bluuebunny/crossref_metadata_2025_split huggingface dataset:
A molecular dynamics study of solvent behavior around a protein
Authors: Komeiji Yuto , Uebayasi Masami , Someya Jun‐ichiro , Yamato Ichiro 
Published: May 2005

AbstractThe solvent structure and behavior around a protein were examined by analyzing a trajectory of molecular dynamics simulation of thetrp‐holorepressor in a periodic box of water. The calculated selfdiffusion coefficient indicated that the solvent within 10 Å of the protein had lower mobility. Examination of the solvent diffusion around different atoms of different kinds of residues showed no general tendency. Thisfact suggested that the solvent mobility is not influenced significantly bythe kind of the atom or residue they solvated. Distribution analysis aroundthe protein revealed two peaks of water oxygen: a sharp one at 2.8 Å around polar and charged atoms and a broad one at ∼3.4 Å aroundapolar atoms. The former was stabilized by water–protein hydrogen bonds, and the latter was stabilized by water‐lwater hydrogen bonds, suggesting the existence of a hydrophobic shell. An analysis of protein atom–water radial distribution functions confirmed these shell structures around polar or charged atoms and apolar ones. © 1993 Wiley‐Liss, Inc.
A comparison of the immunogenicity of a pair of enantiomeric proteins
Authors: Dintzis Howard M. , Symer David E. , Dintzis Renee Z. , Zawadzke Laura E. , Berg Jeremy M. 
Published: May 2005

AbstractThe immunogenicity of a folded, all D‐amino acid protein‐ rubredoxin, has been compared with that for the corresponding L‐protein enantiomer. Following multiple administrations with alum adjuvant, the L‐protein induced a strong, specific lgG antibody response, whereas the D‐protein did not. This relative lack of responsiveness to the D‐protein cannot be attributed to rapid excretion, since it is retained at least 4 times longer than the natural L‐protein. These observations provide the first direct evidence that a folded D‐amino acid protein has low immunogenicity and is long lived in vivo. Proteins with such properties may be useful as molecular platforms in a variety of chemical and pharmaco‐logical applications. © 1993 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray crystallographic analysis of chitinase from barley seeds
Authors: Song Hyun Kyu , Hwang Kwang Yeon , Kim Kyeong Kyu , Suh Se Won 
Published: May 2005

AbstractChitinase from barley seeds has been crystallized at room temperature using polyethylene glycol as precipitant. The crystal is monoclinic, belonging to the space group P21, with unit cell parameters of a = 69.43 Å, b = 44.55 Å, c = 81.41 Å, and β = 111.95 Å. The asymmetric unit seems to contain two molecules of chitinase with a corresponding crystal volume per protein mass (VM) of 2.25 Å3/Da and a solvent content of 45% by volume. The crystal diffracts to at least 2.0 Å with X‐rays from a rotating anode source and is very stable in the X‐ray beam. X‐ray data have been collected to better than 2.2 Å Bragg spacing from a native crystal. © 1993 Wiley‐Liss, Inc.
Organization of turnip yellow mosaic virus investigated by neutron small angle scattering at 80 K: An intermediate state preceding decapsidation of the virion?
Authors: Witz Jean , Timmins Peter A. , Adrian Marc 
Published: May 2005

AbstractThe organization of turnip yellow mosaic virus has been investigated by neutron small angle scattering at 300 K and 80 K in buffers containing various amounts of D2O. We confirm that in native virions, no substantial part of the RNA is located at a radius larger than ca. 100‐110 Å, i.e., that there is very little interpretation of the RNA into the capsid. At 80 K, scattering curves do not depend much upon contrast, from 40% D2O to 100% D2O buffers, but are strongly affected by interparticle interference. We could, however, show that it is not the case for the subsidiary intensity maximum at q ∼ 0.06 Å−1. From the position of this maximum, we conclude that upon freezing, the radius of the capsid expands by c.a. 3.5% and the RNA penetrates deeply into the protein shell. Biological implications of this conformational change immediately preceding decapsidation are dicussed. © 1993 Wiley‐Liss, Inc.
Conformational analysis of protein structures derived from NMR data
Authors: MacArthur Malcolm W. , Thornton Janet M. 
Published: May 2005

