bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving the tolerance of a protein a analogue to repeated alkaline exposures using a bypass mutagenesis approach
Authors: Linhult Martin , Gülich Susanne , Gräslund Torbjörn , Simon Annelie , Karlsson Martin , Sjöberg Anna , Nord Karin , Hober Sophia 
Published: March 2004

AbstractStaphylococcal protein A (SPA) is a cell surface protein expressed by Staphylococcus aureus. It consists of five repetitive domains. The five SPA‐domains show individual interaction to the Fc‐fragment as well as certain Fab‐fragments of immunoglobulin G (IgG) from most mammalian species. Due to the high affinity and selectivity of SPA, it has a widespread use as an affinity ligand for capture and purification of antibodies. One of the problems with proteinaceous affinity ligands in large‐scale purification is their sensitivity to alkaline conditions. SPA however, is considered relatively stable to alkaline treatment. Nevertheless, it is desirable to further improve the stability in order to enable an SPA‐based affinity medium to withstand even longer exposure to the harsh conditions associated with cleaning‐in‐place (CIP) procedures. For this purpose, a protein engineering strategy, which was used earlier for stabilization and consists of replacing the asparagine residues, is employed. Since Z in its “nonengineered” form already has a significant tolerance to alkaline treatment, small changes in stability due to the mutations are difficult to assess. Hence, in order to enable detection of improvements regarding the alkaline resistance of the Z domain, we chose to use a bypass mutagenesis strategy using a mutated variant Z(F30A) as a surrogate framework. Z(F30A) has earlier been shown to possess an affinity to IgG that is similar to the wild‐type but also demonstrates decreased structural stability. Since the contribution of the different asparagine residues to the deactivation rate of a ligand is dependent on the environment and also the structural flexibility of the particular region, it is important to consider all sensitive amino acids one by one. The parental Z‐domain contains eight asparagine residues, each with a different impact on the alkaline stability of the domain. By exchanging asparagine 23 for a threonine, we were able to increase the stability of the Z(F30A) domain in alkaline conditions. Also, when grafting the N23T mutation to the Z scaffold, we were able to detect an increased tolerance to alkaline treatment compared to the native Z molecule. Proteins 2004. © 2004 Wiley‐Liss, Inc.
A method using active‐site sequence conservation to find functional shifts in protein families: Application to the enzymes of central metabolism, leading to the identification of an anomalous isocitrate dehydrogenase in pathogens
Authors: Das Rajdeep , Gerstein Mark 
Published: March 2004

AbstractWe have introduced a method to identify functional shifts in protein families. Our method is based on the calculation of an active‐site conservation ratio, which we call the “ASC ratio.” For a structurally based alignment of a protein family, this ratio is the average sequence similarity of the active‐site region compared to the full‐length protein. The active‐site region is defined as all the residues within a certain radius of the known functionally important groups. Using our method, we have analyzed enzymes of central metabolism from a large number of genomes (35). We found that for most of the enzymes, the active‐site region is more highly conserved than the full‐length sequence. However, for three tricarboxylic acid (TCA)‐cycle enzymes, active‐site sequences are considerably more diverged (than full‐length ones). In particular, we were able to identify in six pathogens a novel isocitrate dehydrogenase that has very low sequence similarity around the active site. Detailed sequence–structure analysis indicates that while the active‐site structure of isocitrate dehydrogenase is most likely similar between pathogens and nonpathogens, the unusual sequence divergence could result from an extra domain added at the N‐terminus. This domain has a leucine‐rich motif similar one in the Yersinia pestis cytotoxin and may therefore confer additional pathogenic functions. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Why are both ends of the polypeptide chain on the outside of proteins?
Authors: Hovmöller Sven , Zhou Tuping 
Published: March 2004

