摘要:

AbstractThe α‐helical, coiled‐coil protein motif is increasingly recognized in a variety of functional classes of proteins. The pitch of a coiled coil, or rate of winding of the α‐helices around each other, is a key determinant of both intra‐ and intermolecular interactions. Experimental measurements of the pitch of parallel two‐stranded coiled coils of muscle proteins, and examination of the recently determined structure of another two‐stranded coiled coil, the GCN4 transcription factor protein, suggest that the pitch has an average value of about 140 Å. This value is consistent with the observed number of residues per turn in α‐helices of globular proteins, the determinant of the inter‐helical packing within the coiled‐coil motif. An understanding of the structural determinants of this value for the pitch and possible variations will be important in defining the interactions of coiled‐coil proteins with other macromolecules.

ISSN:0887-3585    

DOI:10.1002/prot.340140403

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

年代:1992

数据来源: WILEY

摘要:

AbstractProtein secondary structure has been typically classified into four major classes—α‐helices, extended strands, reverse turns, and loops. Available methods for secondary structure analysis utilize predefined structure templates to search for structural matches among proteins. By this approach a significant portion of a proteins backbone conformation is assigned to one of a limited number of conformations or, if unassigned, to random coil. To expand our ability to describe protein secondary structure, we have developed an algorithm that operates independently of a predefined structure template. The procedure uses two geometric descriptors, the linear distance and the backbone dihedral angle, to represent the conformation form the α‐carbon coordinates. The algorithm functions by searching for conformationally equivalent, contiguous fragments without regard to secondary structural classification and is thus independent of the complexity of the backbone fold. The result is a library of conformationally equivalent structure fragments that exhibit some novel characteristics. The library contains features that reproduce the major secondary structure classes as well as defining conformations previously described only as random or undefined conformations. Additionally, the library defines several subclassifications of β‐strands. We present here a validation of this method and a presentation and discussion of the most significant results. In a second study, we report the results of application of this method to spectra‐structure correlations in Fourier transform infrared spectroscopy. © 1992 Wi

ISSN:0887-3585    

DOI:10.1002/prot.340140404

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

年代:1992

数据来源: WILEY

摘要:

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

ISSN:0887-3585    

DOI:10.1002/prot.340140405

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

年代:1992

数据来源: WILEY

摘要:

AbstractIn this paper we present a molecular dynamics (MD) simulation of subtilisin BPN′ in a crystalline environment containing four protein molecules and solvent. Con‐formational and dynamic properties of the molecules are compared with each other and with respect to the X‐ray structure to test the validity of the force field. The agreement between simulated and experimental structure using the GROMOS force field is better than that obtained in the literature using other force fields for protein crystals. The overall shape of the molecule is well preserved, as is the conformation of α‐helices and β‐strands. Structural differences are mainly found in loop regions. Solvent networks found in the X‐ray structure were reproduced by the simulation, which was unbiased with respect to the crystalline hydration structure. These networks seem to play an important role in the stability of the protein; evidence of this is found in the structure of the active site. The weak ion binding site in the X‐ray structure of subtilisin BPN′ is occupied by a monovalent ion. When a calcium ion is placed in the initial structure, three peptide ligands are replaced by 5 water ligands, whereas a potassium ion retains (in part) its original ligands. Existing force fields yield a reliable method to probe local structure and short‐time dynamics of proteins, providing an accuracy of about 0.1 nm. ©

ISSN:0887-3585    

DOI:10.1002/prot.340140406

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

年代:1992

数据来源: WILEY

摘要:

AbstractA directed conformational search algorithm using the program CONGEN (ref. 3), which samples backbone conformers, is described. The search technique uses information from the partially built structures to direct the search process and is tested on the problem of generating a full set of backbone Cartesian coordinates given only α‐carbon coordinates. The method has been tested on six proteins of known structure, varying in size and classification, and was able to generate the original backbone coordinates with RMSs ranging from 0.30–0.87Å for the α‐carbons and 0.5–0.99Å RMSs for the backbone atoms.Cispeptide linkages were also correctly identified. The procedure was also applied to two proteins available with only α‐carbon coordinates in the Brookhaven Protein Data Bank; thioredoxin (SRX) and triacyiglycerol acylhydrolase (TGL). All‐atom models are proposed for the backbone of both these proteins. In addition, the technique was applied to randomized coordinates of flavodoxin to assess the effects of irregularities in the data on the final RMS. This study represents the first time a deterministic conformational search was used on such a large scale. © 199