AbstractA study is presented of the conformational characteristics of NMR‐derived protein structures in the Protein Data Bank compared to X‐ray structures. Both ensemble and energy‐minimized average structures are analyzed. We have addressed the problem using the methods developed for crystal structures by examining the distribution of ϕ, Ψ, and χ angles as indicators of global conformational irregularity. All these features in NMR structures occur to varying degrees in multiple conformational states. Some measures of local geometry are very tightly constrained by the methods used to generate the structure, e.g., proline ϕ angles, α‐helix ϕ, Ψ angles, ω angles, and Cα chirality. The more lightly restrained torsion angles do show increasead clustering as the number of overall experimental observations increases. ϕ, Ψ, and χ1 angle conformational heterogeneity is strongly correlated with accessibility but shows additional differences which reflect the differing number of observations possible in NMR for the various side chains (e.g., many for Trp, few for Ser). In general, we find that the core is defined to a notional resolution of 2.0 to 2.3 Å. Of real interest is the behavior of surface residues and in particular the side chains where multiple rotameric states in different structures can vary from 10% to 88%. Later generation structures show a much tighter definition which correlates with increasing use of J‐coupling information, stereospecific assignments, and heteronumclear techniques. A suite of programs is being developed to address the special needs of NMR‐derived structures which will take into account the existence of increased mobility in solution. © 1993 Wiley‐Liss, Inc.
Recognition of errors in three‐dimensional structures of proteins
Authors: Sippl Manfred J. 
Published: May 2005

AbstractA major problem in the determination of the three‐dimensional structure of proteins concerns the quality of the structural models obtained from the interpretation of experimental data. New developments in X‐ray crystallography and nuclear magnetic resonance spectroscopy have acceleratedd the process of structure determination and the biological community is confronted with a steadily increasing number of experimentally determined protein folds. However, in the recent past several experimentally determined protein structures have been proven to contain major errors, indicating that in some cases the interpretation of experimental data is difficult and may yield incorrect models. Such problems can be avoided when computational methods are employed which complement experimental structure determinations. A prerequisite of such computational tools is that they are independent of the parameters obtained from a particular experiment. In addition such techniques are able to support and accelerate experimental structure determinations. Here we present techniques based on knowledge based mean fields which can be used to judge the quality of protein folds. The methods can be used to identify misfolded structures as well as faulty parts of structural models. The techniques are even applicable in cases where only the Cα trace of a protein conformation is available. The capabilities of the technique are demonstrated using correct and incorrect protein folds. © 1993 Wiley‐Liss, Inc.
A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation: Backbone dynamics of the glucocorticoid receptor DNA‐binding domain
Authors: Eriksson Mats A. L. , Berglund Helena , Härd Torleif , Nilsson Lennart 
Published: May 2005

AbstractThe rapid motions of the backbone of the DNA‐binding domain of the glucocorticoid receptor (GR DBD) have been investigated using proton‐detected heteronuclear NMR experiments on 15N‐labeled protein at pH 6.0 and with a 200 psec molecular dynamics simulation of hydrated GR DBD. The experimental data were interpreted in terms of a generalized order parameter (S2) and an effective correlation time (τe) for the internal motion of each amide bond. A back calculation, using the same model, yielded the {1H}‐15N nuclear Overhauser effects (NOEs) and the 15N spin‐lattice relaxation times (T1) from the simulated data. The rapid motions of the backbone turned out to be rather limited and uniform throughout the protein, with a somewhat reduced mobility in the two major α‐helical regions and a slightly enhanced flexibility for some residues in the first zinc coordinating region. The agreement between the experimental and simulated S2‐values was as good as quantitative for most of the residues, except for some residues that were subject to a more large‐scale, and in the simulation thus poorly sampled, motion. Examples of such motions that were found in the simulation include jumps of the amide bond of Ile‐487 between the charged oxygens of the side chain of Asp‐485 and less distinct large scale motions for some of the residues in the extended regions, that were shown to give rise to noisy and/or fast decaying internal reorientational correlation functions. For these residues large differences in the simulated and experimental τe‐values were found, indicating that motions on different time scales were dominating in the experimental and simulated values. The lower (<0.7) experimental NOEs for these residues could not be reproduced in the simulation and were shown to be a consequence of the lower τe‐values estimated in the simulation. By combining information from the simulation and the experiment a more complete picture of the motions for these residues can be obtained as is illustrated with an estimation of the jump angle and jump frequency for the amide bond of Ile‐487. © 1993 Wiley‐Liss, Inc.
X‐ray structures of fragments from binding and nonbinding versions of a humanized anti‐CD18 antibody: Structural indications of the key role of VH residues 59 to 65
Authors: Eigenbrot Charles , Gonzalez Tania , Mayeda Julia , Carter Paul , Werther Winifred , Hotaling Timothy , Fox Judy , Kessler Jeremy 
Published: May 2005