AbstractProtein folding starts before the whole polypeptide has been synthesized by the ribosome. No matter how long the polypeptide is or how intricate the fold, both ends of the chain always end up on the surface. From a topological point of view, this is surprising; one would have expected to find the starting (N‐terminal) end inside the core of the folded protein, just as in a ball of yarn. We suggest here that the reason for this apparent paradox is that the first amino acid of the emerging polypeptide chain is gripped during protein synthesis, perhaps by the ribosome, and is not released until the whole polypeptide has been synthesized. This binding would greatly decrease the degrees of freedom for the protein‐folding process and could also explain why knots are so rare in proteins. Gripping would also guarantee that the N‐terminal is accessible on the protein surface as required for binding of ubiquitin, which regulates the natural degradation of proteins and avoids buildup of protein aggregates, such as those found in Huntington's, Alzheimer's, Parkinson's, and other neurodegenerative diseases. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Characterization of Arabidopsis thaliana stellacyanin: A comparison with umecyanin
Authors: Harrison Mark D. , Dennison Christopher 
Published: March 2004

AbstractThe cupredoxin domain of a putative type 1 blue copper protein (BCB) from Arabidopsis thaliana was overexpressed and purified. A recursive polymerase chain reaction method was used to synthesize an artificial coding region for the cupredoxin domain of horseradish stellacyanin (commonly known as umecyanin), prior to overexpression and purification. The recombinant proteins were refolded from inclusion bodies and reconstituted with copper, and their in vitro characteristics were studied. Recombinant umecyanin, which is nonglycosylated, has identical spectroscopic and redox properties to the native protein. The UV/Vis and EPR spectra of recombinant BCB and umecyanin demonstrate that they have comparable axial type 1 copper binding sites. Paramagnetic 1H NMR spectroscopy highlights the similarity between the active site architectures of BCB and umecyanin. The reduction potential of recombinant BCB is 252 mV, compared to 293 mV for recombinant umecyanin. Identical pKa values of 9.7 are obtained for the alkaline transitions in both proteins. This study demonstrates that BCB is the A. thaliana stellacyanin and the results form the biochemical basis for a discussion of BCB function in the model vascular plant. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Exploring protein native states and large‐scale conformational changes with a modified generalized born model
Authors: Onufriev Alexey , Bashford Donald , Case David A. 
Published: March 2004

AbstractImplicit solvation models provide, for many applications, a reasonably accurate and computationally effective way to describe the electrostatics of aqueous solvation. Here, a popular analytical Generalized Born (GB) solvation model is modified to improve its accuracy in calculating the solvent polarization part of free energy changes in large‐scale conformational transitions, such as protein folding. In contrast to an earlier GB model (implemented in the AMBER‐6 program), the improved version does not overstabilize the native structures relative to the finite‐difference Poisson–Boltzmann continuum treatment. In addition to improving the energy balance between folded and unfolded conformers, the algorithm (available in the AMBER‐7 and NAB molecular modeling packages) is shown to perform well in more than 50 ns of native‐state molecular dynamics (MD) simulations of thioredoxin, protein‐A, and ubiquitin, as well as in a simulation of Barnase/Barstar complex formation. For thioredoxin, various combinations of input parameters have been explored, such as the underlying gas‐phase force fields and the atomic radii. The best performance is achieved with a previously proposed modification to the torsional potential in the Amber ff99 force field, which yields stable native trajectories for all of the tested proteins, with backbone root‐mean‐square deviations from the native structures being ∼1.5 Å after 6 ns of simulation time. The structure of Barnase/Barstar complex is regenerated, starting from an unbound state, to within 1.9 Å relative to the crystal structure of the complex. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
GEMDOCK: A generic evolutionary method for molecular docking
Authors: Yang Jinn‐Moon , Chen Chun‐Chen 
Published: March 2004

