摘要:

AbstractX‐ray absorption fine structure experiments were performed to study structural and dynamic aspects of the active site of various forms of myoglobin. The structures determined for deoxyMb, MbCO, and MbO2are consistent with the structure established by X‐ray absorption fine structure experiment and X‐ray crystallography. The first shell of ferrous MbNO determined contains 5 nitrogens located at 2.02 Å and a short NO bond length of 1.76 Å. This study focuses on the change of the XAFS Debye–Waller factor with temperature, which is a measure of thermal and static disorder. It was found that the changes of Debye–Waller factor with temperature for the Mb proteins, except deoxyMb, are consistent with a simple Einstein model, in which a single frequency was assumed for the bond stretching modes. In contrast, the temperature dependence of deoxyMb cannot be fitted to the Einstein model and a large disorder was found at low temperatures, which indicates the existence of conformational substates of the

ISSN:0887-3585    

DOI:10.1002/prot.340100402

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

年代:1991

数据来源: WILEY

摘要:

AbstractIt was recently found that some short peptides (including C‐ and S‐peptide fragments of RNase A) can have considerable helicity in solution,1–12which was considered to be surprising. Does the observed helicity require a new explanation, or is it consistent with previous understanding? In this work we show that this helicity is consistent with the physical theory of secondary structure12–19based on an extension of the conventional Zimm‐Bragg model.20Without any special modifications, this theory explains reasonably well almost all the experimentally observed dependencies of helicity on pH, temperature, and amino acid replacements. We conclude that the observed “general level” of helicity of C‐ and S‐peptides (5–30% at room temperature and 10–50% near 0°C) is “normal” for short peptides consisting mainly of helix‐forming and helix‐indifferent residues. The helicity is modified by a multitude of weak specific side chain interactions, many of which are taken into account by the present theory;13–19some discrepancies between the theory and experiment can be explained by weak side‐chain‐side chain interactions that were neglected. A reasonable coincidence of the theory with experiment suggests that it had been used to investigate the role of local interactions in the formation of α‐helic

ISSN:0887-3585    

DOI:10.1002/prot.340100403

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

年代:1991

数据来源: WILEY

摘要:

AbstractThree types of polypeptide surface area (contact, accessible, and molecular) have been studied as a function of the radius of a probe sphere used to map the surface. The surfaces are: (1) three α‐helices, the H‐helix of myoglobin, the E‐helix of leghemoglobin, and an artificial polyalanine helix, each with 26 residues; (2) two globins, myoglobin and leghemoglobin, each with 153 residues: and (3) a two center model system for which the three types of surface area have been calculated analytically. The two globin helices have almost identical surface areas as a function of probe size as do the two globins. The polyalanine helix surface area is smaller but similar in shape to the globin helix areas. All three helix contact areas tend to the same limit as the probe size increases, and the globin contact areas behave similarly. Fractal dimensions were calculated for the helix and globin contact and molecular surfaces. All fractal dimensions showed strong dependence on probe size. The contact fractal dimension peaks at larger values for both the helices and globins. Most residues do not make contact with large probes

ISSN:0887-3585    

DOI:10.1002/prot.340100404

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe effects of ligands on the conformation of yeast phosphoglycerate kinase were explored by introducing cysteinyl residues at different positions in the molecule by site‐directed mutagenesis. Thus several mutants were constructed, each containing a unique cysteinyl residue. Neither the conformation nor the enzyme activity was affected by the substitutions. The reactivity of the thiol groups and the fluorescence of N‐acetyl‐N′‐(5‐sulfo‐1‐naphtyl)ethylene‐diamine covalently linked to these thiols were used to monitor the conformational changes induced upon ligand binding.It was found that the observed changes mainly involve the part of the protein located in the cleft, particularly the environment of residues 35 and 183. No alteration was observed on the external side of the protein. Only 3‐Phosphoglycerate induced these conformational changes. However, when the fluorescent probe was attached to residue 377, the binding of the two substrates was required to induce a modification in the fluorescence of the probe. These results indicate that the substrates separately or together induce discrete molecular motions in phos

ISSN:0887-3585    

DOI:10.1002/prot.340100405

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe different isolates available for HIV‐1 and HIV‐2 were compared for the region of the protease (PR) sequence, and the variations in amino acids were analyzed with respect to the crystal structure of HIV‐1 PR with inhibitor. Based on the extensive homology (39 identical out of 99 residues), models were built of the HIV‐2 PR complexed with two different aspartic protease inhibitors, acetylpepstatin and a renin inhibitor, H‐261. Comparison of the HIV‐1 PR crystal structure and the HIV‐2 PR model structure and the analysis of the changes found in different isolates showed that correlated substitutions occur in the hydrophobic interior of the molecule and at surface residues involved in ionic or hydrogen bond interactions. The substrate binding residues of HIV‐1 and HIV‐2 PRs show conservative substitutions of four residues. The difference in affinity of HIV‐1 and HIV‐2 PRs for the two inhibitors appears to be due in part to the change of Val 32 in HIV‐

ISSN:0887-3585    

DOI:10.1002/prot.340100406

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

年代:1991

数据来源: WILEY

摘要:

AbstractConformational disorder in crystal structures of ribonuclease‐A and crambin is studied by including two independent structures in least‐squares optimizations against X‐ray data. The optimizations are carried out by X‐ray restrained molecular dynamics (simulated annealing refinement) and by conventional least‐squares optimization. Starting from two identical structures, the optimizations against X‐ray data lead to significant deviations between the two, with rms backbone displacements of 0.45 Å for refinement of ribonuclease at 1.53 Å resolution, and 0.31 Å for crambin at 0.945 Å. More than 15 independent X‐ray restrained molecular dynamics runs have been carried out for ribonuclease, and the displacements between the resulting structures are highly reproducible for most atoms. These include residues with two or more conformations with significant dihedral angle differences and alternative hydrogen bonding, as well as groups of residues that undergo displacements that are suggestive of rigid‐body librations. The crystallographicR‐values obtained are ≈ 13%, as compared to 15.3% for a comparable refinement with a single structure. Least‐squares optimization without an intervening restrained molecular dynamics stage is sufficient to reproduce most of the observed displacements. Similar results are obtained for crambin, where the higher resolution of the X‐ray data allows for refinement of unconstrained individual anisotropic temperature factors. These are shown to be correlated with the displacements in th

ISSN:0887-3585    

DOI:10.1002/prot.340100407

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

年代:1991

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340100408

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

年代:1991

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340100401

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

年代:1991

数据来源: WILEY