摘要:

AbstractAmong the known regulatory proteins that are conformationally sensitive to the binding of calcium ions, calmodulin and troponin‐C have the greatest primary sequence homology. This observation has led to the conclusion that the most accurate predicted molecular model of calmodulin would be based on the X‐ray crystallographic coordinates of the highly refined structure of turkey skeletal troponin‐C. This paper describes the structure of calmodulin built from such a premise. The resulting molecular model was subjected to conjugate gradient energy minimization to remove unacceptable intramolecular non‐bonded contacts. In the analysis of the resulting structure, many features of calmodulin, including the detailed conformation of the Ca2+‐binding loops, the amino‐ and carboxy‐terminal hydrophobic patches of the Ca2+‐bound form, and the several clusters of acidic residues can be reconciled with much of the previously published solution data. Calmodulin in missing the N‐terminal helix characteristic of troponin‐C. The deletion of three residues from the central helical linker (denoted D/E in troponin‐D) shortens the molecule and changes the orientation of the two domains of calmodulin by 60° relative to those in troponin‐C. The molecular model has been used to derive two possible binding sites for the antipsychotic drug trifluoperazine, a potent competitive inhibito

ISSN:0887-3585    

DOI:10.1002/prot.340030102

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

年代:1988

数据来源: WILEY

摘要:

AbstractAn orthorhombic crystal form oftrprepressor (aporepressor plus L‐tryptophan ligand) was solved by molecular replacement, refined to 1.65 Å resolution, and compared to the structure of the repressor in trigonal crystals. Even though these two crystal forms of repressor were grown under identical conditions, the refined structures have distinctly different conformations of the DNA‐binding domains. Unlike the repressor/aporepressor structural transition, the conformational shift is not caused by the binding or loss of the L‐tryptophan ligand. We conclude that while L‐tryptophan binding is essential for forming a specific complex withtrpoperator DNA, the corepressor ligand does not lock the repressor into a single conformation that is complementary to the operator. This flexibility may be required by the various binding modes proposed fortrprepressor in its search for and adherence to its three different operat

ISSN:0887-3585    

DOI:10.1002/prot.340030103

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

年代:1988

数据来源: WILEY

摘要:

AbstractElectrostatic interactions between pairs of atoms in proteins are calculated with a model based on the linearized Poisson‐Boltzmann equation. The equation is solved accurately by a method that takes into account the detailed shape of the protein. This paper presents applications to several systems. Experimental data for the interaction of ionized residues with an active site histidine in subtilisin BPN' allow the model to be tested, using various assumptions for the electrical properties of the protein and solvent. The electrostatic stabilization of the active site thiolate or rhodanese is analyzed, with attention to the influence of α‐helices. Finally, relationships between electrostatic potential and charge‐charge distance are reported for large and small globular proteins. The above results are compared with those of simpler electrostatic models, including Coulomb's law with both a distance‐dependent dielectric constant (ϵ = R) and a fixed dielectric constant (ϵ = 2), and Tanford‐Kirkwood theory. The primary conclusions are as follows: (1) The Poisson‐Boltzmann model agrees with the subtilisin data over a range of ionic strengths; (2) two α‐helices generate a large potential in the active site of rhodanese; (3) ϵ = R overestimates weak electrostatic interactions but yields relatively good results for strong ones; (4) Tanford‐Kirkwood theory is a useful approximation to detailed solutions of the linearized Poisson‐Boltzmann equation in globular proteins; and (5) the modified Tanford‐Kirkwood theory overscreens the measured electrostatic in

ISSN:0887-3585    

DOI:10.1002/prot.340030104

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

年代:1988

数据来源: WILEY

摘要:

AbstractPlant ribosome‐inhibiting proteins are shown to be homologous at the domain level to RNase H formEscherichia coliand to two regions of thepolgene product of retroviral reverse transcriptases. One of these regions carries the viral integrase orintfunction, while the other has previously been suggested to contain the viral RNase H exo activity. Several residues conserved among the ribosome inhibitors,E. coliRNase H, and the integrase proteins are seen to occupy a prominent cleft in the tertiary structure of the ribosome inhibitor ricin, suggesting roles in binding or catalysis. It is likely that these homologous sequences represent modern derivatives of an ancient protein‐folding unit capable of nucleic acid binding and modification which has been incorporated into a variety of enzyme functi

ISSN:0887-3585    

DOI:10.1002/prot.340030105

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

年代:1988

数据来源: WILEY

摘要:

AbstractM protein is considered a virulence determinant on the streptococcal cell wall by virtue of its ability to allow the organism to resist attack by human neutrophils. The complete DNA sequence of the M6 gene from streptococcal strain D471 has allowed, for the first time, the study of the structural characteristics of the amino acid sequence of an entire M protein molecule. Predictive secondary structural analysis revealed that the majority of this fibrillar molecule exhibits strong alpha‐helical potential and that, except for the ends, nonpolar residues in the central region of the molecule exhibit the 7‐residue periodicity typical for coiled‐coil proteins. Differences in this heptad pattern of nonpolar residues allow this central rod region to be divided into three subdomains which correlate essentially with the repeat regions A, B, and C/D in the M6 protein sequence. Alignment of the N‐terminal half of the M6 sequence with PepM5, the N‐terminal half of the M5 protein, revealed that 42% of the amino acids were identical. The majority of the identities were “core” nonpolar residues of the heptad periodicity which are necessary for the maintenance of the coiled coil. Thus, conservation of structure in a sequence‐variable region of these molecules may be biologically significant. Results suggest that serologically different M proteins may be built according to a basic scheme: an extended central coiled‐coil rod domain (which may vary in size among strains) flanked by funct

ISSN:0887-3585    

DOI:10.1002/prot.340030106

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

年代:1988

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340030101

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

年代:1988

数据来源: WILEY