AbstractWe have developed an evolutionary approach for flexible ligand docking. This approval, GEMDOCK, uses a Generic Evolutionary Method for molecular DOCKing and an empirical scoring function. The former combines both discrete and continuous global search strategies with local search strategies to speed up convergence, whereas the latter results in rapid recognition of potential ligands. GEMDOCK was tested on a diverse data set of 100 protein–ligand complexes from the Protein Data Bank. In 79% of these complexes, the docked lowest energy ligand structures had root‐mean‐square derivations (RMSDs) below 2.0 Å with respect to the corresponding crystal structures. The success rate increased to 85% if the structure water molecules were retained. We evaluated GEMDOCK on two cross‐docking experiments in which each ligand of a protein ensemble was docked into each protein of the ensemble. Seventy‐six percent of the docked structures had RMSDs below 2.0 Å when the ligands were docked into foreign structures. We analyzed and validated GEMDOCK with respect to various search spaces and scoring functions, and found that if the scoring function was perfect, then the predicted accuracy was also essentially perfect. This study suggests that GEMDOCK is a useful tool for molecular recognition and may be used to systematically evaluate and thus improve scoring functions. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Melittin as model system for probing interactions between proteins and cyclodextrins
Authors: Khajehpour Mazdak , Troxler Thomas , Nanda Vikas , Vanderkooi Jane M. 
Published: March 2004

AbstractCylcodextrin sugars are cyclic sugars that have a hydrophilic exterior and a hydrophobic center. This enables cyclodextrins to solubilize hydrophobic molecules in aqueous media. Cyclodextrins may inhibit aggregation by intercalating surface aromatic residues and competing with interprotein aromatic clusters (π–π interactions). In order to investigate this concept, the interaction of hydroxypropyl‐β‐cyclodextrin (HPBCD) with melittin is studied with steady‐state and time‐resolved fluorescence, fluorescence polarization, circular dichroism, and IR spectroscopy. HPBCD inhibits the aggregation of melittin. This inhibition and the spectroscopic results are consistent with the lone aromatic tryptophan of the peptide being intercalated within HPBCD. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q
Authors: Kihara Daisuke , Skolnick Jeffrey 
Published: March 2004

AbstractThe genome scale threading of five complete microbial genomes is revisited using our state‐of‐the‐art threading algorithm, PROSPECTOR_Q. Considering that structure assignment to an ORF could be useful for predicting biochemical function as well as for analyzing pathways, it is important to assess the current status of genome scale threading. The fraction of ORFs to which we could assign protein structures with a reasonably good confidence level to each genome sequences is over 72%, which is significantly higher than earlier studies. Using the assigned structures, we have predicted the function of several ORFs through “single‐function” template structures, obtained from an analysis of the relationship between protein fold and function. The fold distribution of the genomes and the effect of the number of homologous sequences on structure assignment are also discussed. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Locating the stabilizing residues in (α/β)8 barrel proteins based on hydrophobicity, long‐range interactions, and sequence conservation
Authors: Gromiha M. Michael , Pujadas Gerard , Magyar Csaba , Selvaraj Samuel , Simon Istvan 
Published: March 2004

AbstractIn nature, 1 out of every 10 proteins has an (α/β)8 (TIM)‐barrel fold, and in most cases, pairwise comparisons show no sequence similarity between them. Hence, delineating the key residues that induce very different sequences to share a common fold is important for understanding the folding and stability of TIM‐barrel domains. In this work, we propose a new consensus approach for locating these stabilizing residues based on long‐range interactions, hydrophobicity, and conservation of amino acid residues. We have identified 957 stabilizing residues in 63 proteins from a nonredundant set of 71 TIM‐barrel domains. Most of these residues are located in the 8‐stranded β‐sheet, with nearly one half of them oriented toward the interior of the barrel and the other half oriented toward the surrounding α‐helices. Several stabilizing residues are found in the N‐ and C‐terminal loops, whereas very few appear in the α‐helices that surround the internal β‐sheet. Further, these 957 residues are placed in 434 stabilizing segments of various sizes, and each domain contains 1–10 of these segments. We found that 8 segments per domain is the most abundant one, and two thirds of the proteins have 7–9 stabilizing segments. Finally, we verified the identified residues with experimental temperature factors and found that these residues are among the ones with less mobility in the considered proteins. We suggest that our new protocol serves as a powerful tool to identify the stabilizing residues in TIM‐barrel domains, which can be used as potential candidates for studying protein folding and stability by means of protein engineering experiments. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Temperature dependence of the free energy landscape of the src‐SH3 protein domain
Authors: Guo Weihua , Lampoudi Sotiria , Shea Joan‐Emma 
Published: March 2004

