bluuebunny/crossref_metadata_2025_split huggingface dataset:
A second binding site revealed by C‐terminal truncation of calpain small subunit, a penta‐EF‐hand protein
Authors: Leinala E.K. , Arthur J.S.C. , Grochulski P. , Davies P.L. , Elce J.S. , Jia Z. 
Published: October 2003

AbstractThe subunits in calpain and in the related penta‐EF‐hand (PEF) proteins are bound through contacts between the unpaired EF‐hand 5 from each subunit. To study subunit binding further, a tetra‐EF‐hand 18 kDa N‐ and C‐terminally truncated form of the calpain small subunit was prepared (18k). This protein does not combine with the calpain large subunit to form active calpain, but forms homodimers in solution, as shown by ultracentrifugation. The X‐ray structure of the 18k protein in the presence of cadmium was solved to a resolution of 2.0 Å. The structure of the monomer is almost identical to the known structure of the calpain small subunit, but the 18k protein forms an oligomer in the crystal by the use of two binding sites. One of these sites is an artefact arising from the C‐terminal truncation, but the other is a naturally occurring site that is fully exposed to water in intact purified calpain. The characteristics of this site suggest that it may be important in binding other protein modulators involved in the regulation of calpain and of PEF proteins. Proteins 2003. © 2003 Wiley‐Liss, Inc.
RDOCK: Refinement of rigid‐body protein docking predictions
Authors: Li Li , Chen Rong , Weng Zhiping 
Published: October 2003

AbstractWe present a simple and effective algorithm RDOCK for refining unbound predictions generated by a rigid‐body docking algorithm ZDOCK, which has been developed earlier by our group. The main component of RDOCK is a three‐stage energy minimization scheme, followed by the evaluation of electrostatic and desolvation energies. Ionic side chains are kept neutral in the first two stages of minimization, and reverted to their full charge states in the last stage of brief minimization. Without side chain conformational search or filtering/clustering of resulting structures, RDOCK represents the simplest approach toward refining unbound docking predictions. Despite its simplicity, RDOCK makes substantial improvement upon the top predictions by ZDOCK with all three scoring functions and the improvement is observed across all three categories of test cases in a large benchmark of 49 non‐redundant unbound test cases. RDOCK makes the most powerful combination with ZDOCK2.1, which uses pairwise shape complementarity as the scoring function. Collectively, they rank a near‐native structure as the number‐one prediction for 18 test cases (37% of the benchmark), and within the top 4 predictions for 24 test cases (49% of the benchmark). To various degrees, funnel‐like energy landscapes are observed for these 24 test cases. To the best of our knowledge, this is the first report of binding funnels starting from global searches for a broad range of test cases. These results are particularly exciting, given that we have not used any biological information that is specific to individual test cases and the whole process is entirely automated. Among three categories of test cases, the best results are seen for enzyme/inhibitor, with a near‐native structure ranked as the number‐one prediction for 48% test cases, and within the top 10 predictions for 78% test cases. RDOCK is freely available to academic users at http://zlab.bu.edu/∼rong/dock. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Dissecting subunit interfaces in homodimeric proteins
Authors: Bahadur Ranjit Prasad , Chakrabarti Pinak , Rodier Francis , Janin Joël 
Published: October 2003

AbstractThe subunit interfaces of 122 homodimers of known three‐dimensional structure are analyzed and dissected into sets of surface patches by clustering atoms at the interface; 70 interfaces are single‐patch, the others have up to six patches, often contributed by different structural domains. The average interface buries 1,940 Å2 of the surface of each monomer, contains one or two patches burying 600–1,600 Å2, is 65% nonpolar and includes 18 hydrogen bonds. However, the range of size and of hydrophobicity is wide among the 122 interfaces. Each interface has a core made of residues with atoms buried in the dimer, surrounded by a rim of residues with atoms that remain accessible to solvent. The core, which constitutes 77% of the interface on average, has an amino acid composition that resembles the protein interior except for the presence of arginine residues, whereas the rim is more like the protein surface. These properties of the interfaces in homodimers, which are permanent assemblies, are compared to those of protein‐protein complexes where the components associate after they have independently folded. On average, subunit interfaces in homodimers are twice larger than in complexes, and much less polar due to the large fraction belonging to the core, although the amino acid compositions of the cores are similar in the two types of interfaces. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Elucidation of the disulfide‐folding pathway of hirudin by a topology‐based approach
Authors: Micheletti C. , De Filippis V. , Maritan A. , Seno F. 
Published: October 2003

