bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial optimization of electrostatic interactions between the ionized groups in globular proteins
Authors: Spassov Velin Z. , Atanasov Boris P. 
Published: May 2005

AbstractA model approach is suggested to estimate the degree of spatial optimization of the electrostatic interactions in protein molecules. The method is tested on a set of 44 globular proteins, representative of the available crystallographic data. The theoretical model is based on macroscopic computation of the contribution of charge–charge interactions to the electrostatic term of the free energy for the native proteins and for a big number of virtual structures with randomly distributed on protein surface charge consetellations (generated by a Monte‐Carlo technique). The statistical probability of occurrence of random structures with electrostatic energies lower than the energy of the native protein is suggested as a criterion for spatial optimization of the electrostatic interactions. The results support the hypothesis that the folding process optimizes the stabilizing effect of electrostatic interactions, but to very different degree for different proteins. A parallel analysis of ion pairs shows that the optimization of the electrostatic term in globular proteins has increasingly gone in the direction of rejecting the repulsive short contacts between charges of equal sign than of creating of more salt bridges (in comparison with the statistically expected number of shortrange ion pairs in the simulated random structures). It is observed that the decrease in the spatial optimization of the electrostatic interactions is usually compensated for by an appearance of disulfide bridges in the covalent structure of the examined proteins. © 1994 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray diffraction study of the green flavoenzyme 5‐Hydroxyvaleryl‐CoA dehydratase/dehydrogenase from Clostridium aminovalericum
Authors: Eikmanns Ulrich , Buta Christiane , Buckel Wolfgang , Pai Emil F. 
Published: May 2005

AbstractThe bifunctional flavoenzyme 5‐hydroxyvaleryl‐CoA dehydratase/ dehydrogenase has been crystallized from solutions containing ammonium sulfate (form I) or polyethylene glycol (form II) as precipitant. In both cases, the crystals grew in the monoclinic space group C2. The unit cell dimensions for form I crystals were determined as a = 162.8 Å, b = 71.8 Å, c = 83.5 Å, β = 109.1°. Corresponding values for form II crystals were a = 161.2 Å, b = 71.6 Å, c = 82.2 Å, β = 109.3°. In both cases most probably there are two monomers per asymmetric unit. The crystals diffract to about 2 Å resolution and are rather stable in the X‐ray beam. © 1994 Wiley‐Liss, Inc.
Multiple copy sampling: Rigid versus flexible protein
Authors: Zheng Qiang , Kyle Donald J. 
Published: May 2005

AbstractEffects of protein flexibility on multiple copy conformational sampling were systematically evaluated by studying the side‐chain placement of Phe‐14 in protein Zif268. The multiple copy sampling is shown to be significantly more efficient when a flexible but harmonically constrained protein is used instead of a rigid protein. A range of constraint force from 1 to 25 kcal/mol. Å per atom is determined to be sufficient to prevent the protein from distortion while allowing the protein to fluctuate for enhanced sampling. The protein fluctuations are essential in smoothing the effective energy surface as shown by the opening‐closing of a protein hydrophobic pocket during a multiple copy energy minimization, a phenomenon that has been previously observed only in molecular dynamics. These results provide a practical guidance for applying the multiple copy techniques to molecular modeling and computer‐aided drug design. © 1994 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray diffraction studies of mandelonitrile lyase from almonds
Authors: Lauble Hanspeter , Müller Kirsten , Schindelin Hermann , Förster Siegfried , Effenberger Franz 
Published: May 2005

AbstractSingle crystals of three different isoenzymes of (R)−(+) mandelonitrile lyase (hydroxynitrile lyase) from almonds (Prunus amygdalus) have been obtained by hanging drop vapor diffusion using polyethylene glycol 4000 and isopropanol as co‐precipitants. The crystals belong to the monoclinic space group P2l with unit cell parameters a = 69.9, b = 95.1, c = 95.6 Å, and β = 118.5°. A complete set of diffraction data has been collected to 2.6 Å resolution on native crystals of isoenzyme III. © 1994 Wiley‐Liss, Inc.
Pyrrolidone carboxyl peptidase (Pcp): An enzyme that removes pyroglutamic acid (pGlu) from pGlu‐peptides and pGlu‐proteins
Authors: Awadé A. C. , Cleuziat Ph. , GonzalèS Th. , Robert‐Baudouy J. 
Published: May 2005