AbstractX‐ray crystal structures of fragments from two different humanized antiCD18 antibodies are reported. The Fv fragment of the nonbinding version has been refined in space group C2 with a=64.2 Å, b=61.3 Å, c=51.8 Å, and β=99° to an R‐value of 18.0% at 1.9 Å, and the Fab fragment of the tight‐binding version has been refined in space group P3 with a=101. Å and c=45.5 Å to an R‐value of 17.8% at 3.0 Å resolution. The very large difference in their binding affinity (>1000‐fold) is attributed to large and local structural differences in the C‐terminal part of CDR‐H2, and from this we conclude there is direct contact between this region and antigen when they combine. X‐ray structures of antibody–antigen complexes available in the literature have yet to show this part of CDR‐H2 in contact with antigen, despite its hypervariable sequence. Implications of this result for antibody humanization are discussed. © 1994 John Wiley & Sons, Inc.
Homologous modeling of the lysosomal protective protein/carboxypeptidase L: Structural and functional implications of mutations identified in galactosialidosis patients
Authors: Elsliger Marc‐André , Potier Michel 
Published: May 2005

AbstractThe deficiency of the lysosomal protective protein/carboxypeptidase L (CARB L) causes the lysosomal storage disorder, galactosialidosis, characterized by neuraminidase and β‐galactosidase deficiencies in patients' cells. The three enzymes form a complex inside the lysosome, and the neuraminidase and β‐galactosidase deficiencies are secondary to CARB L deficiency. Sequence similarity and common enzymological properties suggest that the protomeric tertiary structure of CARB L is conserved within a family of serine carboxypeptidases which includes the yeast carboxypeptidase Y, killer expression I gene product and several plant carboxypeptidases. We used this homology to build a model of the CARB L structure based on the recently published X‐ray atomic coordinates of the wheat carboxypeptidase II (CPDW‐II) which shares 32% primary structure identity with CARB L. Small insertions and deletions were accommodated into the model structure by energy minimization using the DREIDING II force field. The Cα atomic‐coordinates of the final CARB L model have a RMS shift of 1.01 Å compared to the corresponding conserved residues in the CPDW‐II template structure. The correct orientation of the homologous catalytic triad residues Ser150, His429 and Asp392, the potential energy calculations and the distribution of hydrophobic and hydrophillic residues in the structure all support the validity of the CARB L model. Most missense mutations identified in galactosialidosis patients were located in secondary structural elements except for the Tyr211→Asn mutation which is in a loop. The other mutant residues have their side chains deeply buried in the central β‐sheet of the model structure except for the Phe412→Val mutation which is located in the dimer interface. The predicted effects of specific mutations on CARB L structural stability correlates well with recently published transient expression studies of mutant CARB L (Shimmoto, M. et al., J. Clin. Invest., 91:2393–2399, 1993). © 1994 John Wiley & Sons, Inc.
Molecular surface representations by sparse critical points
Authors: Lin Shuo Liang , Nussinov Ruth , Fischer Daniel , Wolfson Haim J. 
Published: May 2005

AbstractWe have defined a molecular surface representation that describes precisely and concisely the complete molecular surface. The representation consists of a limited number of critical points disposed at key locations over the surface. These points adequately represent the shape and the important characteristics of the surface, despite the fact that they are modest in number. We expect the representation to be useful in areas such as molecular recognition and visualization. In particular, using this representation, we are able to achieve accurate and efficient protein–protein and protein–small molecule docking. © 1994 John Wiley & Sons, Inc.
Crystallization and structural analysis of bullfrog red cell L‐subunit ferritins
Authors: Trikha J. , Waldo G. S. , Lewandowski F. A. , Ha Y. , Theil E. C. , Weber P. C. , Allewell N. M. 
Published: May 2005