AbstractThe temperature dependence of the free energy landscape of the src‐SH3 protein domain is investigated through fully atomic simulations in explicit solvent. Simulations are performed above and below the folding transition temperature, enabling an analysis of both protein folding and unfolding. The transition state for folding and unfolding, identified from the free energy surfaces, is found to be very similar, with structure in the central hydrophobic sheet and little structure throughout the rest of the protein. This is a result of a polarized folding (unfolding) mechanism involving early formation (late loss) of the central hydrophobic sheet at the transition state. Unfolding simulations map qualitatively well onto low‐temperature free energy surfaces but appear, however, to miss important features observed in folding simulations. In particular, details of the folding mechanism involving the opening and closing of the hydrophobic core are not captured by unfolding simulations performed under strongly denaturing conditions. In addition, free energy surfaces at high temperatures do not display a desolvation barrier found at lower temperatures, involving the expulsion of water molecules from the hydrophobic core. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Data‐based model and parameter evaluation in dynamic transcriptional regulatory networks
Authors: Cavelier German , Anastassiou Dimitris 
Published: March 2004

AbstractFinding the causality and strength of connectivity in transcriptional regulatory networks from time‐series data will provide a powerful tool for the analysis of cellular states. Presented here is the design of tools for the evaluation of the network's model structure and parameters. The most effective tools are found to be based on evolution strategies. We evaluate models of increasing complexity, from lumped, algebraic phenomenological models to Hill functions and thermodynamically derived functions. These last functions provide the free energies of binding of transcription factors to their operators, as well as cooperativity energies. Optimization results based on published experimental data from a synthetic network in Escherichia coli are presented. The free energies of binding and cooperativity found by our tools are in the same physiological ranges as those experimentally derived in the bacteriophage lambda system. We also use time‐series data from high‐density oligonucleotide microarrays of yeast meiotic expression patterns. The algorithm appropriately finds the parameters of pairs of regulated regulatory yeast genes, showing that for related genes an overall reasonable computation effort is sufficient to find the strength and causality of the connectivity of large numbers of them. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Identification of protons position in acid–base enzyme catalyzed reactions: The hepatitis C viral NS3 protease
Authors: Shokhen Michael , Albeck Amnon 
Published: March 2004

AbstractGeneral acid–base catalysis is a key element of the catalytic activity of most enzymes. Therefore, any explicit molecular modeling of enzyme‐catalyzed chemical reactions requires correct identification of protons location on the catalytic groups. In this work, we apply our quantum mechanical/self‐consistent reaction field in virtual solvent [QM/SCRF(VS)] method for identification of the position of protons shared by the enzyme catalytic groups and the polar groups of the inhibitor in a covalent tetrahedral complex (TC) of the hepatitis C virus NS3 protease with a peptidyl α‐ketoacid inhibitor. To identify the relevant protonation states, we have analyzed relative stabilities of R and S configurations of the TC that depend on the specific proton distribution over the polar groups and correlated it with experimental NMR and X‐ray crystallography data, both at low and neutral pH ranges. The tentative assignment of the single resonance in the 13C NMR spectrum of the hemiketal carbon at physiological pH to the S configuration of TC is confirmed. Both R and S configurations are equally stable at acidic pH in our modeling, in good agreement with the 13C NMR observation. Proteins 2004;9999:000–000. © 2004 Wiley‐Liss, Inc.
Expanded turn conformations: Characterization and sequence‐structure correspondence in α‐turns with implications in helix folding
Authors: Dasgupta Bhaskar , Pal Lipika , Basu Gautam , Chakrabarti Pinak 
Published: March 2004

