摘要:

AbstractThe structure of porcine pepsinogen at pH 6.1 has been refined to anR‐factor of 0.173 for data extending to 1.65 Å. The final model contains 180 solvent molecules and lacks density for residues 157–161. The structure of this aspartic proteinase zymogen possesses many of the characteristics of pepsin, the mature enzyme. The secondary structure of the zymogen consists predominantly of β‐sheet, with an approximate 2‐fold axis of symmetry. The activation peptide packs into the active site cleft, and the N‐terminus (IP–9P) occupies the position of the mature N‐terminus (1–9). Thus changes upon activation include excision of the activation peptide and proper relocation of the mature N‐terminus. The activation peptide or residues of the displaced mature N‐terminus make specific interactions with the substrate binding subsites. The active site of pepsinogen is intact; thus the lack of activity of pepsinogen is not due to a deformation of the active site. Nine ion pairs in pepsinogen may be important in the advent of activation and involve the activation peptide or regions of the mature N‐terminus which are relocated in the mature enzyme. The activation peptide–pepsin junction, 44P‐1, is characterized by high thermal parameters and weak density, indicating a flexible structure which would be accessible to cleavage. Pepsinogen is an appropriate model for the structures of other zymogens in the aspartic proteinase fam

ISSN:0887-3585    

DOI:10.1002/prot.340130102

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

年代:1992

数据来源: WILEY

摘要:

AbstractWhile cytochrome P‐450cam, catalyzes the hydroxylation of camphor to 5‐exo‐hydroxycamphor with 100% stereospecificity, norcamphor is hydroxylated by this enzyme yielding 45% 5‐exo‐, 47% 6‐exo‐, and 8% 3‐exo‐hydroxynorcamphor (Atkins, W.M., Sligar, S.G., J. Am. Chem. Soc. 109:3754–3760, 1987). The present study describes a 201‐psec molecular dynamics (MD) simulation of norcamphorbound cytochrome P‐450camto elucidate the relationship between substrate conformational mobility and formation of alternative products. First, these data suggest that the product specificity is, at least partially, due to the mobility of the substrate within the active site. Second, the high mobility of norcamphor in the active site leads to an average increase in separation between the home iron and the substrate of about 1.0 Å; this increase in separation may be the cause of the uncoupling of electron transfer when norcamphor is the substrate. Third, the active site water located in the norcamphor‐bound crystal structure possesses mobility that correlates well with the spin‐state equilibrium of this enzyme–substrate c

ISSN:0887-3585    

DOI:10.1002/prot.340130103

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

年代:1992

数据来源: WILEY

摘要:

AbstractA systematic study of single amino acid substitutions in bacteriophage T4 lysozyme permitted a test of the concept that conserved amino acid residues are more functionally important than nonconserved residues. Substitutions of amino acid residues that are conserved among five bacteriophage‐encoded lysozymes were found to lead more frequently to loss of function than substitutions of nonconserved residues. Of 163 residues tested, only 74 (45%) are sensitive to at least one substitution; however, all 14 residues that are fully conserved are sensitive to substitutions. © 1992 Wiley‐Liss,

ISSN:0887-3585    

DOI:10.1002/prot.340130104

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

年代:1992

数据来源: WILEY

摘要:

AbstractWhile investigating the expression of theSaccharomyces cerevisiaemyristoyl‐CoA:protein N‐myristoyltransferase gene (NMT: E.C. 2.3.1.97) by Northern blot analysis, we observed another RNA transcript whose expression resembled that ofNMT1during meiosis and was derived from a gene located<1 kb immediately upstream ofNMT1. This new gene, designatedPWP1(for periodic tryptophan protein), is divergently transcribed fromNMT1and encodes a 576‐residue protein. Null mutants ofPWP1are viable, but their‐growth is severely retarded and steady‐state levels of several cellular proteins (including at least two proteins that label with exogenous [3H]myristic acid) are drastically reduced. New methods for database searching and assessing the statistical significance of sequence similarities identicPWP1as a member of the β‐transducin protein superfamily. Two other previously unrecognized β‐transducin‐like proteins (S. cerevisiae MAKI1andD. discoideumAAC3) were also identified, and an unexpectedly high degree of sequence homology was found between aChlamydomonasβ‐like polypeptide and the C12.3 gene of chickens. A systematic and quantitative comparative analysis resulted in classifying all β‐transducin‐like sequences into II nonorthologous families. Based on specific sequence attributes, however, not all β‐transducin‐like sequences are expected to be functionally similar, and quantitative criteria for inferring functional analogies are discussed. Possible roles of repetitive tryptophan residues in proteins are also considered.

