bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amino acid substitution analysis of E. coli thymidylate synthase: The study of a highly conserved region at the N‐terminus
Authors: Kim Choll Wan , Michaels Mark Leo , Miller Jeffrey H. 
Published: May 2005

AbstractAmino acid substitution analysis within a highly conserved region of Escherichia coli thymidylate synthase (TS), using suppression of amber mutations by tRNA suppressors, has yielded a bank of 124 new mutationally altered TS proteins. These mutant proteins have been used to study the structure‐function relationship of the Escherichia coli TS protein at the N‐terminus corresponding to residues 20 through 35. This region contains a block of amino acids whose sequence has been well conserved among other known TS proteins from various organisms. Positions 20 through 25 contain a surface loop structure and positions 26 through 35 encompass a β‐strand. We find that residues surrounding a β‐bulge structure within the β‐strand are particularly sensitive to amino acid substitution, suggesting that this structure is maintained by a highly ordered packing arrangement. Three residues in the surface loop that are present at the base of the substrate binding pocket are also sensitive to amino acid substitution. The remainder of the conserved sites, including those at the dimer interface, are tolerant to most, if not all, of the substitutions tested. © 1992 Wiley‐Liss, Inc.
Structural effects induced by mutagenesis affected by crystal packing factors: The structure of a 30–51 disulfide mutant of basic pancreatic trypsin inhibitor
Authors: Eigenbrot Charles , Randal Michael , Kossiakoff Anthony A. 
Published: May 2005

AbstractThe X‐ray structure of the C30V/C51A disulfide mutant of basic pancreatic trypsin inhibitor (BPTI) has been analyzed at 1.6 Å resolution. The mutant crystallizes in a cell having two molecules in the asymmetric unit. The packing environments of these two molecules are quite different, allowing for an assessment of which among the observed structural changes result from the mutation and which are produced by lattice packing considerations. The removal of the 30–51 disulfide bridge has little apparent affect on the B‐factors of segments of adjacent polypeptide chain, although there are distinct differences in the structure compared to wild‐type BPTI crystal structures. Both of the two C30V/C51A molecules show differences at the mutation site when compared to another 30–51 disulfide mutant, C30A/C51A, presumably due to the larger steric bulk of a valine versus an alanine at residue 30. A comparison of the two independent C30V/C51A molecules indicates that there are significant differences between them even at the site of mutation. The description of the specific structural differences of each molecule differs in detail and suggests different conclusions about the nature of structural perturbation near 30–51. In addition, when these two molecules are compared to two different wild‐type structures, which had been determined from different space groups, a somewhat different pattern of changes is observed. These findings indicate that crystal packing can influence the observed perturbations in mutant structures. © 1992 Wiley‐Liss, Inc.
Monte carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space
Authors: Caflisch Amedeo , Niederer Peter , Anliker Max 
Published: May 2005

AbstractA new minimization procedure for the global optimization is cartesian coordinate space of the conformational energy of a polypeptide chain is presented. The Metropolis Monte Carlo minimization is thereby supplemented by a thermalization process, which is initiated whenever a structure becomes trapped in an area containing closely located local minima in the conformational space. The method has been applied to the endogenous opioid pentapeptide methionine enkephalin. Five among 13 different starting conformations led to the same apparent global minimum of an in‐house developed energy function, a type II′ reverse turn, the central residues of which are Gly‐3‐Phe‐4. A comparison between the ECEPP/2 global minimum conformation of methionine enkephalin and the apparent one achieved by the present method shows that minimum‐energy conformations having a certain similarity can be generated by relatively different force fields. © 1992 Wiley‐Liss, Inc.
Overproduction, crystallization, and preliminary X‐ray diffraction studies of the major cold shock protein from Bacillus subtilis, CspB
Authors: Schindelin Hermann , Herrler Michael , Willimsky Gerald , Marahiel Mohamed A. , Heinemann Udo 
Published: May 2005

