bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of morphology on the optical properties of transparent epoxy/montmorillonite composites
Authors: Deng Yuming , Gu Aijuan , Fang Zhengping 
Published: December 2003

AbstractThree kinds of epoxy‐based transparent nanocomposites were prepared by the reaction of alkylammonium‐exchanged montmorillonite (AMT) with diglycidyl ether of bisphenol A (DGEBA) and triethylamine as the curing agent. The morphology of these composites was characterized by X‐ray diffraction, scanning electron microscopy and transmission electron microscopy. The effect of morphology on the optical transparency of epoxy/AMT composites (Ep/AMT) was investigated. The light transmittance of Ep/AMT depended greatly on the exfoliation degree (ED) of AMT in the epoxy matrix, and the transmittance of the composites with higher ED was notably higher than that with lower ED under the same AMT content. The light transmittance of composites prepared with different amounts of curing agent was also studied. Results suggested that the composites prepared with insufficient curing agent were more transparent than those prepared with stoichiometric and higher contents of curing agent because insufficient curing agent was benefitial to the exfoliation of AMT. An equation describes the relationship of the light transmittance of nanocomposites with the concentration, particle size and basal spacing of AMT as well as the wavelength. Theoretical analysis suggested that the effect of morphology on the transparence mainly comes from the changes of the particle size and basal spacing of AMT, and that the effect of the former is more significant than that of the latter Copyright © 2003 Society of Chemical Industry
Class‐specific correlations between protein folding rate, structure‐derived, and sequence‐derived descriptors
Authors: Kuznetsov Igor B. , Rackovsky Shalom 
Published: December 2003

AbstractSmall single‐domain proteins that fold by simple two‐state kinetics have been shown to exhibit a wide variation in their folding rates. It has been proposed that folding mechanisms in these proteins are largely determined by the native‐state topology, and a significant correlation between folding rate and measures of the average topological complexity, such as relative contact order (RCO), has been reported. We perform a statistical analysis of folding rate and RCO in all three major structural classes (α, β, and α/β) of small two‐state proteins and of RCO in groups of analogous and homologous small single‐domain proteins with the same topology. We also study correlation between folding rate and the average physicochemical properties of amino acid sequences in two‐state proteins. Our results indicate that 1) helical proteins have statistically distinguishable, class‐specific folding rates; 2) RCO accounts for essentially all the variation of folding rate in helical proteins, but for only a part of the variation in β‐sheet‐containing proteins; and 3) only a small fraction of the protein topologies studied show a topology‐specific RCO. We also report a highly significant correlation between the folding rate and average intrinsic structural propensities of protein sequences. These results suggest that intrinsic structural propensities may be an important determinant of the rate of folding in small two‐state proteins. Proteins 2003. © 2003 Wiley‐Liss, Inc.
A new pairwise folding potential based on improved decoy generation and side‐chain packing
Authors: Loose C. , Klepeis J. L. , Floudas C. A. 
Published: December 2003

AbstractA new force field for pairwise residue interactions as a function of Cα to Cα distances is presented. The force field was developed through the solution of a linear programming formulation with large sets of constraints. The constraints are based on the construction of >80,000 low‐energy decoys for a set of proteins and requiring the decoy energies for each protein system to be higher than the native conformation of that particular protein. The generation of a robust force field was facilitated by the use of a novel decoy generation process, which involved the rational selection of proteins to add to the training set and included a significant energy minimization of the decoys. The force field was tested on a large set of decoys for various proteins not included in the training set and shown to perform well compared with a leading force field in identifying the native conformation for these proteins. Proteins 2003. © 2003 Wiley‐Liss, Inc.
ProVal: A protein‐scoring function for the selection of native and near‐native folds
Authors: Berglund Anders , Head Richard D. , Welsh Eric A. , Marshall Garland R. 
Published: December 2003

