bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing physical energy functions for protein folding
Authors: Fujitsuka Yoshimi , Takada Shoji , Luthey‐Schulten Zaida A. , Wolynes Peter G. 
Published: December 2003

AbstractWe optimize a physical energy function for proteins with the use of the available structural database and perform three benchmark tests of the performance: (1) recognition of native structures in the background of predefined decoy sets of Levitt, (2) de novo structure prediction using fragment assembly sampling, and (3) molecular dynamics simulations. The energy parameter optimization is based on the energy landscape theory and uses a Monte Carlo search to find a set of parameters that seeks the largest ratio δEs/ΔE for all proteins in a training set simultaneously. Here, δEs is the stability gap between the native and the average in the denatured states and ΔE is the energy fluctuation among these states. Some of the energy parameters optimized are found to show significant correlation with experimentally observed quantities: (1) In the recognition test, the optimized function assigns the lowest energy to either the native or a near‐native structure among many decoy structures for all the proteins studied. (2) Structure prediction with the fragment assembly sampling gives structure models with root mean square deviation less than 6 Å in one of the top five cluster centers for five of six proteins studied. (3) Structure prediction using molecular dynamics simulation gives poorer performance, implying the importance of having a more precise description of local structures. The physical energy function solely inferred from a structural database neither utilizes sequence information from the family of the target nor the outcome of the secondary structure prediction but can produce the correct native fold for many small proteins. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Loss of translational entropy in molecular associations
Authors: Siebert Xavier , Amzel L. Mario 
Published: December 2003

AbstractMolecular associations in solution are opposed by the loss of entropy (ΔS) that results from the restriction of motion of each component in the complex. Theoretical estimates of ΔS are essential for rationalizing binding affinities, as well as for calculating entropic contribution to enzyme catalysis. Recently a statistical–mechanical framework has been proposed for estimating efficiently the translational entropy loss (ΔStrsl), while taking explicitly into account the complex intermolecular interactions between the solute and the solvent. This framework relates the translational entropy of a solute in solution to its “free volume,” defined as the volume accessible to the center of mass of the solute in the presence of the solvent and calculated by using an extension of the cell model (CM) for condensed phases. The translational entropy of pure water, estimated with the CM algorithm, shows good agreement with the experimental information. The free volume of various solutes in water, calculated within the CM by using molecular dynamics simulations with explicit solvent, displays a strong correlation with the solutes' polar and total surface areas. This correlation is used to propose a parameterization that can be used to calculate routinely the translational entropy of a solute in water. We also applied the CM formalism to calculate the free volume and translational entropy loss (ΔStrsl) on binding of benzene to a cavity in a mutant T4‐lysozyme. Our results agree with previously published estimates of the binding of benzene to this mutant T4‐lysozyme. These and other considerations suggest that the cell model is a simple yet efficient theoretical framework to evaluate the translational entropy loss on molecular association in solution. Proteins 2004. © 2003 Wiley‐Liss, Inc.
Molecular dynamics simulations of peptides containing an unnatural amino acid: Dimerization, folding, and protein binding
Authors: Yu Haibo , Daura Xavier , van Gunsteren Wilfred F. 
Published: December 2003

AbstractWe have performed molecular dynamics (MD) simulations to study the dimerization, folding, and binding to a protein of peptides containing an unnatural amino acid. NMR studies have shown that the substitution of one residue in a tripeptide β‐strand by the unnatural amino acid Hao (5‐HO2CCONH‐2‐MeO‐C6H3‐CO‐NHNH2) modifies the conformational flexibility of the β‐strand and the hydrogen‐bonding properties of its two edges: The number of hydrogen‐bond donors and acceptors increases at one edge, whereas at the other, they are sterically hindered. In simulations in chloroform, the Hao‐containing peptide 9 (i‐PrCO‐Phe‐Hao‐Val‐NHBu) forms a β‐sheet–like hydrogen‐bonded dimer, in good agreement with the available experimental data. Addition of methanol to the solution induces instability of this β‐sheet, as confirmed by the experiments. MD simulations also reproduce the folding of the synthetic peptide 1a (i‐PrCO‐Hao‐Ut‐Phe‐Ile‐Leu‐NHMe) into a β‐hairpin–like structure in chloroform. Finally, the Hao‐containing peptide, Ac‐Ala‐Hao‐Ala‐NHMe, is shown to form a stable complex with the Ras analogue, Rap1 A, in water at room temperature. Together with the available experimental data, these simulation studies indicate that Hao‐containing peptides may serve as inhibitors of β‐sheet interactions between proteins. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Detection of functional modules from protein interaction networks
Authors: Pereira‐Leal Jose B. , Enright Anton J. , Ouzounis Christos A. 
Published: December 2003