AbstractThe major co ld shock protein form Bacillus subtilis (CspB) was voerexressed using the bacteriophage T7 RNA polymerase/promotor system and purified to apparent homogeneity from recombinant Escherichia coli cells. CspB was crystallized in two different forms using vapor diffusion methods. The first crystal form obtained with ammonium sulfate as precipitant belongs to the trigonal crystal system, space group P3121 (P3221) with unit cell dimensions a = b = 59.1 Å and c = 46.4 Å. The second crystal form is tetragonal, space group P41212 (P43212) with unit cell dimensionsa = b = 56.9 Å and c = 53.0 Å. These crystals grow with polyethylene glycol 4000 as precipitant. © 1992 Wiley‐Liss, Inc.
The structure of the complex between influenza virus neuraminidase and sialic acid, the viral receptor
Authors: Varghese Joseph N. , McKimm‐Breschkin Jennifer L. , Caldwell James B. , Kortt Alexander A. , Colman Peter M. 
Published: May 2005

AbstractCrystallographic studies of neuraminidase–sialic acid complexes indicate that sialic acid is distorted on binding the enzyme. Three arginine residues on the enzyme interact with the carboxylate group of the sugar which is observed to be equatorial to the saccharide ring as a consequence of its distorted geometry. The glycosidic oxygen is positioned within hydrogen‐bonding distance of Asp‐151, implicating this residue in catalysis. © 1992 Wiley‐Liss, Inc.
Comparative molecular modeling and crystallization of P‐30 protein: A novel antitumor protein of Rana pipiens oocytes and early embryos
Authors: Mosimann Steven C. , Johns Kathy L. , Ardelt Wojciech , Mikulski Stanislaw M. , Shogen Kuslima , James Michael N. G. 
Published: May 2005

AbstractThe P‐30 protein (Onconase™)Onconase™ is a trademark of Alfacell Corporation.
of Rana pipiens oocytes and early embryos is homologous to members of the pancreatic ribonuclease superfamily and exhibits an antitumor activity in vitro and in vivo. It appears that the ribonucleolytic activity of P‐30 protein may be required for its antitumor effects. A comparative molecular model of P‐30 protein has been constructed based upon the known three‐dimensional structure of bovine pancreatic RNase A in order to provide structural information. Functionally, these enzymes hydrolyze oligoribonucleotides to pyrimidine‐3′‐phosphate monoesters and 5′‐OH ribonucleotides. In the modeling procedure, automated sequence alignments were revised based upon the inspection of the RNase A structure before the amino acids of the P‐30 protein were assigned the coordinates of the RNase A template. The inevitable intermolecular steric clashes that result were relieved on an interactive graphics device through theadjustment of side chain torsion angles. This process was followed by energy minimization of the model, which served to optimize stereochemical geometry and to relieve any remaining unacceptably close contacts. The resulting model retains the essential features of RNase A as sequence insertions and deletions are almost exclusively found in exposed surface loops. The all atom superposition of active site residues of the P‐30 protein model and an identically minimized RNase A structure has a root mean square deviation of 0.52 Å. Though tentative, the model is consistent with a pyrimidine specificity. Further, the model suggests Lys9 (P‐30 protein) can donate a hydrogen bond to the active site phosphate, whereas it is unlikely that P‐30 protein binds the 3′‐ribonucleotide in a fashion similar to RNase A. P‐30 protein has been crystallized in an orthorhombic space group, P212121, with unit cell dimensions, a = 40.76, b = 69.77, and c = 32.54 Aring;. The crystals grow as small rosettes from an ammonium sulfate solution at pH 4.5. © 1992 Wiley‐Liss, Inc.
Generation of a substructure library for the description and classification of protein secondary structure. II. Application to spectra–structure correlations in fourier transform infrared spectroscopy
Authors: Prestrelski Steven J. , Byler D. Michael , Liebman Michael N. 
Published: May 2005

AbstractFourier transform infrared spectroscopy has become well known as a sensitive and informative tool for studying secondary structure in proteins. Present analysis of the conformation‐sensitive amide I region in protein infrared spectra, when combined with band narrowing techniques, provides more information concerning protein secondary structure than can be meaningfully interpreted. This is due in part to limited models for secondary structure. Using the algorithm described in the previous paper of this series, we have generated a library of substructures for several trypsin‐like serine proteases. This library was used as a basis for spectra–structure correlations with infrared spectra in the amide I′ region, for five homologous proteins for which spectra were collected. Use of the substructure library has allowed correlations not previously possible with template‐based methods of protein conformational analysis. © 1992 Wiley‐Liss, Inc.
Crystallization, sequence, and preliminary crystallographic data for an antipeptide Fab 50.1 and peptide complexes with the principal neutralizing determinant of HIV‐1 gpl20
Authors: Sturam Enrico A. , Stanfield Robyn L. , Fieser Gail G. , Silver Sandra , Roguska Michael , Hincapie L. Marina , Simmerman Heather K. B. , Profy Albert T. , Wilson Ian A. 
Published: May 2005

