bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimal model for studying prion‐like folding pathways
Authors: Chen Jeff Z. Y. , Lemak Alexander S. , Lepock James R. , Kemp Josh P. 
Published: March 2003

AbstractThe Monte Carlo technique is used to simulate the energy landscape and the folding kinetics of a minimal prion‐like protein model. We show that the competition between hydrogen‐bonding and hydrophobic interactions yields two energetically favored secondary structures, an α‐helix and a β‐hairpin. Folding simulations indicate that the probability of reaching the α‐helix form from a denatured random conformation is much higher than the probability of reaching the β‐sheet form, even though the β‐sheet has a lower energy. The existence of a lower energy β‐sheet state gives the possibility for the normal α‐helix structure to take a structural transformation into the β‐sheet structure under external influences. Proteins 2003;51:283–288. © 2003 Wiley‐Liss, Inc.
Chain length is the main determinant of the folding rate for proteins with three‐state folding kinetics
Authors: Galzitskaya Oxana V. , Garbuzynskiy Sergiy O. , Ivankov Dmitry N. , Finkelstein Alexei V. 
Published: March 2003

AbstractWe demonstrate that chain length is the main determinant of the folding rate for proteins with the three‐state folding kinetics. The logarithm of their folding rate in water (kf) strongly anticorrelates with their chain length L (the correlation coefficient being −0.80). At the same time, the chain length has no correlation with the folding rate for two‐state folding proteins (the correlation coefficient is −0.07). Another significant difference of these two groups of proteins is a strong anticorrelation between the folding rate and Baker's “relative contact order” for the two‐state folders and the complete absence of such correlation for the three‐state folders. Proteins 2003;51:162–166. © 2003 Wiley‐Liss, Inc.
Impact of the tail and mutations G131V and M129V on prion protein flexibility
Authors: Santini Sébastien , Claude Jean‐Baptiste , Audic Stéphane , Derreumaux Philippe 
Published: March 2003

AbstractWithin the “protein‐only” hypothesis, a detailed mechanism for the conversion of a α‐helix to β‐sheet structure is unclear. We have investigated the effects of the tail 90–123 and the point mutations G131V and M129V on prion protein conformational plasticity at neutral pH. Molecular dynamics simulations show that the dynamics of the core 124–226 is essentially independent of the tail and that the point mutation G131V does not affect PrP thermodynamic stability. Both mutations, however, enhance the flexibility of residues that participate in the two‐step process for prion propagation. They also extend the short β‐sheet in the normal protein into a larger sheet at neutral pH. This finding suggests a critical role of the tail for triggering the topological change. Proteins 2003;51:258–265. © 2003 Wiley‐Liss, Inc.
Kinetics of cytochrome C folding: Atomically detailed simulations
Authors: Cárdenas Alfredo E. , Elber Ron 
Published: March 2003

AbstractThe vast range of time scales (from nanoseconds to seconds) during protein folding is a challenge for experiments and computations. To make concrete predictions on folding mechanisms, atomically detailed simulations of protein folding, using potentials derived from chemical physics principles, are desired. However, due to their computational complexity, straightforward molecular dynamics simulations of protein folding are impossible today. An alternative algorithm is used that makes it possible to compute approximate atomically detailed long time trajectories (the Stochastic Difference Equation in Length). This algorithm is used to compute 26 atomically detailed folding trajectories of cytochrome c (a millisecond process). The early collapse of the protein chain (with marginal formation of secondary structure), and the earlier formation of the N and C helices (compare to the 60's helix) are consistent with the experiment. The existence of an energy barrier upon entry to the molten globule is examined as well. In addition to (favorable) comparison to experiments, we show that non‐native contacts drive the formation of the molten globule. In contrast to popular folding models, the non‐native contacts do not form off‐pathway kinetic traps in cytochrome c. Proteins 2003;51:245–257. © 2003 Wiley‐Liss, Inc.
The catalytic mechanism of Drosophila alcohol dehydrogenase: Evidence for a proton relay modulated by the coupled ionization of the active site Lysine/Tyrosine pair and a NAD+ ribose OH switch
Authors: Koumanov Assen , Benach Jordi , Atrian Silvia , Gonzàlez‐Duarte Roser , Karshikoff Andrey , Ladenstein Rudolf 
Published: March 2003