AbstractComplex cellular processes are modular and are accomplished by the concerted action of functional modules (Ravasz et al., Science 2002;297:1551–1555; Hartwell et al., Nature 1999;402:C47–52). These modules encompass groups of genes or proteins involved in common elementary biological functions. One important and largely unsolved goal of functional genomics is the identification of functional modules from genomewide information, such as transcription profiles or protein interactions. To cope with the ever‐increasing volume and complexity of protein interaction data (Bader et al., Nucleic Acids Res 2001;29:242–245; Xenarios et al., Nucleic Acids Res 2002;30:303–305), new automated approaches for pattern discovery in these densely connected interaction networks are required (Ravasz et al., Science 2002;297:1551–1555; Bader and Hogue, Nat Biotechnol 2002;20:991–997; Snel et al., Proc Natl Acad Sci USA 2002;99:5890–5895). In this study, we successfully isolate 1046 functional modules from the known protein interaction network of Saccharomyces cerevisiae involving 8046 individual pair‐wise interactions by using an entirely automated and unsupervised graph clustering algorithm. This systems biology approach is able to detect many well‐known protein complexes or biological processes, without reference to any additional information. We use an extensive statistical validation procedure to establish the biological significance of the detected modules and explore this complex, hierarchical network of modular interactions from which pathways can be inferred. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Gaps in structurally similar proteins: Towards improvement of multiple sequence alignment
Authors: Wrabl James O. , Grishin Nick V. 
Published: December 2003

AbstractAn algorithm was developed to locally optimize gaps from the FSSP database. Over 2 million gaps were identified from all versus all FSSP structure comparisons, and datasets of non‐identical gaps and flanking regions comprising between 90,000 and 135,000 sequence fragments were extracted for statistical analysis. Relative to background frequencies, gaps were enriched in residue types with small side chains and high turn propensity (D, G, N, P, S), and were depleted in residue types with hydrophobic side chains (C, F, I, L, V, W, Y). In contrast, regions flanking a gap exhibited opposite trends in amino acid frequencies, i.e., enrichment in hydrophobic residues and a high degree of secondary structure. Log‐odds scores of residue type as a function of position in or around a gap were derived from the statistics. Three simple experiments demonstrated that these scores contained significant predictive information. First, regions where gaps were observed in single sequences taken from HOMSTRAD structure‐based multiple sequence alignments generally scored higher than regions where gaps were not observed. Second, given the correct pairwise‐aligned cores, the actual positions of gaps could be reproduced from sequence more accurately using the structurally‐derived statistics than by using random pairwise alignments. Finally, revision of the Clustal‐W residue‐specific gap opening parameters with this new information improved the agreement of Clustal‐W alignments with the structure‐based alignments. At least three applications for these results are envisioned: improvement of gap penalties in pairwise (or multiple) sequence alignment, prediction of regions of single sequences likely (or unlikely) to contain indels, and more accurate placement of gaps in automated pairwise structure alignment. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
Proteomic signatures: Amino acid and oligopeptide compositions differentiate among phyla
Authors: Pe'er Itsik , Felder Clifford E. , Man Orna , Silman Israel , Sussman Joel L. , Beckmann Jacques S. 
Published: December 2003