AbstractPyrrolidone carboxyl peptidase (EC 3.4.11.8) is an exopeptidase commonly called PYRase, which hydrolytically removes the pGlu from pGlu‐peptides or pGlu‐proteins.pGlu also known as pyrrolidone carboxylic acid may occur naturally by an enzymatic procedure or may occur as an artifact in proteins or peptides. The enzymatic synthesis of pGlu suggests that this residue may have important biological and physiological functions. Several studies are consistent with this supposition.PYRase has been found in a variety of bacteria, and in plant, animal, and human tissues For over two decades, biochemical and enzymatic properties of PYRase have been investigated. At least two classes of PYRase have been characterized. The first one includes the bacterial and animal type I PYRases and the second one the animal type II and serum PYRases. Enzymes from these two classes present differences in their molecular weight and in their enzymatic properties.Recently, the genes of PYRases from four bacteria, have been cloned and characterized, allowing the study of the primary structure of these enzymes, and their over‐expression in heterelogous organisms. Comparison of the primary structure of these enzymes revealed striking homologies.Type I PYRases and bacterial PYRases are generally soluble enzymes, whereas type II PYRases are membrane‐bound enzymes. PYRase II appears to play as important a physiological role as other neuropeptide degrading enzymes. However, the role of type I and bacterial PYRases remains unclear.The primary application of PYRase has been its utilization for some protein or peptide sequencing. Development of chromogenic substrates for this enzyme has allowed its use in bacterial diagnosis. © 1994 Wiley‐Liss, Inc.
Solvent‐induced organization: A physical model of folding myoglobin
Authors: Callaway David J. E. 
Published: May 2005

AbstractThe essential features of the in vitro refolding of myoglobin are expressed in a solvable physical model. Alpha helices are taken as the fundamental collective coordinates of the system, while the refolding is assumed to be mainly driven by solvent‐induced hydrophobic forces. A quantitative model of these forces is developed and compared with experimental and theoretical results. The model is then tested by being employed in a simulation scheme designed to mimic solvent effects. Realistic dynamic trajectories of myoglobin are shown as it folds from an extended conformation to a close approximation of the native state. Various suggestive features of the process are discussed. The tenets of the model are further tested by folding the single‐chain plant protein leghemoglobin. © 1994 Wiley‐Liss, Inc.
Preliminary crystallographic analysis of an enzyme involved in erythromycin biosynthesis: Cytochrome P450eryF
Authors: Cupp‐Vickery Jill R. , Li Huiying , Poulos Thomas L. 
Published: May 2005

AbstractCytochrome P450eryF was overexpressed in Escherichia coli and purified in high yield. Crystals of the protein in the presence of the substrate, 6‐deoxyerythronolide B, have been obtained by the hanging drop vapor diffusion method, using polyethylene glycol 4000 as a precipitant. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions of a = 54.16 Å, b = 79.67 Å, and c = 99.48 Å and one molecule per asymmetric unit. A complete native data set has been collected to a resolution of 2.1 Å, and anomalous dispersion difference Patterson maps have revealed the location of the single heme iron atom. © 1994 Wiley‐Liss, Inc.
Molecular dynamics simulations of trp apo‐and holorepressors: Domain structure and ligand–protein interaction
Authors: Komeiji Yuto , Uebayasi Masami , Yamato Ichiro 
Published: May 2005

AbstractMolecular dynamics simulations of the apo‐ and holo‐forms of thetrp‐repressor protein were performed under extensively solvated conditions in order to elucidate their dynamic structures and ligand–protein interactions. The root mean square fluctuations calculated from the trajectories agreed with those calculated from X‐ray temperature factors. Distance, distance fluctuation, and dynamic cross‐correlation maps were drawn to provide information on the dynamic structures and communications among the domains. A three‐domain format has been proposed for the crystal structure (Zhang et at., Nature 327:591–597, 1987) namely, helices A–C and F of both subunits make up a central core, and D and E of each subunit forms a DNA binding head. The results of the simulations were mostly consistent with the three‐domain format. However, helix F was more flexible and freer than other parts of the central core. The turn DE, the helix‐turn‐helix DNA binding motif, was free from interactions and correlations with other domains in both forms of the repressor. A comparison of the simulations of the aporepressor and holorepressor showed that tryptophan binding made the DNA‐binding helix D more flexible but helix F less flexible. Several amino acid residues in contact with the bound tryptophan were identified as making concerted motions with it. Interaction energies between the corepressor and the amino acid residues of the protein were analyzed; the results were mostly consistent with the mutational experiments. © 1994 Wiley‐Liss, Inc.
A surface mutant (G82R) of a human α‐glutathione S‐transferase shows decreased thermal stability and a new mode of molecular association in the crystal
Authors: Zeng Ke , Rose John P. , Chen Hong‐Chi , Strickland Corey L. , Tu Chen‐Pei D. , Wang Bi‐Cheng 
Published: May 2005