AbstractFerritin is a 24 subunit protein that controls biomineralization of iron in animals, bacteria, and plants. Rates of mineralization vary among members of the ferritin family, particularly between L and H type subunits of animal ferritins which are differentially expressed in various cell types. To examine ferritin from a highly differentiated cell type and to clarify the relationship between ferritin structure and function, bullfrog red cell L ferritin has been cloned, overexpressed in E. coli, and crystallized under two conditions. Crystals were obtained at high ionic strength in the presence of MnCl2 at a concentration comparable to that of the protein and in the presence of MgCl2 at a concentration much higher than that of the protein. Under both crystallization conditions, the crystals are tetragonal bipyramids in the space group F432 with unit cell dimensions a=b=c= 182 ± 0.5 Å. Crystals obtained in the presence of manganese and ammonium sulfate diffract to 1.9 Å, while those obtained in the presence of magnesium and sodium tartrate diffract to 1.6 Å. Isomorphous crystals have been obtained under similar conditions for a site‐directed mutant with a reduced mineralization rate in which Glu−57, −58, −59, and −61 are all replaced by Ala. The structure of wild type L‐subunit with magnesium has been solved by molecular replacement using the calcium salt of human liver H subunit (Lawson et al., Nature (London) 349:541–544, 1991) as the model. The crystallographic R factor for the 6–2.2 Å shell is 0.21. The overall fold of human H and bullfrog L ferritins is similar with an rms difference in backbone atomic positions of 0.97 Å. The largest structural differences occur in the D helix and the loop connecting the D and E helices of the four helix bundle. Because red cell L ferritin and liver H ferritin show differences in both rates of mineralization and three‐dimensional structure, more detailed comparisons of these structures are likely to shed new light on the relationship between conformation and function. © 1994 John Wiley & Sons, Inc.
Evaluation of the conformational free energies of loops in proteins
Authors: Smith Kenneth C. , Honig Barry 
Published: May 2005

AbstractIn this paper we discuss the problem of including solvation free energies in evaluating the relative stabilities of loops in proteins. A conformational search based on a gas‐phase potential function is used to generate a large number of trial conformations. As has been found previously, the energy minimization step in this process tends to pack charged and polar side chains against the protein surface, resulting in conformations which are unstable in the aqueous phase. Various solvation models can easily identify such structures. In order to provide a more severe test of solvation models, gas phase conformations were generated in which side chains were kept extended so as to maximize their interaction with the solvent. The free energies of these conformations were compared to that calculated for the crystal structure in three loops of the protein E. coli RNase H, with lengths of 7, 8, and 9 residues. Free energies were evaluated with a finite difference Poisson‐Boltzmann (FDPB) calculation for electrostatics and a surface area‐based term for nonpolar contributions. These were added to a gas‐phase potential function. A free energy function based on atomic solvation parameters was also tested. Both functions were quite successful in selecting, based on a free energy criterion, conformations quite close to the crystal structure for two of the three loops. For one loop, which is involved in crystal contacts, conformations that are quite different from the crystal structure were also selected. A method to avoid precision problems associated with using the FDPB method to evaluate conformational free energies in proteins is described. © 1994 John Wiley & Sons, Inc.
Crystallization and preliminary structural studies of a chorismate mutase catalytic antibody complexed with a transition state analog
Authors: Haynes Matthew R. , Stura Enrico A. , Hilvert Donald , Wilson Ian A. 
Published: May 2005

AbstractThe Fab′ fragment of a catalytic antibody with chorismate mutase activity has been crystallized as a complex with the transition‐state analog hapten. The complex was crystallized by the vapor diffusion method using ammonium sulfate as the precipitant. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions a = 37.1 Å, b = 63.3 Å, c = 178.5 Å, and there is one Fab' molecule per asymmetric unit. The crystals diffract X‐rays to at least 3.0 Å and are suitable for X‐ray crystallographic studies. © 1994 John Wiley & Sons, Inc.
Thermodynamics of ubiquitin unfolding
Authors: Wintrode Patrick L. , Makhatadze George I. , Privalov Peter L. 
Published: May 2005