AbstractA theoretical model for the folding of proteins containing disulfide bonds is introduced. The model exploits the knowledge of the native state to favor the progressive establishment of native interactions. At variance with traditional approaches based on native topology, not all native bonds are treated in the same way; in particular, a suitable energy term is introduced to account for the special strength of disulfide bonds, as well as their ability to undergo intramolecular reshuffling. The model thus possesses the minimal ingredients necessary to investigate the much debated issue of whether the refolding process occurs through partially structured intermediates with native or non‐native disulfide bonds. This strategy is applied to a context of particular interest, the refolding process of hirudin, a thrombin‐specific protease inhibitor, for which conflicting folding pathways have been proposed. We show that the only two parameters in the model (temperature and disulfide strength) can be tuned to reproduce well a set of experimental transitions between species with different number of formed disulfides. This model is then used to provide a characterization of the folding process and a detailed description of the species involved in the rate‐limiting step of hirudin refolding. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
Many residues in cytochrome c populate alternative states under equilibrium conditions
Authors: Williamson Michael P. 
Published: October 2003

AbstractA curved temperature dependence of an amide proton NMR chemical shift indicates that it explores discrete alternative conformations at least 1% of the time; that is, it accesses conformations that lie within 5 kcal/mol−1 of the ground state. The simulations presented show how curvature varies with the nature of the alternative state, and are compared to experimental results. From studies in different denaturant concentrations, it is concluded that at least 25% of residues in reduced horse cytochrome c, covering most of the protein, with the exception of the center of the N‐ and C‐terminal helices, visit alternative states under equilibrium conditions. The conformational ensemble of the protein therefore has high structural entropy. The density of alternative states is particularly high near the heme ligand Met80, which is of interest because both redox change and the first identified stage in unfolding are associated with change in Met80 ligation. By combining theoretical and experimental approaches, it is concluded that the alternative states each comprise approximately five residues, have in general less structure than the native state, and are accessed independently. They are therefore locally unfolded structures. The locations of the alternative states match what is known of the global unfolding pathway of cytochrome c, suggesting that they may determine the pathway. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
The intracellular domain of the Drosophila cholinesterase‐like neural adhesion protein, gliotactin, is natively unfolded
Authors: Zeev‐Ben‐Mordehai Tzviya , Rydberg Edwin H. , Solomon Ariel , Toker Lilly , Auld Vanessa J. , Silman Israel , Botti Simone , Sussman Joel L. 
Published: October 2003

AbstractDrosophila gliotactin (Gli) is a 109‐kDa transmembrane, cholinesterase‐like adhesion molecule (CLAM), expressed in peripheral glia, that is crucial for formation of the blood‐nerve barrier. The intracellular portion (Gli‐cyt) was cloned and expressed in the cytosolic fraction of Escherichia coli BLR(DE3) at 45 mg/L and purified by Ni‐NTA (nitrilotriacetic acid) chromatography. Although migration on sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE), under denaturing conditions, was unusually slow, molecular weight determination by matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry (MS) confirmed that the product was consistent with its theoretical size. Gel filtration chromatography yielded an anomalously large Stokes radius, suggesting a fully unfolded conformation. Circular dichroism (CD) spectroscopy demonstrated that Gli‐cyt was >50% unfolded, further suggesting a nonglobular conformation. Finally, 1D‐1H NMR conclusively demonstrated that Gli‐cyt possesses an extended unfolded structure. In addition, Gli‐cyt was shown to possess charge and hydrophobic properties characteristic of natively unfolded proteins (i.e., proteins that, when purified, are intrinsically disordered under physiologic conditions in vitro). Proteins 2003. © 2003 Wiley‐Liss, Inc.
Accessibility of oxygen with respect to the heme pocket in horseradish peroxidase
Authors: Khajehpour Mazdak , Rietveld Ivo , Vinogradov Sergei , Prabhu Ninad V. , Sharp Kim A. , Vanderkooi Jane M. 
Published: October 2003