AbstractA chimeric enzyme (GST121) of the human α‐glutathione S‐transferases GST1‐1 and GST2‐2, which has improved catalytic efficiency and thermostability from its wild‐type parent proteins, has been crystallized in a space group that is isomorphous with that reported for crystals of GST1‐1. However, a single‐site (G82R) mutant of GST121, which exhibits a significant reduction both in vitro and in vivo in protein thermostability, forms crystals that are not isomorphous with GST1‐1. The mutant protein crystallizes in space group P212121, with cell dimensions a = 49.5, b = 92.9, c = 115.9 Å, and one dimer per asymmetric unit. Preliminary crystallographic results show that a mutation of the surface residue Gly 82 from a neutral to a charged residue causes new salt bridges to be formed among the GST dimers, suggesting that the G82R mutant might aggregate more readily than does GST121 in solution resulting in a change of its solution properties. © 1994 Wiley‐Liss, Inc.
Crystallization and preliminary crystallographic study of human CksHs1: A cell cycle regulatory protein
Authors: Arvai Andrew S. , Bourne Yves , Williams DeWight , Reed Steve I. , Tainer John A. 
Published: May 2005

AbstractThe cell cycle regulatory protein CksHs1 has been crystallized in a form suitable for X‐ray studies. CksHsl crystals were grown in the presence of vanadate, a phos‐phatase inhibitor, but were also obtained with phosphate or tungstate as a cofactor. They belong to the hexagonal space group P6122 with unit cell dimensions: a=b=94 Å, c=131.6 Å, and γ =120. The crystals grown in the presence of vanadate diffract X‐rays to at least 2.8 Å. Molecular replacement results from the homologous human CksHs2 structure reveal that a dimer forms the crystal habit, giving the unusual Vm value of 4.4 Å3/Da or a solvent content of 72%. © 1995 Wiley‐Liss, Inc.
Crystals of an antibody FV fragment against an integral membrane protein diffracting to 1.28 Å resolution
Authors: Ostermeier Christian , Essen Lars‐Oliver , Michel Hartmut 
Published: May 2005

AbstractThe Fv fragment of a monoclonal antibody, 7E2 (IgG1, κ, murine), which is directed against the integral membrane protein cytochrome c oxidase (EC 1.9.3.1) from Paracoccus denitrificans, was cloned and produced in Escherichia coli. Crystals suitable for highresolution X‐ray analysis were obtained by microdialysis under low salt conditions. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions of a = 51.51 Å, b = 56.15 Å, c = 99.86 Å (1 Å = 0.1 nm) and contain one F v fragment per asymmetric unit. Using synchrotron radiation diffraction data were collected up to 1.28 Å resolution. This high resolution is very unusual for a heterodimeric protein. The crystals should open the way for refining not only the atomic positions, but also for obtaining information about internal dynamics. © 1995 Wiley‐Liss, Inc.
Packing constraints of hydrophobic side chains in (α/β)8 barrels
Authors: Vtyurin Nickolie , Panov Victor 
Published: May 2005

AbstractAn analysis of possible tight packing of hydrophobic groups simultaneously at the both surfaces of β‐hyperboloid‐8 was conducted. This analysis shows that the disposition of amino acid side chains at the real β‐structure's surface is unique. If we sign the mean distance between adjacent β‐strands as “a,” and the mean distance along β‐strand between Cα atoms, whose side chains are directed to one side of the β‐sheet, as “b,” the ratio b/a = √2 very precisely. This ratio ensures the most efficient packing of side hydrophobic groups at the outer surface of β‐hyperboloid‐8, forming, at the same time, the second by efficiency packing at its inner surface. © 1995 Wiley‐Liss, Inc.
Preliminary X‐ray diffraction analysis of crystals of tomato aspermy virus (TAV)
Authors: Canady Mary A. , Leja Catherine A. , Day John , McPherson Alexander 
Published: May 2005