ISSN:0887-3585    

DOI:10.1002/prot.340130105

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

年代:1992

数据来源: WILEY

摘要:

AbstractA recently developed algorithm, called Convex Constraint Analysis (CCA), was successfully applied to determine the circular dichroism (CD) spectra of thepureβ‐pleated sheetin globular proteins. On the basis of X‐ray diffraction determined secondary structures, the original data set used (Perczel, A., Hollosi, M., Tusnady, G. Fasman, G.D. Convex constraint analysis: A natural deconvolution of circular dichroism curves of proteins, Prot. Eng.,4:‐669–679, 1991), was improved by the addition of proteins with high β‐pleated sheet content. The analysis yielded CD curves of the pure components of the main secondary structural elements (α‐helix, antiparallel β‐pleated sheet, β‐turns, and unordered conformation), as well as a curve attributed to the “aromatic contribution” in the wavelength range of 195–240 nm. Upon deconvolution the curves obtained were assigned to various secondary structures. The calculated weights (percentages determining the contributions of each pure component curve in the measured CD spectra of a given protein) were correlated with the X‐ray diffraction determined percentages in an assignment procedure and were evaluated. The Pearson product correlation coefficients (R) are significant for all five components. The new pure component curves, which were obtained through deconvolution of the protein CD spectra alone, are promising candidates for determining the percentages of the secondary structural components in globular proteins without the necessity of adopting an X‐ray database. The CD spectrum of the CheY protein was interesting because it has the characteristic shape associated with the α‐helical structure, but upon analysis yielded a considerable amount of β‐sheet in agreement with the X

ISSN:0887-3585    

DOI:10.1002/prot.340130106

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

年代:1992

数据来源: WILEY

摘要:

AbstractComputer simulation of the conformations of short antigenic peptides (5–10 residues) either free or bound to their receptor, the major histocompatibility complex (MHC)‐encoded glycoprotein H‐2 Ld, was employed to explain experimentally determined differences in the antigenic activities within a set of related peptides. Starting for each sequence from the most probable conformations disclosed by a pattern‐recognition technique, several energy‐minimized structures were subjected to molecular dynamics simulations (MD) either in vacuo or solvated by water molecules. Notably, antigenic potencies were found to correlate to the peptides propensity to form and maintain an overall α‐helical conformation through regulari,i+4 hydrogen bonds. Accordingly, less active or inactive peptides showed a strong tendency to formi,i+3 hydrogen bonds at their N‐terminal end. Experimental data documented that the C‐terminal residue is critical for interaction of the peptide with H‐2 Ld. This finding could be satisfactorily explained by a 3‐D Q.S.A.R. analysis postulating interactions between ligand and receptor by hydrophobic forces. A 3‐D model is proposed for the complex between a high‐affinity nonapeptide and the H‐2 Ldreceptor. First, the H‐2 Ldmolecule was built from X‐ray coordinates of two homologous proteins: HLA‐A2 and HLA‐Aw68, energy‐minimized and studied by MD simulations. With HLA‐A2 as template, the only realistic simulation was achieved for a solvated model with minor deviations of the MD mean structure from the X‐ray conformation. Water simulation of the H‐2 Ldprotein in complex with the antigenic nonapeptide was then achieved with the template‐derived optimal parameters. The bound peptide retains mainly its α‐helical conformation and binds to hydrophobic residues of H‐2 Ldthat correspond to highly polymorphic positions of MHC proteins. The orientation of the nonapeptide in the binding cleft is in accordance with the experimentally determined distribution of its MHC receptor‐binding residues (agretope residues). Thus, computer simulation was successfully employed to explain functional data and predicts α‐helical conf

ISSN:0887-3585    

DOI:10.1002/prot.340130107

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.340130101

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

年代:1992

数据来源: WILEY