AbstractOxygen and other molecules of similar size take part in a variety of protein reactions. Therefore, it is critical to understand how these small molecules penetrate the protein matrix. The protein system studied in this case is horseradish peroxidase (HRP). We have converted the native HRP into a phosphorescent analog by replacing the heme prosthetic group by Pd‐mesoporphyrin. Oxygen readily quenches the phosphorescence of Pd porphyrins, and this can be used to characterize oxygen diffusion through the protein matrix. Our measurements indicate that solvent viscosity and pH modulate the accessibility of the heme pocket relative to small molecules. The binding of the substrate benzohydroxamic acid (BHA) to the protein drastically impedes oxygen access to the heme pocket. These results indicate that, first, the penetration of small molecules through the protein matrix is a function of protein dynamics, and second, there are specific pathways for the diffusion of these molecules. The effect of substrate and pH on protein dynamics has been investigated with the use of molecular dynamics calculations. We demonstrate that the model of a “fluctuating entry point,” as suggested by Zwanzig (J Chem Phys 1992;97:3587–3589), properly describes the diffusion of oxygen through the protein matrix. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
Crystal‐state 3D‐structural characterization of novel 310‐helical peptides
Authors: Crisma Marco , Moretto Alessandro , Rainaldi Mario , Formaggio Fernando , Broxterman Quirinus B. , Kaptein Bernard , Toniolo Claudio 
Published: October 2003

AbstractThe crystal‐state conformations of two octapeptides, pBrBz‐(D‐Iva)8‐OtBu (8I) and Ac‐[L‐(αMe)Val]8‐OH (8II), the heptapeptide Z‐[L‐(αMe)Val]7‐OH (7), the hexapeptide Z‐[L‐(αMe)Leu]6‐OtBu (6) and the tetrapeptide alkylamide Z‐(Aib)2‐L‐Glu(OMe)‐L‐Ala‐L‐Lol (5) were assessed by x‐ray diffraction analyses. Two independent molecules are observed in the asymmetric unit of each L‐(αMe)Val homo‐peptide. All four homo‐peptides are folded in a regular 310‐helical structure (only the C‐terminal H‐bonded conformation of the D‐Iva octapeptide is distorted to a type‐I β‐turn). The hydroxyl groups of the C‐terminal carboxyl moieties of the two L‐(αMe)Val homo‐peptides participate in an oxy‐analogue of the type‐III β‐turn conformation. While the two L‐(αMe)Val 310‐helices are right‐handed, the D‐Iva and L‐(αMe)Leu helices are left‐handed. The tetrapeptide alkylamide is 310‐helical at the N‐terminus, but it is mixed 310/α‐helical at the C‐terminus. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Synthesis, conformation and biological activity of dermorphin and deltorphin I analogues containing N‐alkylglycine in place of residues in position 1, 3, 5 and 6
Authors: Biondi Laura , Giannini Elisa , Filira Fernando , Gobbo Marina , Marastoni Mauro , Negri Lucia , Scolaro Barbara , Tomatis Roberto , Rocchi Raniero 
Published: October 2003

AbstractSyntheses are described of new dermorphin and [D‐Ala2]deltorphin I analogues in which the phenylalanine, the tyrosine or the valine residues have been substituted by the corresponding N‐alkyl‐glycine residues. Structural investigations by CD measurements in different solvents and preliminary pharmacological experiments were carried out on the resulting peptide–peptoid hybrids. The contribution from aromatic side chain residues is prominent in the CD spectra of dermorphin analogues and the assignment of a prevailing secondary structure could be questionable. In the CD spectra of deltorphin analogues the aromatic contribution is lower and the dichroic curves indicate the predominance of random conformer populations. The disappearance of the aromatic contribution in the [Ntyr1,D‐Ala2]‐deltorphin spectrum could be explained in terms of high conformational freedom of the N‐terminal residue. The kinetics of degradation of the synthetic peptoids digestion by rat and human plasma enzymes were compared with that of [Leu5]‐enkephalin. The binding to opioid receptors was tested on crude membrane preparations from CHO cells stably transfected with the µ‐ and δ‐opioid receptors. The biological potency of peptoids was compared with that of dermorphin in GPI preparations and with that of deltorphin I in MVD preparations. All the substitutions produced a dramatic decrease in the affinity of the peptide–peptoid hybrids for both the µ‐ and δ‐opioid receptors. Nval5 and/or Nval6 containing hybrids behaved as µ‐opioid receptor agonists and elicit a dose‐dependent analgesia (tail‐flick test) when injected i.c.v. in rats. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Potent side‐chain to side‐chain cyclized dermorphin analogues containing a carbonyl bridge
Authors: Filip Katarzyna , Oleszczuk Marta , Pawlak Danuta , Wójcik Jacek , Chung Nga N. , Schiller Peter W. , Izdebski Jan 
Published: October 2003