AbstractX‐ray quality crystals of an Fab fragment from an antipeptide monoclonal antibody (R/V3‐50.1) that recognizes the principal neutralizing determinant (PND) of the gpl20 glycoprotein of human immunodeficiency virus type 1 (HIV‐1) (MN isolate) were grown as uncomplexed and peptide complexed forms. Crystals of the free Fab grew from high salt in orthorhombic space groups P212121 and I222 and from polyethylene glycol in space groups P1 and P21. Seeds from either the P1 and P21 native (uncomplexed) Fab crystals induced nucleation of crystals of the Fab complexed to a 16‐residue synthetic peptide corresponding to the PND when streak seeded into preequilibrated solutions of this complex. Data were collected from these complex crystals and from each of the four native Fab forms to at least 2.8Å resolution. The genes for the variable domain of the Fab were cloned and sequenced and the primary amino acid sequence was deduced from this information. Knowledge of the three‐dimensional structure of this Fab–pep‐tide complex will be important in the understanding of the PND of HIV‐1 and its recognition by neutralizing monoclonal antibodies. © 1992 Wiley‐Liss, Inc.
The quaternary structure of carbonmonoxy hemoglobin ypsilanti
Authors: Janin Joël , Wodak Shoshana J. 
Published: May 2005

AbstractWe present a geometric analysis of the allosteric interface in the new Y state quaternary structure observed in liganded mutant hemoglobin Ypsilanti (β99 Asp → Tyr) by Smith, F.R., Lattman, E.E., Carter, C.W., Jr. (Proteins 10:81–91, 1991). The classical T to R quaternary structure change being a rotation of αβ dimers about an axis which is approximately parallel to the dimer axis of pseudosym‐metry, the new quaternary structure is obtained by applying to R an additional rotation about an axis orthogonal to the first. This suggests that Y is a modified R state rather than an intermediate on the T to R pathway. Computer docking experiments designed to simulate the quaternary structure change support this suggestion. © 1993 Wiley‐Liss, Inc.
The contribution of cross‐links to protein stability: A normal mode analysis of the configurational entropy of the native state
Authors: Tidor Bruce , Karplus Martin 
Published: May 2005

AbstractThe vibrational entropy of native BPTI, with three disulfide bonds, was determined by use of normal mode calculations and compared with that of folded variants having either one less disulfide bond or lacking a peptide bond at the trypsin‐reactive site. Favorable contributions to the free energy of 2.5–5.1 kcal/mol at 300 K were calculated for the reduction of disulfide bonds in the folded state, whereas no favorable contribution was found for the hydrolysis of the peptide bond cleaved by trypsin. This is on the order of the effect of disulfides in the unfolded state. The implications of these results for the stabilization of a folded protein by the introduction of crosslinks are discussed. © 1993 Wiley‐Liss, Inc.
Studies of the zein‐like α‐prolamins based on an analysis of amino acid sequences: Implications for their evolution and three‐dimensional structure
Authors: Garratt Richard , Oliva Glaucius , Caracelli Ignez , Leite Adilson , Arruda Paulo 
Published: May 2005