AbstractAvailability of complete genome sequences allows in‐depth comparison of single‐residue and oligopeptide compositions of the corresponding proteomes. We have used principal component analysis (PCA) to study the landscape of compositional motifs across more than 70 genera from all three superkingdoms. Unexpectedly, the first two principal components clearly differentiate archaea, eubacteria, and eukaryota from each other. In particular, we contrast compositional patterns typical of the three superkingdoms and characterize differences between species and phyla, as well as among patterns shared by all compositional proteomic signatures. These species‐specific patterns may even extend to subsets of the entire proteome, such as proteins pertaining to individual yeast chromosomes. We identify factors that affect compositional signatures, such as living habitat, and detect strong eukaryotic preference for homopeptides and palindromic tripeptides. We further detect oligopeptides that are either universally over‐ or underabundant across the whole proteomic landscape, as well as oligopeptides whose over‐ or underabundance is phylum‐ or species‐specific. Finally, we report that species composition signatures preserve evolutionary memory, providing a new method to compare phylogenetic relationships among species that avoids problems of sequence alignment and ortholog detection. Proteins 2004. © 2003 Wiley‐Liss, Inc.
First principles computational study of the active site of arginase
Authors: Ivanov Ivaylo , Klein Michael L. 
Published: December 2003

AbstractAb initio density functional theory (DFT) methods were used to investigate the structural features of the active site of the binuclear enzyme rat liver arginase. Special emphasis was placed on the crucial role of the second shell ligand interactions. These interactions were systematically studied by performing calculations on models of varying size. It was determined that a water molecule, and not hydroxide, is the bridging exogenous ligand. The carboxylate ligands facilitate the close approach of the Mn (II) ions by attenuating the metal–metal electrostatic repulsion. Of the two metals, MnA was shown to carry a larger positive charge. Analysis of the electronic properties of the active site revealed that orbitals involving the terminal Asp234 residue, as well as the flexible μ‐1,1 bridging Asp232, lie at high energies, suggesting weaker coordination. This is reflected in certain structural variability present in our models and is also consistent with recent experimental findings. Finally, implications of our findings for the biological function of the enzyme are delineated. Proteins 2004. © 2003 Wiley‐Liss, Inc.
Sequence‐based study of two related proteins with different folding behaviors
Authors: Favrin Giorgio , Irbäck Anders , Wallin Stefan 
Published: December 2003

AbstractZSPA–1 is an engineered protein that binds to its parent, the three‐helix‐bundle Z domain of staphylococcal protein A. Uncomplexed ZSPA–1 shows a reduced helix content and a melting behavior that is less cooperative, compared with the wild‐type Z domain. Here we show that the difference in folding behavior between these two sequences can be partly understood in terms of an off‐lattice model with 5–6 atoms per amino acid and a minimalistic potential, in which folding is driven by backbone hydrogen bonding and effective hydrophobic attraction. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
The influence of uniaxial stress on the electrical properties of TMA‐CuBr4 crystals
Authors: Kallaev S. N. , Kamilov I. K. , Djabrailov A. M. , Sadykov S. A. , Amirova A. A. 
Published: December 2003

AbstractAnomalously large variations in the electrical properties of [N(CH3)4]2CuBr4 crystals are manifested by the disappearance of the spontaneous polarization (ferroelectricity) under the action of small uniaxial mechanical stresses. The observed effect is reversible and non‐linear. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
EPR of [Li]0, [Na]0, and [K]0 centres in SrS and CaS polycrystals
Authors: Seeman V. , Danilkin M. , Ots A. , Pedak E. , Pung L. , Pärnoja E. 
Published: December 2003

AbstractConnected with alkaline metal impurities axial V centres were studied by EPR in SrS and CaS polycrystals. A paramagnetic S− ion arises near an alkaline metal ion substituting for a cation of the host lattice after a hole produced by X‐raying at 77 K is captured. The centres are observable at low temperatures of 10–25 K. The superhyperfine structure from a 23Na nucleus and a 7Li nucleus was observed. Parameters of V centres (g‐tensor and A‐tensor values, thermal decay) are determined. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of gallium doping on the electronic structure of lead‐telluride‐based alloys
Authors: Skipetrov E. , Zvereva E. , Kovalev B. , Slyn'ko E. 
Published: December 2003