AbstractA new family of cyclic opioid peptide analogues related to the 1–4 sequence of dermorphin/deltorphin (Tyr‐D‐Aaa2‐Phe‐Aaa4‐NH2) has been synthesized. The synthesis of the linear precursor peptides was accomplished by the solid‐phase method and ring formation was achieved via a ureido group incorporating the side chain amino functions of D‐Aaa2 (D‐Lys, D‐Orn) and Aaa4 (Lys, Orn, Dab, Dap). The peptides were tested in the guinea‐pig ileum (GPI) and mouse vas deferens (MVD) assays. Most showed very high agonist potency in the GPI assay. The peptide containing D‐Lys in position 2 and Dab in position 4 was 210 times more active than enkephalin, and that containing Orn and Dab, respectively, was 150 times more active than enkephalin. The latter peptide was also very active in the MVD assay, and showed an IC50 MVD/GPI ratio of 0.816. NMR spectra of selected peptides were recorded, and structural parameters were determined. The conformational space of the peptides was examined using the electrostatically driven Monte Carlo method. With the help of the NMR spectra each peptide was described as an ensemble of conformations. The conformations have been interpreted with regard to the opioid activities, and comparisons have been made with a model proposed earlier for enkephalin analogues. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
High‐pressure and high‐temperature study of phase transitions in solid germanium
Authors: Di Cicco Andrea , Frasini Anna Chiara , Minicucci Marco , Principi Emiliano , Itiè Jean‐Paul , Munsch Pascal 
Published: October 2003

AbstractA detailed investigation of the pressure and temperature dependence of the structure of stable and metastable solid Ge phases in the 0–15 GPa and 295–500 K ranges is presented. Structural results including the equation of state, characteristic of coexistence regions of diamond and β‐tin structures, and appearance of metastable phases are discussed and compared with the results presently available in the literature. The isothermal bulk modulus and its derivative are evaluated using temperature‐dependent equations of state for Ge I (cubic) and Ge II (β‐Sn), and for the Ge III (ST12) metastable polymorph at 400 K. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structure and properties of As25Te35Si40 glass
Authors: Lörinczi A. , Sava F. , Iovu M. , Leonovici M. , Halm Th. , Popescu M. , Hoyer W. 
Published: October 2003

AbstractThe glassy composition As25Te35Si40 was investigated by differential scanning calorimetry (DSC), X‐ray diffraction (XRD), Raman spectroscopy, and infrared absorption (IR) measurements. X‐ray diffraction patterns at room temperature and at temperatures around Tg were recorded and the radial distribution functions have been calculated. A continuous random network model for the ideal homogeneous glass structure has been proposed.
An extended KPS method for calculating multipole polarizabilities – application to crystalline ions
Authors: Yousif Al‐Mulla S. Y. 
Published: October 2003

AbstractThe improvement proposed by Shukla and Easa to the variational calculation of the multipole polarizabilities of atoms and ions has been applied to the Kirkwood–Pople–Schofield approach, to derive a general form of this variational techniqes. This form has been applied to calculate the polarizabilities of free atoms and ions and for atoms and ions in crystalline environments. The accuracy of the results in the KPS method depends on the quality of the initial wavefunction of a given system.
Electrical resistivity of RNi4B compounds (R = Y or rare earth)
Authors: Toliński T. , Kowalczyk A. , Ivanov V. 
Published: October 2003

AbstractElectrical resistivity studies of RNi4B compounds (R = Y, Ce, Pr, Nd, Sm, Dy, Ho, Er) are presented. The ordering temperatures are well established in the case of the ferromagnetic compounds. YNi4B shows a presence of an impurity carbon‐rich phase with a transition to the superconducting state at temperature of 12 K. This compound was treated as the isostructural non‐magnetic reference compound for the RNi4B series. CeNi4B reveals a shallow Kondo‐like minimum at low temperatures. Spin‐disorder contributions are derived for the compounds and the resistivity in the ferromagnetic region is analysed including the influence of anisotropy effects. In the case of SmNi4B the effect of the crystal field was taken into consideration.
Acoustic studies of the ferroelastic phase transition in the K3Na(CrO4)2 crystal
Authors: Charnaya E. V. , Mroz B. , Radzhabov A. K. , Tien C. , Tylczynski Z. , Wur C. S. 
Published: October 2003