AbstractTomato aspermy virus (TAV) is a member of the T = 3 cucumovirus group, and the chrysanthemum strain (C‐TAV) has been crystallized in a form suitable for X‐ray structural analysis. The crystals, which grow in 14–17% ethanol at pH 8.5, are of orthorhombic space group I222 with unit cell dimensions of a = 295.1 Å, b = 320.5 Å, and c = 383.6 Å. There are two T = 3 virus particles in the unit cell, which means that they must be centered at 0,0,0 and 1/2, 1/2, 1/2 with icosahedral 222 symmetry elements coincident with crystallographic symmetry operators. The asymmetric unit of the crystals, therefore, contains one quarter of a virus particle, or 45 capsid subunits. Native diffraction data to 4 Å resolution have been collected using synchrotron radiation, though data appear to be present beyond that resolution. © 1995 Wiley‐Liss, Inc.
An analysis of side chain interactions and pair correlations within antiparallel β‐sheets: The differences between backbone hydrogen‐bonded and non‐hydrogen‐bonded residue pairs
Authors: Wouters Merridee A. , Curmi Paul M. G. 
Published: May 2005

AbstractCross‐strand pair correlations are calculated for residue pairs in antiparallel β‐sheet for two cases: pairs whose backbone atoms are hydrogen bonded together (H‐bonded site) and pairs which are not (non‐H‐bonded site). The statistics show that this distinction is important. When glycine is located on the edge of a sheet, it shows a 3:1 preference for the H‐bonded site. Thestrongest observed correlations are for pairs of disulfide‐bonded cystines, many of which adopt a close‐packed conformation with each cystine in a spiral conformation of opposite chirality to its partner. It is likely that these pairs are a signature for the family of small, cystine‐rich proteins. Most other strong positive and negative correlations involve charged and polar residues. It appears that electrostatic compatibility is the strongest factor affecting pair correlation. Significant correlations are observed for β‐ and γ‐branched residues inthe non‐H‐bonded site. An examination of the structures showsa directionality in side chain packing. There is a correlation between (1) the directionality in the packing interactions of non‐H‐bonded β‐ and γ‐branched residue pairs, (2) the handedness of the observed enantiomers of chiral β‐branched side chains, and (3) the handedness of the twist of β‐sheet. These findings have implications for the formation of β‐sheets during protein folding and the mechanism by which the sheet becomes twisted. © 1995 Wiley‐Liss, Inc.
Structural basis for serpin inhibitor activity
Authors: Wright H. Tonie , Scarsdale J. Neel 
Published: May 2005

AbstractThe mechanism of formation and the structures of serpin–inhibitor complexes are not completely understood, despite detailed knowledge of the structures of a number of cleaved and uncleaved inhibitor, noninhibitor, and latent serpins. It has been proposed from comparison of inhibitor and noninhibitor serpins in the cleaved and uncleaved forms that insertion of strand s4A into preexisting β‐sheet A is a requirement for serpin inhibitor activity. We have investigated the role of this strand in formation of serpin–proteinase complexes and in serpin inhibitor activity through homology modeling of wild type inhibitor, mutant substrate, and latent serpins, and of putative serpin–proteinase complexes. These models explain the high stability of the complexes and provide an understanding of substrate behavior in serpins with point mutations in s4A and of latency in plasmingoen activator inhibitor I. © 1995 Wiley‐Liss, Inc.
A Continuum theory for the prediction of lateral and rotational positioning of α‐helices in membrane proteins: Bacteriorhodopsin
Authors: Suwa Makiko , Hirokawa Takatsugu , Mitaku Shigeki 
Published: May 2005

AbstractWe have developed a new method for the prediction of the lateral and the rotational positioning of transmembrane helices, based upon the present status of knowledge about the dominant interaction of the tertiary structure formation. The basic assumption about the interaction is that the interhelix binding is due to the polar interactions and that very short extramembrane loop segments restrict the relative position of the helices. Another assumption is made for the simplification of the prediction that a helix may be regarded as a continuum rod having polar interaction fields around it. The polar interaction field is calculated by a probe helix method, using a copolymer of serine and alanine as probe helices. The lateral position of helices is determined by the strength of the interhelix binding estimated from the polar interaction field together with the length of linking loop segments. The rotational positioning is determined by the polar interaction field, assuming the optimum lateral configuration. The structural change due to the binding of a prosthetic group is calculated, fixing the rotational freedom of a helix that is connected to the prosthetic group. Applying this method to bacteriorhodopsin, the optimum lateral and rotational positioning of transmembrane helices that are very similar to the experimental configuration was obtained. This method was implemented by a software system, which was developed for this work, and automatic calculation became possible for membrane proteins comprised of several transmembrane helices. © 1995 Wiley‐Liss, Inc.
The heat capacity of proteins
Authors: Gómez Javier , Hilser Vincent J. , Xie Dong , Freire Ernesto 
Published: May 2005