ISSN:0887-3585    

DOI:10.1002/prot.340140407

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe function of the cellulosebinding domain (CBD) of the cellobiohydrolase I ofTrichoderma reeseiwas studied by site‐directed mutagenesis of two amino acid residues identified by analyzing the 3D structure of this domain. The mutant enzymes were produced in yeast and tested for binding and activity on crystalline cellulose. Mutagenesis of the tyrosine residue (Y492) located at the tip of the wedge‐shaped domain to alanine or aspartate reduced the binding and activity on crystalline cellulose to the level of the core protein lacking the CBD. However, there was no effect on the activity toward small oligosaccharide (4‐methylumbellifery1 β‐D‐lactoside). The mutation tyrosine to histidine (Y492H) lowered but did not destroy the cellulose binding, suggesting that the interaction of the pyranose ring of the substrate with an aromatic side chain is important. However, the catalytic activity of this mutant on crystalline cellulose was identical to the other two mutants. The mutation P477R on the edge of the other face of the domain reduces both binding and activity of CBHI. These results support the hypothesis that both surfaces of the CBD are involved in the interaction of the binding domain with crystalline cellulose. © 1992 Wile

ISSN:0887-3585    

DOI:10.1002/prot.340140408

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

年代:1992

数据来源: WILEY

摘要:

AbstractA model for an antibody specific for the carcinoembryonic antigen (CEA) has been constructed using a method which combines the concept of canonical structure with conformational search. A conformational search technique is introduced which couples random generation of backbone loop conformations to a simulated annealing method for assigning side chain conformations. This technique was used both to verify conformations selected from the set of known canonical structures and to explore conformations available at the H3 loop in CEA ab initio. Canonical structures are not available for H3 due to its variability in length, sequence, and observed conformation in known antibody structures Analysis of the results of conformational search resulted in three equally probable conformations for H3 loop in CEA. Force field energies, solvation free energies, exposure of charged residues and burial of hydrophobic residues, and packing of hydrophobic residues at the base of the loop were used as selection criteria. The existence of three equally plausible structures may reflect the high degree of flexibility expected for an exposed loop of this length. The nature of the combining site and features which could be important to interaction with antigen are discussed. © 1992 Wiley‐Liss, I

ISSN:0887-3585    

DOI:10.1002/prot.340140409

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

年代:1992

数据来源: WILEY

摘要:

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 groupsP212121andI222 and from polyethylene glycol in space groupsP1 andP21. Seeds from either theP1 andP21native (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. © 199

ISSN:0887-3585    

DOI:10.1002/prot.340140410

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

年代:1992

数据来源: WILEY

摘要:

AbstractMethods have recently been developed to present vast libraries of random peptides on the surface of filamentous phage. To introduce a degree of conformational constraint into random peptides, a library of hexapeptides flanked by cysteine residues (capable of forming cyclic disulfides) was constructed. This library was screened using the platelet glycoprotein, IIb/IIIa, which mediates the aggregation of platelets through binding of fibrinogen. A variety of peptides containing the sequence Arg‐Gly‐Asp or Lys‐Gly‐Asp were discovered and synthesized. The cyclic, disulfide bonded forms of the peptides bound IIb/IIIa with dissociation constants in the nanomolar range, while reduced forms or an analogue in which Ser replaced the Cys residues bound considerably less tightly. These results demonstrate the feasibility for introducing conformational constraints into random peptide libraries and also demonstrates the potential for using phage peptide libraries to discover pharmacologically active lead compounds. © 1992 Wiley

ISSN:0887-3585    

DOI:10.1002/prot.340140411

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.340140402

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

年代:1992

数据来源: WILEY