AbstractThe ionization properties of the active site residues in Drosophila lebanonensis alcohol dehydrogenase (DADH) were investigated theoretically by using an approach developed to account for multiple locations of the hydrogen atoms of the titratable and polar groups. The electrostatic calculations show that (a) the protonation/deprotonation transition of the binary complex of DADH is related to the coupled ionization of Tyr151 and Lys155 in the active site and (b) the pH dependence of the proton abstraction is correlated with a reorganization of the hydrogen bond network in the active site. On this basis, a proton relay mechanism for substrate dehydrogenation is proposed in which the O2′ ribose hydroxyl group from the coenzyme has a key role and acts as a switch. The proton relay chain includes the active site catalytic residues, as well as a chain of eight water molecules that connects the active site with the bulk solvent. Proteins 2003;51:289–298. © 2003 Wiley‐Liss, Inc.
Non‐intertwined binary patterns of hydrophobic/nonhydrophobic amino acids are considerably better markers of regular secondary structures than nonconstrained patterns
Authors: Hennetin Jérôme , Le Tuan Khanh , Canard Luc , Colloc'h Nathalie , Mornon Jean‐Paul , Callebaut Isabelle 
Published: March 2003

AbstractPatterns of hydrophobic and hydrophilic residues (binary patterns) play an important role in protein architecture and can be roughly categorized into two classes regarding their preferential participation in α‐helices or β‐strands. However, a single binary pattern can be embedded into different longer patterns carrying opposite structural information and thus cannot be as much informative as expected. Here, we consider conditional binary patterns, or hydrophobic clusters, whose existence is conditioned by the presence of a minimum number of nonhydrophobic residues, called the connectivity distance, that separate two hydrophobic amino acids assumed to belong to two distinct patterns. Conditional binary patterns are distinct from simple ones in that they are not intertwined, i.e., they can not include or be included in other conditional patterns and therefore carry a much more differentiated information, in particular being dramatically better correlated with regular secondary structures (especially β ones). The distribution of these nonintertwined binary patterns in natural proteins was assessed relative to randomness, evidencing the structural bricks that are favored and disfavored by evolutionary selection. Several connectivity distances as well as several hydrophobic alphabets were tested, evidencing the clear superiority of a connectivity distance of 4, which mimics the minimum current length of loops in globular domains, and of the VILFMYW alphabet, selected from structural data (secondary structure propension and Voronoï tesselation), in highlighting fundamental properties of protein folds. Proteins 2003;51:236–244. © 2003 Wiley‐Liss, Inc.
Conservation and amyloid formation: A study of the gelsolin‐like family
Authors: Benyamini Hadar , Gunasekaran K. , Wolfson Haim , Nussinov Ruth 
Published: March 2003

AbstractThe mechanism through which globular proteins transform into amyloid fibrils is still not understood. Here we analyze the structure and sequence conservation to assess the differential stability of segments from two structurally related protein families: the amyloidogenic gelsolin‐like and its structurally related cofilin‐like. The two families belong to the actin depolymerizing proteins, with a central β‐sheet stacked between 2 and 4 α‐helices. Although sequentially remote, the two families share regions of high and low conservation and stability. Our results show a highly conserved hydrophobic and aromatic cluster, located at a central buried β‐hairpin. The geometry of the aromatic residues with respect to each other is strictly conserved, suggesting involvement in strand registering and β‐sheet stabilization. Consistent with experiment, we find a region of weak conservation and stability at one of the exposed β‐strands (strand B in the gelsolin‐like family). This region was recently found to be affected by a point mutation‐mediated destabilization of the human gelsolin domain 2, which facilitates the first proteolytic event in the formation of the amyloidogenic fragment. Thus, both experimental and computational conservation analyses suggest that this unstable region may constitute a first step in amyloid formation. Our analysis uses a recently developed multiple‐structure comparison algorithm in which molecules are aligned simultaneously. Proteins 2003;51:266–282. © 2003 Wiley‐Liss, Inc.
Large contact surface interactions between proteins detected by time series analysis methods: Case study on C‐phycocyanins
Authors: Giuliani Alessandro , Benigni Romualdo , Colafranceschi Mauro , Chandrashekar Indu , Cowsik Sudha M. 
Published: March 2003