AbstractA low‐resolution scoring function for the selection of native and near‐native structures from a set of predicted structures for a given protein sequence has been developed. The scoring function, ProVal (Protein Validate), used several variables that describe an aspect of protein structure for which the proximity to the native structure can be assessed quantitatively. Among the parameters included are a packing estimate, surface areas, and the contact order. A partial least squares for latent variables (PLS) model was built for each candidate set of the 28 decoy sets of structures generated for 22 different proteins using the described parameters as independent variables. The Cα RMS of the candidate structures versus the experimental structure was used as the dependent variable. The final generalized scoring function was an average of all models derived, ensuring that the function was not optimized for specific fold classes or method of structure generation of the candidate folds. The results show that the crystal structure was scored best in 64% of the 28 test sets and was clearly separated from the decoys in many examples. In all the other cases in which the crystal structure did not rank first, it ranked within the top 10%. Thus, although ProVal could not distinguish between predicted structures that were similar overall in fold quality due to its inherently low resolution, it can clearly be used as a primary filter to eliminate ∼90% of fold candidates generated by current prediction methods from all‐atom modeling and further evaluation. The correlation between the predicted and actual Cα RMS values varies considerably between the candidate fold sets. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
Type I collagen N‐Telopeptides adopt an ordered structure when docked to their helix receptor during fibrillogenesis*
Authors: Malone James P. , George Anne , Veis Arthur 
Published: December 2003

AbstractThe in vitro rate and specificity of fibrillogenesis in type I collagen depends on the integrity of the amino (N)‐telopeptide domain. In vivo an intact N‐telopeptide domain is also required for normal fibril assembly. Although Chou–Fasman predictions and NMR studies suggested that a type I β‐turn could be induced in α1(I) N‐telopeptide chains, computer modeling did not identify ordered structures. Nevertheless, X‐ray analysis and electron tomography studies have shown that the N‐telopeptide is in one of the most highly ordered fibril domains. This study was undertaken to determine if the docking of the N‐telopeptide to its helix receptor domain could induce the telopeptides to take up a specific conformation. With use of molecular modeling suite of programs, a (Gly‐Pro‐Pro)n triple‐helical structure was built on the basis of high‐resolution X‐ray crystallographic coordinates and then replaced with the actual bovine collagen residues 924–938, the triple‐helical α1(I)‐N‐telopeptide‐receptor sequences. Energy minimization produced a modified triple‐helical conformation. The bovine α1(I) N‐telopeptide sequence was similarly minimized and docked to this receptor. The docking induced an ordered conformation with a stabilizing hydrogen bond in the N‐telopeptide and, importantly, a reciprocal reordering of the triple‐helical conformation in the binding domain. This docked structure placed Lys residues in both telopeptide and helix in the correct locations for cross‐link formation. The modeling has been extended to the three‐chain N‐telopeptide domain and finally to the construction of the Hulmes–Miller quasi‐hexagonal packing structure. Each N‐telopeptide domain can form linkages with two adjacent, aligned helix receptor domains. The telopeptides and the order of staggering of the three chains in the helix play crucial roles in the packing and intrafibrillar cross‐linking patterns and the relative azimuthal orientations of adjacent molecules in the fibril. The models confirm the high order in the N‐telopeptide 4D overlap zone. Proteins 2003;9999:000–000. © 2003 Wiley‐Liss, Inc.
Evaluation of protein fold comparison servers
Authors: Novotny Marian , Madsen Dennis , Kleywegt Gerard J. 
Published: December 2003

AbstractWhen a new protein structure has been determined, comparison with the database of known structures enables classification of its fold as new or belonging to a known class of proteins. This in turn may provide clues about the function of the protein. A large number of fold comparison programs have been developed, but they have never been subjected to a comprehensive and critical comparative analysis. Here we describe an evaluation of 11 publicly available, Web‐based servers for automatic fold comparison. Both their functionality (e.g., user interface, presentation, and annotation of results) and their performance (i.e., how well established structural similarities are recognized) were assessed. The servers were subjected to a battery of performance tests covering a broad spectrum of folds as well as special cases, such as multidomain proteins, Cα‐only models, new folds, and NMR‐based models. The CATH structural classification system was used as a reference. These tests revealed the strong and weak sides of each server. On the whole, CE, DALI, MATRAS, and VAST showed the best performance, but none of the servers achieved a 100% success rate. Where no structurally similar proteins are found by any individual server, it is recommended to try one or two other servers before any conclusions concerning the novelty of a fold are put on paper. Proteins 2004. © 2003 Wiley‐Liss, Inc.
Effective scoring function for protein sequence design
Authors: Liang Shide , Grishin Nick V. 
Published: December 2003

