摘要:

AbstractWe report the first atomic resolution structure of an insect virus determined by single crystal X‐ray diffraction. Black beetle virus has a bipartite RNA genome encapsulated in a single particle. The capsid contains 180 protomers arranged on aT= 3 surface lattice. The quaternary organization of the protomers is similar to that observed in theT= 3 plant virus structures. The protomers consist of a basic, crystallographically disordered amino terminus (64 residues), a β‐barrel as seen in other animal and plant virus subunits, an outer protrusion composed predominantly of β‐sheet and formed by three large insertions between strands of the barrel, and a carboxy terminal domain composed of two distorted helices lying inside the shell. The outer surfaces of quasi‐threefold related protomers form trigonal pyramidyl protrusions. A cleavage site, located 44 residues from the carboxy terminus, lies within the central cavity of the protein shell.The structural motif observed in BBV (a shell composed of 180 eight‐stranded antiparallel β‐barrels) is common to all nonstatellite spherical viruses whose structures have so far been solved. This highly conserved shell architecture suggests a common origin for the coat protein of spherical viruses, while the primitive genome structure of BBV suggests that this insect virus represents an early stage in the evolution of spherical viruses from

ISSN:0887-3585    

DOI:10.1002/prot.340020302

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

年代:1987

数据来源: WILEY

摘要:

AbstractThe intron/exon organization of the human gene for glycogen phosphorylase has been determined. The segments of the polypeptide chain that corresponds to the 19 exons of the gene are examined for relationships between the three‐dimensional structure to the protein and gene structure. Only weak correlations are observed between domains of phosphorylase and exons. The nucleotide binding domains that are found in phosphorylase and other glycolytic enzymes are examined for relationships between exons of the genes and structures of the domains. When mapped to the three‐dimensional structures, the intron/exon boundaries are shown to be widely distributed in this family of protein doma

ISSN:0887-3585    

DOI:10.1002/prot.340020303

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

年代:1987

数据来源: WILEY

摘要:

AbstractA method to build a three‐dimensional protein model from nuclear magnetic resonance (NMR) data using fragments from a data base of crystallographically determined protein structures is presented. The interproton distances derived from the nuclear Overhauser effect (NOE) data are compared to the precalculated distances in the known protein structures. An efficient search algorithm is used, which arranges the distancs in matrices akin to a Cα diagonal distance plot, and compares the NOE distance matrices for short sequential zones of the protein to the data base matrices. After cluster analysis of the fragments found in this way, the structure is built by aligning fragments in overlapping zones. The sequentially long‐range NOEs cannot be used in the initial fragments search but are vital to discriminate between several possible combinations of different groups of fragments. The method has been tested on one simulated NOE data set derived from a crystal structure and one experimental NMR data set. The method produces models that have good local structure, but may contain larger global errors. These models can be used as the starting point for further refinement, e.g., by restrained molecular dynamics or interactive grap

ISSN:0887-3585    

DOI:10.1002/prot.340020304

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

年代:1987

数据来源: WILEY

摘要:

AbstractA method is described for rapidly surveying the effects of modifying individual amino acid residues of a protein on its ability to interact specifically with another macromolecule. The procedure has been used to examine the individual roles of the seven lysyl residues of calmodulin in its ability to bind to smooth muscle myosin light chain kinase; previous studies by Jackson et al. (J. Biol. Chem. 261:1226–12232, 1986) have suggested that certain lysines may be located close to the interaction site. Trace [3H]‐acetylated calmodulin, consisting predominantly of molecules acetylated at single sites together with unmodified protein, was incubated in excess (five‐ to 20‐fold) with smooth muscle MLC kinase to allow the modified and unmodified molecules to compete for binding to the enzyme. Subsequently, the calmodulin‐enzyme complex was separated from unbound calmodulin, and the level of acetylation of each of the seven lysines of the bound fraction of calmodulin was determined and compared to that of each corresponding group of the starting preparation. Significant changes were found at only two of the lysines, 21 and 75, where the extent of acetylation in the bound fraction was three‐ and fivefold lower, respectively, than that in the original preparation. These results were reproducible in three separate selection experiments employing both chicken and turkey gizzard MLC kinase. It is concluded that acetylation of calmodulin at either lysine 21 or 75 markedly reduces its affinity for MLC kinase, but acetylation at any of the other lysines (13, 30, 77, 94, or 148) has only minor effects. This finding supports the proposal that the face of the central helix containing lysine 75 is involved in interaction with MLC kinase and suggests also that additional contact near Ca2‐binding