AbstractA purely sequence‐dependent approach to the modeling of protein–protein interaction was applied to the study of C‐phycocyanin αβ dimers. The interacting pairs (α and β subunits) share an almost complete structural homology, together with a general lack of sequence superposition; thus, they constitute a particularly relevant example for protein–protein interaction prediction. The present analysis is based on a description posited at an intermediate level between sequence and structure, that is, the hydrophobicity patterning along the chains. Based on the description of the sequence hydrophobicity patterns through a battery of nonlinear tools (recurrence quantification analysis and other sequence complexity descriptors), we were able to generate an explicit equation modeling α and β monomers interaction; the model consisted of canonical correlation between the hydrophobicity autocorrelation structures of the interacting pairs. The general implications of this holistic approach to the modeling of protein–protein interactions, which considers the protein primary structures as a whole, are discussed. Proteins 2003;51:299–310. © 2003 Wiley‐Liss, Inc.
Functional role for Tyr 31 in the catalytic cycle of chicken dihydrofolate reductase
Authors: Shrimpton Paul , Mullaney Alex , Allemann Rudolf K. 
Published: March 2003

AbstractDespite much work, many key aspects of the mechanism of the dihydrofolate reductase (DHFR) catalyzed reduction of dihydrofolate remain unresolved. In bacterial forms of DHFR both substrate and water access to the active site are controlled by the conformation of the mobile M20 loop. In vertebrate DHFRs only one conformation of the residues corresponding to the M20 loop has been observed. Access to the active site was proposed to be controlled by residue 31. MD simulations of chicken DHFR complexed with substrates and cofactor revealed a closing of the side chain of Tyr 31 over the active site on binding of dihydrofolate. This conformational change was dependent on the presence of glutamate on the para‐aminobenzoylamide moiety of dihydrofolate. In its absence, the conformation remained open. Although water could enter the active site and hydrogen bond to N5 of dihydrofolate, indicating the feasibility of water as the proton donor, this was not controlled by the conformation of Tyr 31. The water accessibility of the active site was low for both conformations of Tyr 31. However, when hydride was transferred from NADPH to C6 of dihydrofolate before protonation, the average time during which water was found in hydrogen bonding distance to N5 of dihydrofolate in the active site increased almost fivefold. These results indicated that water can serve as the Broensted acid for the protonation of N5 of dihydrofolate during the DHFR catalyzed reduction. Proteins 2003;51:216–223. © 2003 Wiley‐Liss, Inc.
Disordering effect on optical absorption processes in CuInP2S6 layered ferrielectrics
Authors: Studenyak I. P. , Mitrovcij V. V. , Kovacs Gy. S. , Gurzan M. I. , Mykajlo O. A. , Vysochanskii Yu. M. , Cajipe V. B. 
Published: March 2003

AbstractThe optical absorption edge of CuInP2S6 crystals is studied between 77 and 573 K. The nature of optical transitions, resulting in absorption edge formation in ferrielectric and paraelectric phases, is elucidated. The temperature variation of the energy gap in the ferrielectric phase transition range and the temperature behavior of the Urbach absorption edge in the paraelectric phase are studied. The effect of temperature and structural disordering on the absorption edge energy position and shape is analyzed.
Structural modulation induced by the incommensurate antiferromagnetic phase transitionin ZnCr2Se4
Authors: Hidaka M. , Yoshimura M. , Tokiwa N. , Akimitsu J. , Park Yong Jun , Park Jae Hyun , Ji Sung Dae , Lee Ki Bong 
Published: March 2003

AbstractThe structural properties of normal‐type spinel ZnCr2Se4 have been studied as a function of temperature by means of X‐ray diffraction using synchrotron radiation. It is found that a structural phase transition from cubic to orthorhombic symmetry occurs at 22.5 K (Tc). It is also found that, below Tc, Se ions are cooperatively displaced in a pseudo‐tetragonal (001) plane. Since the Cr3+ ion has no orbital angular momentum, a CrSe6 octahedron is not distorted by a crystal field produced by surrounding Se2– anions. It is interpreted that the pseudo‐tetragonal displacements of Se ions are induced by magnetostriction among Cr3+ ions in CrSe2 chains, in which Cr ions share two Se2– with each other along 〈110〉.
ESR studies on Er3+‐doped YBiPt compound
Authors: Güner S. , Rameev B. , Aktaş B. 
Published: March 2003