AbstractWe have developed an effective scoring function for protein design. The atomic solvation parameters, together with the weights of energy terms, were optimized so that residues corresponding to the native sequence were predicted with low energy in the training set of 28 protein structures. The solvation energy of non‐hydrogen‐bonded hydrophilic atoms was considered separately and expressed in a nonlinear way. As a result, our scoring function predicted native residues as the most favorable in 59% of the total positions in 28 proteins. We then tested the scoring function by comparing the predicted stability changes for 103 T4 lysozyme mutants with the experimental values. The correlation coefficients were 0.77 for surface mutations and 0.71 for all mutations. Finally, the scoring function combined with Monte Carlo simulation was used to predict favorable sequences on a fixed backbone. The designed sequences were similar to the natural sequences of the family to which the template structure belonged. The profile of the designed sequences was helpful for identification of remote homologues of the native sequence. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
A Shannon entropy‐based filter detects high‐ quality profile–profile alignments in searches for remote homologues
Authors: Capriotti Emidio , Fariselli Piero , Rossi Ivan , Casadio Rita 
Published: December 2003

AbstractDetection of homologous proteins with low‐sequence identity to a given target (remote homologues) is routinely performed with alignment algorithms that take advantage of sequence profile. In this article, we investigate the efficacy of different alignment procedures for the task at hand on a set of 185 protein pairs with similar structures but low‐sequence similarity. Criteria based on the SCOP label detection and MaxSub scores are adopted to score the results. We investigate the efficacy of alignments based on sequence–sequence, sequence–profile, and profile–profile information. We confirm that with profile–profile alignments the results are better than with other procedures. In addition, we report, and this is novel, that the selection of the results of the profile–profile alignments can be improved by using Shannon entropy, indicating that this parameter is important to recognize good profile–profile alignments among a plethora of meaningless pairs. By this, we enhance the global search accuracy without losing sensitivity and filter out most of the erroneous alignments. We also show that when the entropy filtering is adopted, the quality of the resulting alignments is comparable to that computed for the target and template structures with CE, a structural alignment program. Proteins 2004. © 2003 Wiley‐Liss, Inc.
Crystal structure of the C67A mutant of isopentenyl diphosphate isomerase complexed with a mechanism‐based irreversible inhibitor
Authors: Wouters J. , Oudjama Y. , Stalon V. , Droogmans L. , Poulter C.D. 
Published: December 2003

AbstractIsopentenyl diphosphate:dimethylallyl diphosphate (IPP:DMAPP) isomerase is a key enzyme in the biosynthesis of isoprenoids. The mechanism of the isomerization reaction involves protonation of the unactivated carbon‐carbon double bond in the substrate. Analysis of the 1.97 Å crystal structure of the inactive C67A mutant of E. coli isopentenyl diphosphate:dimethylallyl diphosphate isomerase complexed with the mechanism‐based inactivator 3,4‐epoxy‐3‐methyl‐1‐butyl diphosphate is in agreement with an isomerization mechanism involving Glu 116, Tyr 104, and Cys 67. In particular, the results are consistent with a mechanism where Glu116 is involved in the protonation step and Cys67 in the elimination step. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
Picosecond dynamics of the glutamate receptor in response to agonist‐induced vibrational excitation
Authors: Kubo Minoru , Shiomitsu Eiji , Odai Kei , Sugimoto Tohru , Suzuki Hideo , Ito Etsuro 
Published: December 2003