AbstractGalvanomagnetic and photoelectric properties of the Pb1−ySnyTe (0 ≤ y ≤ 0.06) and Pb1−xGexTe (0.04 ≤ x ≤ 0.08) single crystals doped with gallium (CGa = 0.3–3 mol%) have been investigated. Low‐temperature activation ranges of the impurity conductivity on the dark curves of the resistivity ρ(1/T) and Hall coefficient RH(1/T) were revealed and attributed to the appearance of gallium‐induced deep levels in the gap of the alloys. It was shown that the alloys possess high infrared photosensitivity at temperatures below Tc = 50–60 K. The results are discussed in the frame of the model assuming that doping with gallium leads to the formation of two different gallium‐related defect levels in the energy spectrum of the PbTe‐based alloys. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Expanded Bethe–Peierls approximation for the Ising model with S = 1/2 and 1
Authors: Du A. , Liu H. J. , Yü Y. Q. 
Published: December 2003

AbstractA expanded Bethe–Peierls approximation has been used to study the Ising model on honeycomb lattice, square lattice, kagomé lattice, triangular lattice and simple cubic lattice with spin S = 1/2 and 1. The spatial dimensionality of system is distinguished for different lattices. It is found that the transition temperatures on different lattices are much closer to the real values than those obtained by the effective field theory and the Bethe lattice approximation, and the transition temperatures of systems on kagomé lattice (z = 4) and trianguilar lattice (z = 6) are lower than those on square lattice (z = 4) and simple cubic lattice (z = 6), respectively. The static magnetic susceptibilities are also calculated. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interlayer coupling in magnetic superlattices with electron density inhomogeneities
Authors: Gruhn W. , Bąk Z. 
Published: December 2003

AbstractWe discuss the influence of spatial inhomogeneities of the free electron density on the magnetic interaction between magnetic layers of the superlattice, mediated across nonmagnetic, metallic spacer. Using the modified total energy approach, we prove that the TM or RE superlattices the additional scattering of free electrons on magnetic ion multipole moment increases the ferroquadrupolar biquadratic coupling between magnetic layers. It is shown also that the nonuniform free electron density generates contribution to the interlayer coupling being of the Dzialoshinsky‐Moriya type. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spin surfaces and trajectories in valence bands of tetrahedral semiconductors
Authors: Dargys A. 
Published: December 2003

AbstractSurfaces and trajectories traced out by spin vectors in spin space are calculated and systematized for holes in tetrahedral semiconductors. It is shown how various trajectories are related to the wave‐function phases and amplitudes of the doubly degenerated heavy‐mass, light‐mass, or split‐off bands. Relations between hole wave vectors and spin surface shapes are examined for high symmetry directions. The presented results may be useful in ultrafast spintronics, where both the spin state and the wave vector of a hole should be taken into account simultaneously in the description of the hole spin dynamics. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ionic conductivity and chemical diffusion in superionic LixCu2−xS (0 ≤ x ≤ 0.25)
Authors: Balapanov M. Kh. , Gafurov I. G. , Mukhamed'yanov U. Kh. , Yakshibaev R. A. , Ishembetov R. Kh. 
Published: December 2003

AbstractThe ionic conductivity and the conjugate chemical diffusion of cations and electron holes in LixCu2−xS (0 ≤ x ≤ 0.25) compositions are studied in the temperature range 623–467 K. In accordance with prediction of the known “mixed mobile ions effect” the partial substitution of copper by lithium in copper sulfide leads to decreasing of the ionic conductivity and it is linked to an increase of activation energy of the ionic conductivity. In comparison with pure copper sulfide the chemical diffusion coefficients in the lithium‐contained compounds are smaller too. The observed values of the activation energy of the chemical diffusion are close to those of the activation energy of the ionic conductivity. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effective susceptibility exponent in transverse Ising thin films
Authors: Kaneyoshi T. 
Published: December 2003