Abstractα‐Prolamins are the major seed storage proteins of species of the grass tribe Andropogonea. They are unusually rich in glutamine, proline, alanine, and leucine residues and their sequences show a series of tandem repeats presumed to be the result of multiple intragenic duplication. Two new sequences of α‐prolamin clones from Coix (pBCX25.12 and pBCX25.10) are compared with similar clones from maize and Sorghum in order to investigate evolutionary relationships between the repeat motifs and to propose a schematic model for their three‐dimensional structure based on hydrophobic membrane‐helix propensities and helical “wheels.” A scheme is proposed for the most recent events in the evolution of the central part of the molecule (repeats 3 to 8) which involves two partial intragenic duplications and in which contemporary odd‐numbered and even‐numbered repeats arise from common ancestors, respectively. Each pair of repeats is proposed to form an antiparallel α‐helical hairpin and that the helices of the molecule as a whole are arranged on a hexagonal net. The majority of helices show six faces of alternating hydrophobic and polar residues, which give rise to intersticial holes around each helix which alternate in chemical character. The model is consistent with proteins which contain different numbers of repeats, with oligomerization and with the dense packaging of α‐prolamins within the protein body of the seed endosperm. © 1993 Wiley‐Liss, Inc.
Crystal structure of CTP‐ligated T state aspartate transcarbamoylase at 2.5 Å resolution: Implications for ATCase mutants and the mechanism of negative cooperativity
Authors: Kosman Richard P. , Gouaux J. Eric , Lipscomb William N. 
Published: May 2005

AbstractThe X‐ray crystal structure of CTP‐ligated T state aspartate transcarbamoylase has been refined to an R factor of 0.182 at 2.5 Å resolution using the computer program X‐PLOR. The structure contains 81 sites for solvent and has rms deviations from ideality in bond lengths and bond angles of 0.018 Å and 3.722°, respectively. The cytosine base of CTP interacts with the main chain carbonyl oxygens of rTyr‐89 and rIle‐12, the main chain NH of rIle‐12, and the amino group of rLys‐60. The ribose hydroxyls form polar contacts with the amino group of rLys‐60, a carboxylate oxygen of rAsp‐19, and the main chain carbonyl oxygen of rVal‐9. The phosphate oxygens of CTP interact with the amino group of rLys‐94, the hydroxyl of rThr‐82, and an imidazole nitrogen of rHis‐20. Recent mutagenesis experiments evaluated in parallel with the structure reported here indicate that alterations in the hydrogen bonding environment of the side chain of rAsn‐111 may be responsible for the homotropic behavior of the pAR5 mutant of ATCase. The location of the first seven residues of the regulatory chain has been identified for the first time in a refined ATCase crystal structure, and the proximity of this portion of the regulatory chain to the allosteric site suggests a potential role for these residues in nucleotide binding to the enzyme. Finally, a series of amino acid side chain rearrangements leading from the R1 CTP allosteric to the R6 CTP allosteric site has been identified which may constitute the molecular mechanism of distinct CTP binding sites on ATCase. © 1993 Wiley‐Liss, Inc.
Purification, crystallization, and preliminary X‐ray studies on the rhizome lectin from stinging nettle and its complex with NN′N″‐triacetylchitotriose
Authors: Loris Remy , Thi Minh Hoa Dao , Lisgarten John , Wyns Lode 
Published: May 2005

AbstractSingle crystals were grown from affinity‐purified stinging nettle lectin and from its complex with the specific trisaccharide NN′N″ ‐triacetylchitotriose by vapor diffusion at room temperature. The lectin crystallizes in space group P212121 with unit cell dimensions a = 54.3 (1) Å, b = 62.2 (1) Å, and c = 92.4 (2) Å, and diffracts to 3.0 Å resolution. The asymmetric unit contains three lectin monomers. The crystals of the lectin‐trisaccharide complex have space group P212121 with cell constants a = 37.69 (4) Å, b = 48.97 (6) Å, and c = 57.32 (4) Å. These crystals diffract to at least 2.0 Å resolution and the asymmetric unit contains one lectin monomer. A three‐dimensional X‐ray structure determination is on its way. © 1993 Wiley‐Liss, Inc.
On the calculation of pKas in proteins
Authors: Yang An‐Suei , Gunner M. R. , Sampogna Rosemary , Sharp Kim , Honig Barry 
Published: May 2005