AbstractConformational changes of proteins are dominated by the excitation and relaxation processes of their vibrational states. To elucidate the mechanism of receptor activation, the conformation dynamics of receptors must be analyzed in response to agonist‐induced vibrational excitation. In this study, we chose the bending vibrational mode of the guanidinium group of Arg485 of the glutamate receptor subunit GluR2 based on our previous studies, and we investigated picosecond dynamics of the glutamate receptor caused by the vibrational excitation of Arg485 via molecular dynamics simulations. The vibrational excitation energy in Arg485 in the ligand‐binding site initially flowed into Lys730, and then into the J‐helix at the subunit interface of the ligand‐binding domain. Consequently, the atomic displacement in the subunit interface around an intersubunit hydrogen bond was evoked in about 3 ps. This atomic displacement may perturb the subunit packing of the receptor, triggering receptor activation. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Quantifying the effect of burial of amino acid residues on protein stability
Authors: Zhou Hongyi , Zhou Yaoqi 
Published: December 2003

AbstractThe average contribution of individual residue to folding stability and its dependence on buried accessible surface area (ASA) are obtained by two different approaches. One is based on experimental mutation data, and the other uses a new knowledge‐based atom–atom potential of mean force. We show that the contribution of a residue has a significant correlation with buried ASA and the regression slopes of 20 amino acid residues (called the buriability) are all positive (pro‐burial). The buriability parameter provides a quantitative measure of the driving force for the burial of a residue. The large buriability gap observed between hydrophobic and hydrophilic residues is responsible for the burial of hydrophobic residues in soluble proteins. Possible factors that contribute to the buriability gap are discussed. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Evolutionary trace analysis of scorpion toxins specific for K‐channels
Authors: Zhu Shunyi , Huys Isabelle , Dyason Karin , Verdonck Fons , Tytgat Jan 
Published: December 2003

AbstractScorpion α‐K+ channel toxins are a large family of polypeptides with a similar structure but diverse pharmacological activities. Despite many structural and functional data available at present, little progress has been made in understanding the toxin′s molecular basis responsible for the functional diversification. In this paper, we report the first complete cDNA sequences of toxins belonging to subfamily 6 and identify five new members, called α‐KTx 6.6‐6.10. By analyzing the rates of mutations that occurred in the corresponding cDNAs, we suggest that accelerated evolution in toxin‐coding regions may be associated with the functional diversification of this subfamily. To pinpoint sites probably involved in the functional diversity of α‐KTx family, we analyzed this family of sequences using the evolutionary trace method. This analysis highlighted one channel‐binding surface common for all the members. This surface is composed of one conserved lysine residue at position 29 assisted by other residues at positions 10, 26, 27, 32, 34, and 36. Of them, the positions 29, 32, and 34 have been reported to be the most major determinants of channel specificity. Interestingly, another contrary surface was also observed at a higher evolutionary time cut‐off value, which may be involved in the binding of ERG (ether‐a‐go‐go‐related gene) channel‐specific toxins. The good match between the trace residues and the functional epitopes of the toxins suggested that the evolutionary trace results reported here can be applied to predict channel‐binding sites of the toxins. Because, the side‐chain variation in the trace positions is strongly linked with the functional alteration and channel‐binding surface transfer of α‐KTx family, we conclude that our findings should also be important for the rational design of new toxins targeting a given potassium channel with high selectivity. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Strand‐loop‐strand motifs: Prediction of hairpins and diverging turns in proteins
Authors: Kuhn Michael , Meiler Jens , Baker David 
Published: December 2003

Abstractβ‐sheet proteins have been particularly challenging for de novo structure prediction methods, which tend to pair adjacent β‐strands into β‐hairpins and produce overly local topologies. To remedy this problem and facilitate de novo prediction of β‐sheet protein structures, we have developed a neural network that classifies strand‐loop‐strand motifs by local hairpins and nonlocal diverging turns by using the amino acid sequence as input. The neural network is trained with a representative subset of the Protein Data Bank and achieves a prediction accuracy of 75.9 ± 4.4% compared to a baseline prediction rate of 59.1%. Hairpins are predicted with an accuracy of 77.3 ± 6.1%, diverging turns with an accuracy of 73.9 ± 6.0%. Incorporation of the β‐hairpin/diverging turn classification into the ROSETTA de novo structure prediction method led to higher contact order models and somewhat improved tertiary structure predictions for a test set of 11 all‐β‐proteins and 3 αβ‐proteins. The β‐hairpin/diverging turn classification from amino acid sequences is available online for academic use (Meiler and Kuhn, 2003; www.jens‐meiler.de/turnpred.html). Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
A Semantics for Distributed Execution of Statemate
Authors: Fränzle Martin , Niehaus Jürgen , Metzner Alexander , Damm Werner 
Published: December 2003