AbstractThe semi‐metallic cubic compound YBiPt doped by Er3+ (4f11) has been studied by ESR technique between 4 and 300 K. X‐band and Q‐band measurements have been performed. The angular dependence of the ESR spectra on the crystal orientation with respect to the static magnetic field has been measured. Two anisotropic lines with hyperfine peaks coming from the interaction between electronic and nuclear spins of 167Er3+ (I = 7/2) isotopes have been observed below 30 K in the spectra. Computer modeling showed that these lines are the ESR signals from the quadruplet ground state of Er3+ ions in the cubic crystal field. The values of crystal field parameters B4 = –5.68 × 10–4 cm–1 and B6 = –6.64 × 10–6 cm–1 have been extracted. Also an isotropic line near g = 2 have been observed in both frequency bands. Dysonian lineshape of the spectra components due to the skin‐depth effect shows the conducting property of the sample under study. The temperature dependence of the spectra intensity obeys the well‐known Curie law for paramagnetism arising from the unpaired electrons of Er3+ ion.
Semi‐empirical descriptions of temperature dependences of band gaps in semiconductors
Authors: Pässler Roland 
Published: March 2003

AbstractStarting from general foundations of the semi‐empirical theory of monotonic temperature dependences of band gaps in semiconductors, we devote ourselves in this article to further analytical development and applications of the power function model. On the basis of a detailed analytical study of asymptotic low and high temperature behaviors, including numerical comparisons for intermediate temperatures, we devise a novel analytical (higher order root) expression. Applications to least‐mean‐square fittings of fundamental band gap data available for a variety of group IV, III–V, and II–VI materials are shown to provide, both for regimes of moderate and large phonon dispersion, self‐consistent values for basic dispersion‐related parameters. This is essential for detailed comparisons of the power function model with other elaborate semi‐empirical models developed in last years, which differ above all by qualitatively different types of low temperature asymptotes. An exemplification for bulk samples of Si and GaAs shows that it is rather difficult to distinguish clearly between T → 0 asymptotes, [E(0) – E(T)] ∝ T p, that are controlled by system‐specific fractional exponents (2 < p < 3) and other dispersion‐related descriptions that admit exclusively quadratic asymptotes (p = 2). Novel high‐precision data for single quantum dot luminescence peak positions are found to give us better chances for distinguishing between qualitatively different types of low temperature asymptotes.
Ordering in undoped hexagonal AlxGa1–xN grown on sapphire (0001) with 0.09 < x < 0.247
Authors: Laügt M. , Bellet‐Amalric E. , Ruterana P. , Omnès F. 
Published: March 2003

AbstractMultiple ordering has been observed both by high resolution X‐ray diffraction (HRXRD) and transmission electron microscopy (TEM) in AlxGa1–xN grown by low pressure metal‐organic vapor phase epitaxy (LP‐MOVPE) on sapphire (0001) with x varying from 9 to 25 percent. This is shown to take place even simultaneously in the same sample; beside the disordered alloy, AlGaN2 (1:1), and Al0.25Ga0.75N (3:1), there is an additional type which a quite large unit cell. In the latter, the c parameter is six times larger than that of the disordered alloy. Through the analysis of X‐ray diffraction data and comparison with TEM observations, a structure model is proposed. Taking into account the super‐lattice reflections intensity and symmetry, we conclude that this ordered phase contains two consecutive AlN monolayers in the 3.1 nm unit cell that corresponds to Al0.16Ga0.84N (10:2).
Morbidity measures in the presence of recurrent composite endpoints
Authors: Scott Martin , Möcks Joachim , Givens Sam , Köhler Walter , Maurer Jörg , Budde Michael 
Published: March 2003