AbstractThe heat capacity plays a major role in the determination of the energetics of protein folding and molecular recognition. As such, a better understanding of this thermodynamic parameter and its structural origin will provide new insights for the development of better molecular design strategies. In this paper we have analyzed the absolute heat capacity of proteins in different conformations. The results of these studies indicate that three major terms account for the absolute heat capacity of a protein: (1) one term that depends only on the primary or covalent structure of a protein and contains contributions from vibrational frequencies arising from the stretching and bending modes of each valence bond and internal rotations; (2) a term that contains the contributions of noncovalent interactions arising from secondary and tertiary structure; and (3) a term that contains the contributions of hydration. For a typical globular protein in solution the bulk of the heat capacity at 25°C is given by the covalent structure term (close to 85% of the total). The hydration term contributes about 15 and 40% to the total heat capacity of the native and unfolded states, respectively. The contribution of non‐covalent structure to the total heat capacity of the native state is positive but very small and does not amount to more than 3% at 25°C. The change in heat capacity upon unfolding is primarily given by the increase in the hydration term (about 95%) and to a much lesser extent by the loss of noncovalent interactions (up to ∼5%). It is demonstrated that a single universal mathematical function can be used to represent the partial molar heat capacity of the native and unfolded states of proteins in solution. This function can be experimentally written in terms of the molecular weight, the polar and apolar solvent accessible surface areas, and the total area buried from the solvent. This unique function accurately predicts the different magnitude and temperature dependences of the heat capacity of both the native and unfolded states, and therefore of the heat capacity changes associated with folding/unfolding transitions. © 1995 Wiley‐Liss, Inc.
Effects of cavity‐creating mutations on conformational stability and structure of the dimeric 4‐α‐helical protein ROP: Thermal unfolding studies
Authors: Steif Christian , Hinz Hans‐Jürgen , Cesareni Giovanni 
Published: May 2005

AbstractThe structural and energetic perturbations caused by cavity‐creating mutations (Leu‐41 → Val and Leu‐41 → Ala) in the dimeric 4‐α‐helical‐bundle protein ROP have been characterized by CD spectroscopy and differential scanning calorimetry (DSC). Deconvolution of the CD spectra showed a decrease in α ‐helicity as a result of the amino acid exchanges that follows qualitatively the overall decrease in conformational stability. Transition enthalpies are sensitive probes of the energetic change associated with point mutations. ΔH0 values at the respective transition temperatures, T1/2 (71.0, 65.3, and 52.9°C at 0.5 mg/ml) decrease from 580 ± 20 to 461 ± 20 kJ/(mol of dimmer) and 335 ± 20 kJ/(mol of dimmer) for wildtype ROP (Steif, C., Weber, P., Hinz, H.‐J., Flossdorf, J., Cesareni, G., Kokkinidis, M. Biochemistry 32:3867‐3876, 1993), L41V, and L41A, respectively. The conformational stabilities at 25°C expressed by the standard Gibbs energies of denaturation, ΔG, are 71.7, 61.1, and 46.1 kJ/(mol of dimmer). The corresponding transition enthalpies have been obtained from extrapolation using the c(T)and c(T) functions. Their values at 25°C are 176.3, 101.9, and 141.7 kJ/(mol of dimmer) for wild‐type ROP, L41V, and L41A, respectively. When the stability perturbation resulting from the cavity creating mutations is referred to the exchange of 1 mol of CH2 group, the average ΔΔG value is −5.0 ± 1 kJ/(mol of CH2 group). This decrease in conformation stability suggests that dimeric ROP exhibits the same susceptibility to Leu → Yal and Leu → Ala exchanges as small monomeric proteins. Careful determinations of the partial specific heat capacities of wild‐type and mutated protein solutions suggest that the mutational effects are predominantly manifested in the native rather than the unfolded state. © 1995 Wiley‐Liss, Inc.