Abstract.
We present a semantics for the statechart variant implemented in the Statemate product of i-Logix. Our semantics enables distributed code generation for Statemate models in the context of rapid prototyping for embedded control applications. We argue that it seems impossible to efficiently generate distributed code using the original Statemate semantics. The new, distributed semantics has the advantages that, first, it enables the generation of efficient distributed code, second, it preserves many aspects of the original semantics for those parts of a model that are not distributed, and third, the changes made regarding the interaction of distributed model parts are similar to the interaction between the model and its environment in the original semantics, thus giving designers a familiar execution model. The semantics has been implemented in Grace, a framework for rapid prototyping code generation for embedded control applications.
Redesign of a Systems Engineering Language: Formalisation of χ
Authors: Bos Victor , Kleijn Jeroen 
Published: December 2003

Abstract.
This paper describes the redesign of a systems engineering language called χ. This is an engineering language designed to specify and analyse industrial systems. The main objective of this redesign was to enable mathematical reasoning about χ specifications. We discuss the original χ language, the requirements and design decisions, and the resulting syntax and semantics of the new version of χ, called χ. In particular, we elaborate on semantical aspects of χ’s time model.
Intensional and Extensional Semantics of Dataflow Programs
Authors: Gay Simon , Nagarajan Rajagopal 
Published: December 2003

Abstract.
We compare two semantic models of dataflow programs: a synchronous version of the classical Kahn semantics, and a new semantics in a category of synchronous processes. We consider the Kahn semantics to be extensional, as it describes the functions computed by dataflow nodes, and the categorical semantics to be intensional, as it describes the step-by-step production of output tokens from input tokens. Assuming that programs satisfy Wadge’s cycle sum condition and are therefore deadlock-free, we prove that the two semantics are equivalent. This equivalence result amounts to a proof that function composition in the extensional semantics is faithfully modelled by the detailed interactions of the intensional semantics, and provides further insight into the nature of dataflow computation.
Hearing loss in Fabry disease: The effect of agalsidase alfa replacement therapy
Authors: Hajioff D. , Enever Y. , Quiney R. , Zuckerman J. , Mackermot K. , Mehta A. 
Published: December 2003

AbstractSummary: The aim of this study was to describe the nature and prevalence of hearing loss in Fabry disease (McKusick 301500), a rare X‐linked lysosomal storage disorder, and its response to enzyme replacement therapy with agalsidase alfa. Fifteen hemizygous male Fabry patients (aged 25–49 years) were randomized to receive placebo or enzyme replacement therapy for 6 months; all have received open‐label enzyme replacement therapy for an additional 24 months thus far. Pure‐tone audiometry, impedance audiometry and otoacoustic emission testing were performed at 0 (baseline), 6, 18 and 30 months. Four patients (27%) had bilateral and 7 (47%) had unilateral high‐frequency sensorineural hearing loss (SNHL). Two (13%) had unilateral middle ear effusions with conductive losses persisting beyond 6 months. Only 3 (20%) had normal hearing. High‐frequency SNHL deteriorated over the first 6 months in both placebo and active treatment groups by a median 4.3 dB (p=0.002, Wilcoxon matched pairs). This hearing loss subsequently improved above baseline by 2.1 dB at 18 months (p=0.02) and by 4.9 dB at 30 months (p=0.004). In conclusion, significant hearing loss, usually high‐frequency SNHL, is a common manifestation of Fabry disease in adults. α‐Galactosidase A replacement therapy with agalsidase alfa appears to reverse the hearing deterioration in these patients. This improvement is gradual, however, suggesting the need for long‐term enzyme replacement therapy.