ISSN:0887-3585    

DOI:10.1002/prot.340020305

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

年代:1987

数据来源: WILEY

摘要:

AbstractThe tertiary structure of the α‐subunit of tryptophan synthase was proposed using a combination of experimental data and computational methods. The vacuum‐ultraviolet circular dichroism spectrum was used to assign the protein to the α/β‐class of supersecondary structures. The two‐domain structure of the α‐subunit (Miles et al.:Biochemistry21:2586, 1982; Beasty and Matthews:Biochemistry24:3547, 1985) eliminated consideration of a barrel structure and focused attention on a β‐sheet structure. An algorithm (Cohen et al.:Biochemistry22:4894, 1983) was used to generate a secondary structure prediction that was consistent with the sequence data of the α‐subunit from five species. Three potential secondary structures were then packed into tertiary structures using other algorithms. The assumption of nearest neighbors from second‐site revertant data eliminated 97% of the possible tertiary structures; consideration of conserved hydrophobic packing regions on the β‐sheet eliminated all but one structure. The native structure is predicted to have a parallel β‐sheet flanked on both sides by α‐helices, and is consistent with the available data on chemical cross‐linking, chemical modification, and limited proteolysis. In addition, an active site region containing appropriate residues could be identified as well as an interface for β2‐subunit association. The ability of experimental data to facilitate the predictio

ISSN:0887-3585    

DOI:10.1002/prot.340020306

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

年代:1987

数据来源: WILEY

摘要:

AbstractGlycogen phosphorylases catalzye the regulated breakdown of glycogen to glucose‐1‐phosphate. In mammals, glycogen phosphorylase occurs in three different isozymes called liver, muscle and brain after the tissues in which they are prefer entially expressed. The muscle isozyme binds and is activated cooperatively by AMP. In contrast, the liver enzyme binds AMP noncooperatively and is poorly activated. The amino acid sequence of human liver phosphorylase is 80% identical with rabbit muscle phosphorylase, and those residues which contact AMP are conserved. Using computer graphics software, we replaced side chains of the known rabbit muscle structure with those of human liver phosphorylase and interpreted the effects of these changes in order to account for the biochemical differences between them. We have identified two substitutions in liver phosphorylase potentially important in altering the cooperative binding and activation of this isozyme by

ISSN:0887-3585    

DOI:10.1002/prot.340020307

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

年代:1987

数据来源: WILEY

摘要:

AbstractPositional probability density functions (pdf) for the atomic fluctuations are determined from a molecular dynamics simulation for hen egg‐white lysozyme. Most atoms are found to have motions that are highly anisotropic but only slightly anharmonic. The largest deviations from harmonic motion are in the direction of the largest rms fluctuations in the local principal axis frame. Backbone atoms tend to be more nearly harmonic than sidechain atoms. The atoms with the largest anharmonicities tend to have pdfs with multiple peaks, each of which is close to harmonic. Several model pdfs are evaluated on the basis of how well they fit probability densities from the dynamics simulations when parameterized in terms of the moments of the distribution. Gram‐Charlier and Edgeworth perturbation expansions, which have been successful in describing the motions of small molecules in crystals, are shown to be inadequate for the distributions found in the dynamics of proteins. Multipeaked distribution functions are found to be more appropri

ISSN:0887-3585    

DOI:10.1002/prot.340020308

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

年代:1987

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340020309

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

年代:1987

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340020301

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

年代:1987

数据来源: WILEY