AbstractThe analysis of recurrent event data in clinical trials presents a number of difficulties. The statistician is faced with issues of event dependency, composite endpoints, unbalanced follow‐up times and informative dropout. It is not unusual, therefore, for statisticians charged with responsibility for providing reliable and valid analyses to need to derive new methods specific to the clinical indication under investigation. One method is proposed that appears to have possible advantages over those that are often used in the analysis of recurrent event data in clinical trials. Based on an approach that counts periods of time with events instead of single event counts, the proposed method makes an adjustment for patient time on study and incorporates heterogeneity by estimating an individual per‐patient risk of experiencing a morbid event. Monte Carlo simulations demonstrate that, with use of a real clinical study data, the proposed method consistently outperforms other measures of morbidity. Copyright © 2003 John Wiley & Sons, Ltd.
Software for non‐linear mixed effects modelling: a review of several packages
Authors: Smith Michael K. 
Published: March 2003

AbstractThis paper gives some background information on what non‐linear mixed effects models are, why they can be useful in analysing repeated measures and what makes analysing such data challenging. Various software packages and routines are available to perform this kind of analysis, and this paper will compare and contrast these. Copyright © 2003 John Wiley & Sons, Ltd.
Case study in the Bayesian analysis of a cost‐effectiveness trial in the evaluation of health care technologies: Depression
Authors: Stevens John W. , O'Hagan Anthony , Miller Paul 
Published: March 2003

AbstractWe present a case study based on a depression study that will illustrate the use of Bayesian statistics in the economic evaluation of cost‐effectiveness data, demonstrate the benefits of the Bayesian approach (whilst honestly recognizing any deficiencies) with respect to frequentist methods, and provide details of using the methods, including computer code where appropriate. Copyright © 2003 John Wiley & Sons, Ltd.
Numerical methods for multicenter integrals for numerically defined basis functions applied in molecular calculations
Authors: Talman James D. 
Published: March 2003

AbstractAn alternative approach to using functions defined analytically as basis functions for molecular orbital calculations is to use functions defined numerically on some mesh. It is then necessary to evaluate various integrals involving products of such functions that are centered at different points in space, usually the nuclei. This article discusses in detail the problem of evaluating overlap and kinetic energy integrals, nuclear attraction three‐center integrals, and electron–electron repulsion four‐center integrals for such functions. The problem of evaluating these functions in translated coordinate systems, which arises in density functional theory applications, and the associated convergence problems are also discussed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
First‐principles molecular dynamics simulations in a continuum solvent
Authors: Fattebert Jean‐Luc , Gygi François 
Published: March 2003

AbstractA new continuum solvation model for density functional theory first‐principles simulations is presented in the context of plane wave Car–Parrinello molecular dynamics. The Poisson problem—with dielectric function representing the solvent effects—is solved by a compact finite difference method on a regular grid. The smoothness of the solute–solvent transition, and the density‐based solute cavity, provide good numerical properties to the model and allow for total energy calculations, reaction barriers calculations, and energy‐conserving molecular dynamics. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
High‐resolution detection of adulteration of maize oil using multi‐component compound‐specificδ13C values of major and minor components and discriminant analysis
Authors: Mottram Hazel R. , Woodbury Simon E. , Rossell J. Barry , Evershed Richard P. 
Published: March 2003

AbstractMaize oil commands a premium price and is thus a target for adulteration with cheaper vegetable oils. Detection of this activity presents a particular challenge to the analyst because of the natural variability in the fatty acid composition of maize oils and because of their high sterol and tocopherol contents. This paper describes a method that allows detection of adulteration at concentrations of just 5% (m/m), based on the Mahalanobis distances of the principal component scores of theδ13C values of major and minor vegetable oil components. The method makes use of a database consisting ofδ13C values and relative abundances of the major fatty acyl components of over 150 vegetable oils. The sterols and tocopherols of 16 maize oils and 6 potential adulterant oils were found to be depleted in13C by a constant amount relative to the bulk oil. Moreover, since maize oil contains particularly high levels of sterols and tocopherols, theirδ13C values were not significantly altered when groundnut oil was added up to 20% (m/m) and it is possible to use the values for the minor components to predict the values that would be expected in a pure oil; therefore, comparison of the predicted values with those obtained experimentally allows adulteration to be detected. A refinement involved performing a discriminant analysis on theδ13C values of the bulk oil and the major fatty acids (16:0, 18:1 and 18:2) and using the Mahalanobis distances to determine the percentage of adulterant oil present. This approach may be refined further by including theδ13C values of the minor components in the discriminant analysis thereby increasing the sensitivity of the approach to concentrations at which adulteration would not be attractive economically. Copyright © 2003 John Wiley & Sons, Ltd.