摘要:

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‐L

ISSN:0887-3585    

DOI:10.1002/prot.340140302

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractFree energies of oxygen‐linked subunit assembly and cooperative interaction have been determined for 34 molecular species of human hemoglobin, which differ by amino acid alterations as a result of mutation or chemical modification at specific sites. These studies required the development of extensions to our earlier methodology. In combination with previous results they comprise a data base of 60 hemoglobin species, characterized under the same conditions. The data base was analyzed in terms of the five following issues. (1) Range and sensitivity to site modifications. Deoxy tetramers showed greater average energetic response to structural modifications than the oxy species, but the ranges are similar for the two ligation forms. (2) Structural localization of cooperative free energy. Difference free energies of dimer‐tetramer assembly (oxy minus deoxy) yielded ΔGcfor each hemoglobin, i.e., thefree energy used for modulation of oxygen affinity over all four binding steps. A structure‐energy map constructed from these results shows that the α1β2interface is a unique structural location of the noncovalent bonding interactions that are energetically coupled to cooperativity. (3) Relationship of cooperativity to intrinsic binding. Oxygen binding energetics for dissociated dimers of mutants strongly indicates that cooperativity and intrinsic binding are completely decoupled by tetramer to dimer dissociation. (4) Additivity, site‐site coupling and adventitious perturbations. All these are exhibited by individual‐site modifications of this study. Large nonadditivity may be correlated with global (quaternary) structure change.(5) Residue position vs. chemical nature. Functional response is solely dictated by structural location for a subset of the sites, but varies with side‐chain type at other sites. The current data base provides a unique framework for further analyses and modeling of fundamental issues in the structural chemistry of proteins and allosteric mechanisms. © 1992

ISSN:0887-3585    

DOI:10.1002/prot.340140303

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractRecent crystallographic studies on the mutant human hemoglobin Ypsilanti (β99 Asp→xsTyr) have revealed a previously unknownquaternary structure called “quaternary Y” and suggested that the new structure may represent an important intermediate in the cooperative oxygenationpathway of normal hemoglobin.15Here we measure the oxygenation and subunit assembly properties of hemoglobin Ypsilanti and five additionalβ99 mutants (Asp β99→Val, Gly, Asn, Ala, His) totest for consistency between their energetics and those of the intermediatespecies of normal hemoglobin.Overall regulation of oxygen affinity in hemoglobin Ypsilanti is found to originate entirely from 2.6 kcal of quaternary enhancement, such that thetetramer oxygenation affinity is 85‐fold higher than for binding to the dissociated dimers. Equal partitioning of this regulatory energy among the four tetrameric binding steps (0.65 kcal per oxygen) leads toa noncooperative isotherm with extremely high affinity (pmedian= .14 torr). Temperature and pH studies of dimer‐tetramer assembly and sulfhydryl reaction kinetics suggest that oxygenation‐dependent structural changes in hemoglobin Ypsilanti are small. These properties are quite different from the recently characterized allosteric intermediate, which has two ligands bound on the same side of the α1β2interface (see ref. 1 for review). The combined results do, however, support the view that quaternary Y may represent the intermediate cooperativity state of normal hemoglobin that binds the last oxygen. © 1

ISSN:0887-3585    

DOI:10.1002/prot.340140304

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractThe three‐dimensional structure of the human immunoglobulin fragment Fab New (IgG1,λ) has been refined to a crystal‐lographicR‐factor of 16.9% to 2Å resolution. Rms deviations of the final model from ideal geometry are 0.014 Å for bond distances and 3.03° for bond angles. Refinement was based on a new X‐ray data set including 28,301 reflections withF>2.5σ(F) from 6.0 to 2.0 Å resolution. The starting model for the refinement procedure reported here is from the Brookhaven Protein Data Bank entry 3FAB (rev. 1981). Differences between the initial and final models include modified polypeptide‐chain folding in the third complementarity‐determining region (CDR3) and the third framework region (FR3) of VHand in some exposed loops of CLand CHl. Amino acid sequencechanges were determined at a number of positions by inspection of difference electron density maps. The incorporation of amino acid sequence changes results inan improved VHframework model for the “humanization” of