AbstractUltrasonic studies of the K3Na(CrO4)2 crystal were carried out within a temperature range of 185 to 295 K. Temperature dependences of the velocity and attenuation coefficient for the xx and zz longitudinal acoustic waves and the yx and zx transverse waves were measured. Noticeable anomalies in velocity and attenuation for transverse as well as for longitudinal waves were found near the ferroelastic phase transition which temperature was 235.5 K. The anomalies in the c44 and c66 elastic moduli were treated on the base of the Landau theory assuming the component ε4 as the primary order parameter and (ε2–ε1)/2 as the secondary one. Six elastic moduli, c11, c33, c44, c66, c12, and c14 were evaluated at room temperature.
Effect of charge carrier–phonon coupling on the energy of shallow donors in CdSe quantum dots
Authors: Feddi E. , El Haouari M. , Assaid E. , Stébé B. , El Khamkhami J. , Dujardin F. 
Published: October 2003

AbstractThe effects of low electric field and finite‐barrier height on the ground state energy of a donor impurity confined in a polar CdSe spherical quantum dot embedded in a non‐polar matrix were studied. Calculations were carried out in the framework of the effective mass approximation using the Hassé variational approach. The effect of the quantum confinement was described by a finite deep potential taking into account the interactions between the charge carriers (electron and ion) and the confined longitudinal optical phonons (LO‐phonons). It was found that the binding energy and the polarizability depend strongly on LO‐phonon effects. So, the phonon corrections should not be ignored or neglected whatever the dot size and the degree of confinement. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Topological excitations near a spinless atom in layered antiferromagnets with an axial magnetic field
Authors: Fonseca M. P. P. , Pereira A. R. 
Published: October 2003

AbstractWe have investigated the effect of a nonmagnetic impurity on the configuration and energy of topological excitations in the isotropic two‐dimensional Heisenberg antiferromagnet in the presence of an external uniform magnetic field applied perpendicular to the XY plane. This model is expected to have the XY‐like low‐temperature phase and show the Kosterlitz–Thouless transition due to a XY‐like degeneracy of a canted spin‐flop ground state. The spins in the spin‐flop state may simultaneously tip into the out‐of‐plane directions while forming a vortex. Thus, we consider as the excitation for our study, the out‐of‐plane vortex. Our calculations show that an effective interaction between the two defects, the out‐of‐plane vortex and the nonmagnetic impurity, can be attractive at short range. These results can also be applied to two‐dimensional easy‐plane ferromagnets with weak anisotropy. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A method for phase diagrams of spin‐1 Ising ferromagnetic systems
Authors: Polat H. , Akįncį Ü. , Sökmen İ. 
Published: October 2003

AbstractA method in Ising models is introduced by using the effective field theory (EFT) with correlations. In the present method, for the spin‐1 Ising ferromagnetic systems with three coordination numbers q (q = 3, 4 and 6), we have derived a set of linear equations by taking as a basis the thermal averages of a central spin and a perimeter spin at the site i, which is defined within spin identities and differential operator technique. By solving numerically the set of linear equations derived individually for the Ising systems, we have evaluated the phase diagrams of both the spin‐1 Ising ferromagnetic systems with a single‐ion anisotropy and the spin‐1 transverse Ising ferromagnetic systems with a transverse field. The present results of critical transverse field for the spin‐1 transverse Ising systems improve those obtained by the pair approximation. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interpretation of the optical spectra and EPR parameters for Yb3+ in LiYF4 crystal
Authors: Dong H. N. , Zheng W. C. , Wu S. Y. 
Published: October 2003

AbstractIn this paper, the crystal‐field energy levels, the EPR g‐factors g∥, g⟂ of Yb3+ and hyperfine structure constants A∥, A⟂ of 171Yb3+ and 173Yb3+ isotopes in LiYF4 crystal are calculated from the crystal‐field theory. All the calculated results (seven energy levels and six EPR parameters) are in reasonable agreement with the observed values. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)