AbstractThe energetics of ubiquitin unfolding have been studied using differential scanning microcalorimetry. For the first time it has been shown directly that the enthalpy of protein unfolding is a nonlinear function of temperature. Thermodynamic parameters of ubiquitin unfolding were correlated with the structure of the protein. The enthalpy of hydrogen bonding in ubiquitin was calculated and compared to that obtained for other proteins. It appears that the energy of hydrogen bonding correlates with the average length of the hydrogen bond in a given protein structure. © 1994 John Wiley & Sons, Inc.
Hydrogen bond strength and β‐sheet propensities: The role of a side chain blocking effect
Authors: Bai Yawen , Englander S. Walter 
Published: May 2005

AbstractAmino acid side chains can enhance peptide group hydrogen bond strength in protein structures by obstructing the competing hydrogen bond to solvent in the unfolded state. Available data indicate that the steric blocking effect contributes an average of 0.5 kJ per residue to protein hydrogen bond strength and accounts for the intrinsic α‐sheet propensities of the amino acids. In available data for helical models, the contribution to α‐helix propensities is obscured especially by large context‐dependent effects. These issues are all related by a common side chain‐dependent steric clash which disfavors peptide to water H‐bond formation, peptide to catalyst complexation in hydrogen exchange reactions (Bai et al., Proteins 17:75–86, 1993), and peptide to peptide H‐bonding in the helical main chain conformation (Creamer and Rose, Proc. Natl. Acad. Sci. U.S.A. 89:5937–5941, 1992) but not in α‐strands. © 1994 John Wiley & Sons, Inc.
A method for α‐helical integral membrane protein fold prediction
Authors: Taylor William R. , Jones David T. , Green N. Michael 
Published: May 2005

AbstractIntegral membrane proteins (of the α‐helical class) are of central importance in a wide variety of vital cellular functions. Despite considerable effort on methods to predict the location of the helices, little attention has been directed toward developing an automatic method to pack the helices together. In principle, the prediction of membrane proteins should be easier than the prediction of globular proteins: there is only one type of secondary structure and all helices pack with a common alignment across the membrane. This allows all possible structures to be represented on a simple lattice and exhaustively enumerated. Prediction success lies not in generating many possible folds but in recognizing which corresponds to the native. Our evaluation of each fold is based on how well the exposed surface predicted from a multiple sequence alignment fits its allocated position. Just as exposure to solvent in globular proteins can be predicted from sequence variation, so exposure to lipid can be recognized by variable‐hydrophobic (variphobic) positions. Application to both bacteriorhodopsin and the eukaryotic rhodopsin/opsin families revealed that the angular size of the lipid‐exposed faces must be predicted accurately to allow selection of the correct fold. With the inherent uncertainties in helix prediction and parameter choice, this accuracy could not be guaranteed but the correct fold was typically found in the top six candidates. Our method provides the first completely automatic method that can proceed from a scan of the protein sequence databanks to a predicted three‐dimensional structure with no intervention required from the investigator. Within the limited domain of the seven helix bundle proteins, a good chance can be given of selecting the correct structure. However, the limited number of sequences available with a corresponding known structure makes further characterization of the method difficult. © 1994 John Wiley & Sons, Inc.
Crystallization and preliminary crystallographic studies of the precursor and mature forms of a neutral lipase from the fungus Rhizopus delemar
Authors: Swenson Lora , Green Ruth , Joerger Rolf , Haas Michael , Scott Karen , Wei Yunyi , Derewenda Urszula , Lawson David M. , Derewenda Zygmunt S. 
Published: May 2005

AbstractA neutral lipase from the filamentous fungus Rhizopus delemar has been crystallized in both its proenzyme and mature forms. Although the latter crystallizes readily and produces a variety of crystal forms, only one was found to be suitable for X‐ray studies. It is monoclinic (C2, a = 92.8 Å, b = 128.9 Å, c = 78.3 Å, β = 135.8) with two molecules in the asymmetric unit related by a noncrystallographic diad. The prolipase crystals are orthorhombic (P212121, with a = 79.8 Å, b = 115.2 Å, c = 73.0 Å) and also contain a pair of molecules in the asymmetric unit. Initial results of molecular replacement calculations using the refined coordinates of the related lipase from Rhizomucor miehei identified the correct orientations and positions of the protein molecules in the unit cells of crystals of both proenzyme and the mature form. © 1994 John Wiley & Sons, Inc.