AbstractBy the use of both the standard mean field theory and the effective field theory with correlations the phase transition of the transverse Ising thin films is investigated with special emphasis to the behavior of the susceptibility χ(T) outside the critical regime. The exchange interaction and transverse field at the surfaces of the thin film take values different from those in the bulk. Various non‐monotonic temperature dependences of the effective exponent γ(T) introduced by Kouvel and Fisher are found, depending on the ratios of these properties between the surfaces and the bulk as well as the value of film thickness L. They are clearly different from the behavior in the bulk. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interwell exciton dispersion engineering, coherent phonons generation and optical detection of exciton condensate
Authors: Lozovik Yu. E. , Ovchinnikov I. V. , Ostroumov R. P. , Wang K. L. 
Published: December 2003

AbstractWe propose to use dispersion engineering of interwell excitons in coupled quantum wells with external electric and magnetic fields in order to generate coherent phonons and to detect exciton condensate. A parallel magnetic field moves the dispersion minimum of interwell excitons away from the radiative zone and thus reduces their recombination rate. Normal electric field moves an interwell excitons dispersion minimum on the energy scale. These two fields effect can be used to tune the resonance condition of the interwell excitons recombination process via an in‐well excitons level, which results in acoustic phonon emission. We show, that one can change recombination rate as well as intensity and angular distribution of the interwell excitons photoluminescence in the wide range by controlling the external fields. Based on this principle we propose and theoretically evaluate a procedure to detect the condensate of interwell excitons, as well as a scheme to obtain a coherent and monochromatic phonon beam (saser). The statistics of the phonon emission from the condensate of interwell excitons is studied. Numerical estimate for GaAs/AlGaAs coupled quantum wells is provided. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hopping transport in 1D chains (DNA vs. DLC)
Authors: Kohary K. , Cordes H. , Baranovskii S. D. , Thomas P. , Wendorff J.‐H. 
Published: December 2003

AbstractWe discuss charge transport in one‐dimensional organic solids (DNA and discotic liquid‐crystalline glass (DLC)), focusing on the effects of static and dynamic disorder. In the presence of static disorder it can be shown that the temperature dependence of the low‐field mobility is μ ∝ exp [−(T0/T)2], with characteristic temperature T0 depending on the scale of the energy distribution of localized states responsible for transport. In the case of both static and dynamic disorder the situation is different. We obtain a temperature independent mobility in our molecular dynamics calculations in the case of large static and dynamic disorder compared to the energy overlap integral between the neighbouring sites. The theoretical results are in good agreement with experimental data. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Shot noise in mesoscopic transport through localised states
Authors: Savchenko A. K. , Safonov S. S. , Roshko S. H. , Bagrets D. A. , Jouravlev O. N. , Nazarov Y. V. , Linfield E. H. , Ritchie D. A. 
Published: December 2003

AbstractWe show that shot noise can be used for studies of hopping and resonant tunnelling between localised electron states. In hopping via several states, shot noise is seen to be suppressed compared with its classical Poisson value SI = 2eI (I is the average current) and the suppression depends on the distribution of the barriers between the localised states. In resonant tunnelling through a single impurity an enhancement of shot noise is observed. It has been established, both theoretically and experimentally, that a considerable increase of noise occurs due to Coulomb interaction between two resonant tunnelling channels. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interwell exciton dispersion engineering, coherent phonons generation and optical detectionof exciton condensate
Authors: Lozovik Yu. E. , Ovchinnikov I. V. , Ostroumov R. P. , Wang K. L. 
Published: December 2003

AbstractThis issue's Editor's Choice [1] discusses interwell excitons in coupled quantum wells as a candidate for observation of different phases in an exciton system, including the very interesting phenomenon of Bose condensation.The cover picture shows schematically how the generation of coherent phonons and the angular distribution of the exciton photoluminescence (PL) from the quantum well system can be controlled by the external electric and magnetic fields.The first author, Yurii E. Lozovik, is head of the Laboratory of Spectroscopy of Nanostructures at the Institute of Spectroscopy and also Professor of Physics at the Moscow Physical and Technical Institute. His main interests are electron and electron–hole systems in nanostructures, cluster physics, quantum electrodynamics in a cavity, matter in strong magnetic fields, nanotechnology, ultrafast and near field optics, and computer simulations.