AbstractThis paper describes a general method to calculate the pKas of ionizable groups in proteins. Electrostatic calculations are carried out using the finite difference Poisson–Boltzmann (FDPB) method. A formal treatment of the calculation of pKas within the framework of the FDPB method is presented. The major change with respect to previous work is the specific incorporation of the complete charge distribution of both the neutral and charged forms of each ionizable group into the formalism. This is extremely important for the treatment of salt bridges. A hybrid statistical mechanical/Tanford–Roxby method, which is found to be significantly faster than previous treatments, is also introduced. This simplifies the problem of summing over the large number of possible ionization states for a complex polyion. Applications to BPTI and serine proteases suggest that the calculations can be quite reliable. However, the necessity of including bound waters in the treatment of the Asp‐70…His‐31 salt bridge in T4 lysozyme and experience with other proteins suggest that additional factors ultimately need to be considered in a comprehensive treatment of pKas in proteins. © 1993 Wiley‐Liss, Inc.
Multiple‐site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins
Authors: Gilson Michael K. 
Published: May 2005

AbstractComputer models of proteins frequently treat the energies and forces associated with ionizable groups as if they were purely electrostatic. This paper examines the validity of the purely electrostatic approach, and concludes that significant errors in energies can result from the neglect of ionization changes. However, a complete treatment of ionizable groups presents substantial computational obstacles, because of the large number of ionization states which must be examined in systems having multiple interacting titratable groups. In order to address this problem, two novel methods for treating the energetics and forces associated with ionizable groups with a minimum of computer time have been developed. The most rapid method yields approximate energies by computing the free energy of a single highly occupied ionization state. The second method separates ionizable groups into clusters, and treats intracluster interactions exactly, but intercluster interactions approximately. This method yields both accurate energies and fractional charges. Good results are obtained in tests of both methods on proteins having has many as 123 ionizable groups. The more rapid method requires computer times of 0.01 to 0.34 sec, while the more accurate method requires 0.7 to 15 sec. These methods may be fast enough to permit the incorporation of ionization effects in iterative computations, such as energy minimizations and conformational searches. © 1993 Wiley‐Liss, Inc.
The structure of a thermally stable 3‐phosphoglycerate kinase and a comparison with its mesophilic equivalent
Authors: Davies Gideon J. , Gamblin Steven J. , Littlechild Jennifer A. , Watson Herman C. 
Published: May 2005

AbstractThe structure of the phosphoglycerate kinase (PGK) from Bacillus stearothermophilus, a moderate thermophile, has been determined and compared with that of its mesophilic equivalent from yeast. The Bacillus enzyme structure was solved by molecular replacement and improved using constrained rigid‐body, molecular dynamics and conventional refinement procedures. The refinement residual, calculated using all the measured data between 8 and 1.65 Å, is 0.18(1). The stereo chemical deviations of the final model from ideality are 0.01 Å for both bonds and planes.The mid‐point temperatures of the Bacillus and yeast enzymes are 67 and 53°C, respectively. Differential scanning calorimetry indicates that the energy difference (ΔΔG) between the mesophilic and thermophilic enzymes is of the order of 5 kcal mol−1 at room temperature. The structure comparison indicates that the features most likely to be responsible for the increased thermal stability of the Bacillus enzyme are the increased internal hydrophobicity, additional ion pairs, and better α‐helix stability resulting from the removal of helix destablising residues and extra helix–dipole/helix side chain ionic interactions. © 1993 Wiley‐Liss, Inc.
Small effects of amino acid replacements on the reduced and unfolded state of pancreatic trypsin inhibitor
Authors: Goldenberg David P. , Zhang Jian‐Xin 
Published: May 2005

AbstractThe effects of amino acid replacements on the hydrodynamic volume of reduced and unfolded bovine pancreatic trypsin inhibitor (BPTI) have been examined by gel electrophoresis. The electrophoretic mobilities of the reduced forms of 46 BPTI variants were compared at room temperature in the absence of denaturants. The single substitutions examined include many different types of replacements at sites throughout the polypeptide, and, collectively, alter 22 of the 58 residues of the wild‐type protein. The only substitutions found to alter the electrophoretic mobility of the reduced protein by more than ∼3% are those that change the net charge of the protein. For nine mutants, the rates of disulfide formation in the reduced protein were also examined and found to be very similar to that of the wild‐type protein. These results suggest that any structure that may be present in the reduced protein is either relatively insensitive to amino acid replacements or does not greatly influence the averaged properties of the polypeptide chain. © 1993 Wiley‐Liss, Inc.