AbstractLike the β‐turns, which are characterized by a limiting distance between residues two positions apart (i, i+3), a distance criterion (involving residues at positions i and i+4) is used here to identify α‐turns from a database of known protein structures. At least 15 classes of α‐turns have been enumerated based on the location in the ϕ,ψ space of the three central residues (i+1 to i+3)—one of the major being the class AAA, where the residues occupy the conventional helical backbone torsion angles. However, moving towards the C‐terminal end of the turn, there is a shift in the ϕ,ψ angles towards more negative ϕ, such that the electrostatic repulsion between two consecutive carbonyl oxygen atoms is reduced. Except for the last position (i+4), there is not much similarity in residue composition at different positions of hydrogen and non‐hydrogen bonded AAA turns. The presence or absence of Pro at i+1 position of α‐ and β‐turns has a bearing on whether the turn is hydrogen‐bonded or without a hydrogen bond. In the tertiary structure, α‐turns are more likely to be found in β‐hairpin loops. The residue composition at the beginning of the hydrogen bonded AAA α‐turn has similarity with type I β‐turn and N‐terminal positions of helices, but the last position matches with the C‐terminal capping position of helices, suggesting that the existence of a “helix cap signal” at i+4 position prevents α‐turns from growing into helices. Our results also provide new insights into α‐helix nucleation and folding. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Theoretical studies of the spin‐Hamiltonian parameters for Er3+ in CaWO4 and SrWO4
Authors: Wu Shao‐Yi , Dong Hui‐Ning , Yan Wei‐Zi , Gao Xiu‐Ying 
Published: March 2004

AbstractThe spin‐Hamiltonian parameters g factors g‖, g⟂ and hyperfine structure parameters A‖ and A⟂ for Er3+ (167Er) in CaWO4 and SrWO4 are theoretically studied by using the perturbation formulas of the spin‐Hamiltonian parameters for a 4f11 ion in tetragonal symmetry. In these formulas, the contributions to the spin‐Hamiltonian parameters arising from the second‐order perturbation terms and the admixture of various states are considered. The crystal‐field parameters for the tetragonally distorted tetrahedra are calculated from the superposition model and the local structural data of the impurity Er3+ ions at the host Ca2+ and Sr2+ sites. The theoretical parameters are in agreement with the experimental values. The validity of the results is discussed. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
PbS nanoparticles in Langmuir–Blodgett films: kinetics of formation and growth
Authors: Savin Yu. N. , Vitushkina S. V. 
Published: March 2004

AbstractThe formation and growth of lead sulfide nanocrystals in lead stearate Langmuir–Blodgett (LB) films are investigated by optical absorption spectroscopy. Kinetics of the concentration changes of lead ions in the different states formed during the growth process, as well as the evolution of the nanocrystal average size versus growth time, are studied. A nonlinear dependence of the nanoparticle growth rate versus time is found. The idea of diffusive decomposition of solid solutions is used to analyze the experimental results. It is shown that high concentrations of metal ions at the interfaces of monolayers of LB films, as well as diffusion restrictions of mass‐transfer processes, play a decisive role in the formation and growth of nanocrystals in ordered organic matrices. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Exchange and correlation effects in strained‐layer semiconductor quantum wells
Authors: Tong C. , Kim M. R. , Kim S. K. , Han B. H. , Rhee J. K. 
Published: March 2004

AbstractWe examine the exchange and the correlation effects for a quasi‐two‐dimensional InxGa1−xAs/InGaAsP QW systems with strain, considering the complexities related to the effect of valence‐band mixing. The many‐body effects due to exchange interaction and screening of Coulomb interaction are calculated within the random‐phase approximation. The valence‐band structure is obtained by solving the Luttinger–Kohn Hamiltonian to evaluate the valence‐band mixing and the strain effects properly. The dependence of the many‐body effects on strain and sheet carrier density is shown to become more important as the screening of the Coulomb interaction is included. Also, it is shown that the exchange and correlation energy becomes important as indium mole fraction and sheet carrier density increase. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The diluted transverse Ising model with competing bulk and surface ordering
Authors: Khaya L. , Benayad N. , Dakhama A. 
Published: March 2004

AbstractThe phase diagram of the three‐dimensional transverse Ising system with competing surface and bulk exchange interactions is studied by the use of an effective‐field method within the framework of a single‐site cluster theory. In addition to this pure case, which shows qualitatively interesting features, we investigated the effects of the bond dilution on the obtained phase diagram. In particular, we studied the influence of the surface dilution parameter on the surface transitions. We find a number of characteristic behaviours of the surface both in the absence and in the presence of the surface transverse field. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)