent hydrophobicity, the juxtaposition of stabilizing hydrophobes leads to a synergistic effect, and thus a clustering effect. The addition of a third stabilizing hydrophobe to the cassette (•••) resulted in a further synergistic gain in stability of 1.7 kcal/mole (Tm = 54.1°C and Urea1/2 = 3.3M). Therefore, the role of hydrophobicity in the hydrophobic core of coiled‐coils is extremely context dependent and clustering is an important aspect of protein folding and stability.