ISSN:0887-3585    

DOI:10.1002/prot.340140305

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractUsing a backpropagation neural network model we have found a limit for secondary structure prediction from local sequence. By including only sequences from whole α‐helix and non‐α‐helixstructures in our training and test sets—sequences spanning boundaries between these two structures were excluded—it was possible to investigate directly the relationship between sequence and structure for α‐helix. A group of non‐α‐helix sequences, that was disrupting overall prediction success, was indistinguishable to the network from α‐helix sequences. These sequences were found to occur at regions adjacent to the termini of α‐helices with statistical significance, suggesting that potentially longer α‐helices are disrupted by global constraints. Some of these regions spanned more than 20 residues. On these whole structure sequences, 10 residues in length, a comparatively high prediction success of 78% with a correlation coefficient of 0.52 was achieved. In addition, the structure of the input space, the distribution of β‐sheet in this space, and the effect of segment length were also inves

ISSN:0887-3585    

DOI:10.1002/prot.340140306

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractThe structure of the retroviral proteinase from avian myeloblastosisassociated virus (MAV) has been determined and refined at 2.2 Å resolution. This structure is compared with those of homologous proteinases from Rous sarcoma virus (RSV) and human immunodeficiency type 1 virus (HIV). Through comparison with the structure of a proteinase‐inhibitor complex from HIV, a model of a complex between MAV proteinase and a peptide substrate has been generated. Examination of this model suggests structural basis for the diverse specifications of viral proteinases. © 1992 Wiley‐Liss

ISSN:0887-3585    

DOI:10.1002/prot.340140307

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractThe P‐30 protein (Onconase™)Onconase™ is a trademark of Alfacell Corporation.ofRana pipiensoocytes 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, andc= 32.54 Aring;. The crystals grow as small rosettes from an ammonium sulfate soluti

ISSN:0887-3585    

DOI:10.1002/prot.340140308

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractHexameric insulin has been crystallized from different conditions ina variety of crystalline modifications. In the presence of ∼1%phenol and at a pH of 8.5, a new rhom‐bohedral form is produced, space group R3, a = 79.92 Åand c = 40.39 Å, in whichthe asymmetric unit consists of a dimer. The structur has been solved and refined, using data between 8.0 and 2.5 Å resolution, to a residual of0.157. The two monomers in the asymmetric unit have nearly identical R conformations, that is, residues Bl through B8 are α‐helical, producing a continuous α‐helix from Bl through B19. A phenol molecule is hydrogen bonded to the carbonyl oxygen of A6 Cys of each monomer. Small differences in conformation and the final (2Fo‐Fc) and difference electron density maps suggest that an additional phenol molecule is coordinated to one of the

ISSN:0887-3585    

DOI:10.1002/prot.340140309

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractA method is presented for generating folded chains of specific aminoacid sequences on a simple cubic lattice. Monte Carlo simulations are used to transform extended geometries of simplified α‐carbon chainsfor eight small monomeric globular proteins into folded states. Permitted chain transitions are limited to a few types of moves, all restricted to occur on the lattice. Crude residue–residue potentials derived from statistical structure data are used to describe the energies for each conformer. The low resolution structures obtained by this procedure contain many of the correct gross features of the native folded architectures with respect to average residue energy per nonbonded contact, segment density, and location of surface loops and disulfide pairs. Rms deviations between these and the native X‐ray structures and percentage of native long‐range contacts found in these final folded structures are 7.6 ± 0.7 Å and 48 ± 3%, respectively. This procedure can be useful for predicting approximate tertiary interactions from amino acid sequence. © 1992 Wil

ISSN:0887-3585    

DOI:10.1002/prot.340140310

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340140312

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY