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1.
Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin 总被引:5,自引:0,他引:5
A new methodology for theoretically predicting the native, three-dimensional structure of a polypeptide is presented. Based on equilibrium statistical mechanics, an algorithm has been designed to determine the probable conformation of a polypeptide by calculating conditional free-energy maps for each residue of the macromolecule. The conditional free-energy map of each residue is computed from a set of probability integrals, obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. By locating the region(s) of lowest free energy for each map, the probable conformation for each residue can be identified. The native structure of the polypeptide is assumed to be the combination of the probable conformations of the individual residues. All multidimensional probability integrals are evaluated by an adaptive Monte Carlo algorithm (SMAPPS —Statistical-Mechanical Algorithm for Predicting Protein Structure). The Monte Carlo algorithm searches the entire conformational space, adjusting itself automatically to concentrate its sampling in regions where the magnitude of the integrand is largest (“importance sampling”). No assumptions are made about the native conformation. The only prior knowledge necessary for the prediction of the native conformation is the amino acid sequence of the polypeptide. To test the effectiveness of the algorithm, SMAPPS was applied to the prediction of the native conformation of the backbone of Met-enkephalin, a pentapeptide. In the calculations, only the backbone dihedral angles (? and ψ) were allowed to vary; all side-chain (χ) and peptide-bond (ω) dihedral angles were kept fixed at the values corresponding to the alleged global minimum energy previously determined by direct energy minimization. For each conformation generated randomly by the Monte Carlo algorithm, the total conformational energy of the polypeptide was obtained from established empirical potential energy functions. Solvent effects were not included in the computations. With this initial application of SMAPPS , three distinct low-free-energy β-bend structures of Met-enkephalin were found. In particular, one of the structures has a conformation remarkably similar to the one associated with the previously alleged global minimum energy. The two additional structures of the pentapeptide have conformational energies lower than the previously computed low-energy structure. However, the Monte Carlo results are in agreement with an improved energy-minimization procedure. These initial results on the backbone structure of Met-enkephalin indicate that an equilibrium statistical-mechanical procedure, coupled with an adaptive Monte Carlo algorithm, can overcome many of the problems associated with the standard methods of direct energy minimization. 相似文献
2.
Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. II. Average backbone structure of enkephalin 总被引:3,自引:0,他引:3
The average conformation of Met-enkephalin was determined by using an adaptive, importance-sampling Monte Carlo algorithm (SMAPPS—Statistical Mechanical Algorithm for Predicting Protein Structure). In the calculation, only the backbone dihedral angles (? and ψ) were allowed to vary; i.e., all side-chain (χ) and peptide-bond (ω) dihedral angles were kept fixed at the values corresponding to a low-energy structure of the pentapeptide. The total conformational energy for each randomly generated structure of the polypeptide was obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. The interaction energies were computed by the program ECEPP/2 (Empirical Conformational Energy Program for Peptides). Solvent effects were not included in the computation. The calculation was repeated until a total of 10 independent average conformations were established. The regions of conformational space occupied by the average structures were compared with the regions of low conditional free energy obtained by SMAPPS in the first paper of this series. Such a comparison provides an analysis of the capacity of SMAPPS to adjust the Monte Carlo search to regions of highest probability. The results demonstrate that the ability of SMAPPS to focus the Monte Carlo search is excellent. Finally, the 10 independent average conformations and the mean of the 10 average structures were utilized as the initial conformations for a direct energy minimization of the pentapeptide. Of the 11 final energy-minimized structures, three of the conformations were found to be equivalent to the conformation of lowest energy determined previously. In addition, all but two of the remaining energy-minimized structures were found to correspond to one of the two other conformations of high probability obtained in the first paper of this series. These results indicate that a set of independent average conformations can provide a rational, unbiased choice for the initial conformation, to be used in a direct energy minimization of a polypeptide. The final energy-minimized structures consequently constitute a set of low-energy conformations, which include the global energy minimum. 相似文献
3.
M D Shenderovich G V Nikiforovich A A Golbraikh 《International journal of peptide and protein research》1991,37(4):241-251
Theoretical conformational analysis was carried out for several tetrapeptide analogues of beta-casomorphin and dermorphin containing a Phe residue in position 3. Sets of low-energy backbone structures of the mu-selective peptides [N-Me-Phe3, D-Pro4]-morphiceptin and Tyr-D-Orn-Phe-Asp-NH2 were obtained. These sets of structures were compared for geometrical similarity between themselves and with the low-energy conformations found for the delta-selective peptide Tyr-D-Cys-Phe-D-Pen-OH and nonactive peptide Tyr-Orn-Phe-Asp-NH2. Two pairs of geometrically similar conformations of mu-selective peptides, sharing no similarity with the conformations of peptides showing low affinity to the mu-receptor, were selected as two alternative models of probable mu-receptor-bound backbone conformations. Both models share geometrical similarity with the low-energy structures of the linear mu-selective peptide Tyr-D-Ala-Phe-Phe-NH2. Putative binding conformations of Tyr1 and Phe3 side chains are also discussed. 相似文献
4.
Methionine enkephalin and isosteric analogues. Part II.: Receptor conformation of methionine enkephalin 总被引:1,自引:0,他引:1
D Hudson R Sharpe M Szelke 《International journal of peptide and protein research》1980,15(2):122-129
Biological activities are reported for two different types of analogues of methionine enkephalin. Cyclic analogues, bridged between the amino- and carboxy- terminals of the parent peptide, are inactive. In contrast, significant levels of activity are displayed by linear isosterically modified analogues in which the Tyr1-Gly2 peptide bond is replaced by either -CH2NH- or -CH2CH2-. Similar replacements of the Gly2-Gly3 peptide bond yield compounds with much reduced potency. These modifications serve as useful probes of the receptor conformation. Based on these findings, a model is proposed for interaction between enkephalin and its receptor. 相似文献
5.
Conformational energy calculations were carried out for beta-endorphin. Its spatial structure can be described by nine low-energy conformations. The calculations yielded the values of all dihedral angles of the backbone and side chains of these forms as well as intra- and inter-residue interaction energies. 相似文献
6.
P P Batra 《Biochimie》1991,73(11):1397-1402
Ovalbumin was reacted with a 960-fold molar excess of citraconic anhydride, and 91% of the epsilon-amino groups, representing 18 of the 20 lysine residues, were citraconylated. As detected by fluorescence and far-ultraviolet circular dichroic (CD) measurements, the modified protein displayed significant disruption of the native conformation. Treatment at pH 2.2 for 5 h resulted in the hydrolysis of 10 of the 18 citraconyl groups, but when subjected to the acid conditions for 12 h, all 18 modifying groups were removed. Electrophoretically, the 5-h and the 12-h acid-treated proteins were homogeneous and showed decreasing anodic mobility at pH 8.3; indeed, the anodic mobility of the 12-h acid-treated protein was identical to that of the native protein. Similarly, the 12-h acid-treated protein possessed conformational properties almost indistinguishable from the native protein. These properties included similar emission fluorescence spectra and far-ultraviolet CD spectra, similar resistance to undergoing helix-to-coil transition at pH 12.2, and identical urea unfolding curves, and thus identical urea transition mid-point of about 8.0 M. These observations indicate that the protein with all the epsilon-amino groups regenerated by acid treatment has the same conformational stability as the native ovalbumin. 相似文献
7.
Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide. 总被引:2,自引:1,他引:2
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A. Liwo M. R. Pincus R. J. Wawak S. Rackovsky H. A. Scheraga 《Protein science : a publication of the Protein Society》1993,2(10):1715-1731
Based on the concept that hydrophobic interactions cause a polypeptide chain to adopt a compact structure, a method is proposed to predict the structure of a protein. The procedure is carried out in four stages: (1) use of a virtual-bond united-residue approximation with the side chains represented by spheres to search conformational space extensively using specially designed interactions to lead to a collapsed structure, (2) conversion of the lowest-energy virtual-bond united-residue chain to one with a real polypeptide backbone, with optimization of the hydrogen-bond network among the backbone groups, (3) perturbation of the latter structure by the electrostatically driven Monte Carlo (EDMC) procedure, and (4) conversion of the spherical representation of the side chains to real groups and perturbation of the whole molecule by the EDMC procedure using the empirical conformational energy program for peptides (ECEPP/2) energy function plus hydration. Application of this procedure to the 36-residue avian pancreatic polypeptide led to a structure that resembled the one determined by X-ray crystallography; it had an alpha-helix starting at residue 13, with the N-terminal portion of the chain in an extended conformation packed against the alpha-helix. Similar structures with slightly higher energies, but looser packing, were also obtained. 相似文献
8.
9.
Peterson JR Bickford LC Morgan D Kim AS Ouerfelli O Kirschner MW Rosen MK 《Nature structural & molecular biology》2004,11(8):747-755
Current drug discovery efforts focus primarily on proteins with defined enzymatic or small molecule binding sites. Autoregulatory domains represent attractive alternative targets for small molecule inhibitors because they also occur in noncatalytic proteins and because allosteric inhibitors may avoid specificity problems inherent in active site-directed inhibitors. We report here the identification of wiskostatin, a chemical inhibitor of the neural Wiskott-Aldrich syndrome protein (N-WASP). Wiskostatin interacts with a cleft in the regulatory GTPase-binding domain (GBD) of WASP in the solution structure of the complex. Wiskostatin induces folding of the isolated, unstructured GBD into its autoinhibited conformation, suggesting that wiskostatin functions by stabilizing N-WASP in its autoinhibited state. The use of small molecules to bias conformational equilibria represents a potentially general strategy for chemical inhibition of autoinhibited proteins, even in cases where such sites have not been naturally evolved in a target. 相似文献
10.
The secondary structures of the histones, H1, H2A, H2B, H3, and H4 have been predicted utilizing the predictive scheme of Chou and Fasman (Biochemistry 13:211, 222[1974]) and a new set of conformational parameters based on the X-ray data of 29 protein structures. The alpha-helical, beta-sheet, reverse beta-turns, and random coil regions of these proteins are carefully delineated. Structures are specified which are most probably under various environmental conditions, i.e., for changes in ionic strength, association between histones and in association with DNA. Potential conformational changes within these histones are also predicted. 相似文献
11.
Using a semi-empirical method, an a priori conformational analysis of the [Met]-enkephalin molecule was carried out. Calculations yielded the values of all dihedral angles of the backbone and side chains of the peptide's forms as well as intra- and inter-residue interaction energies. 相似文献
12.
Fluorescence study on the conformation of a cyclic enkephalin analog in aqueous solution 总被引:1,自引:0,他引:1
P W Schiller 《Biochemical and biophysical research communications》1983,114(1):268-274
Certain patients with ovarian germ cell tumors develop a specific antibody reacting with glycoprotein-bound large carbohydrates of murine teratocarcinoma cells. The antigenic determinant was found to involve an alpha-galactosyl residue, since alpha-galactosidase from coffee bean, but not other glycosidases abolished the antigenic activity of the large glycan isolated from F9 and OTT6050 cells. Several evidences excluded the possibility that the antigen is blood group B or P1 antigen. These results indicate tumor-associated expression of an unusual alpha-galactosyl residue in human ovarian germ cell tumors. 相似文献
13.
Necleoside conformations. 19. Temperature and pH effects on the conformation of guanosine phosphates.
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Proton magnetic resonance spectra at 250 MHz were measured as a function of temperature and pH of the three guanosine phosphates. From these data and previously published work the conformational parameters of these compounds were determinated. The phosphate group of Guo-5'-P changes its conformation around the C-O bond and its rotation is relatively slow at 20 degrees. At neutral pD the S conformation is favoured and the N form at acid pD. This conformational change is paralleled by a change in exocyclic rotamer distribution and takes place at the pK of the protonation of the base on N-7. Although correlation appears to exist between the various conformations, notable exceptions exist. 相似文献
14.
A new approach of predicting structural classes of protein domain sequences is presented in this paper. Besides the amino acid composition, the composition of several dipeptides, tripeptides, tetrapeptides, pentapeptides and hexapeptides are taken into account based on the stepwise discriminant analysis. The result of jackknife test shows that this new approach can lead to higher predictive sensitivity and specificity for reduced sequence similarity datasets. Considering the dataset PDB40-B constructed by Brenner and colleagues, 75.2% protein domain sequences are correctly assigned in the jackknife test for the four structural classes: all-alpha, all-beta, alpha/beta and alpha + beta, which is improved by 19.4% in jackknife test and 25.5% in resubstitution test, in contrast with the component-coupled algorithm using amino acid composition alone (AAC approach) for the same dataset. In the cross-validation test with dataset PDB40-J constructed by Park and colleagues, more than 80% predictive accuracy is obtained. Furthermore, for the dataset constructed by Chou and Maggiona, the accuracy of 100% and 99.7% can be easily achieved, respectively, in the resubstitution test and in the jackknife test merely taking the composition of dipeptides into account. Therefore, this new method provides an effective tool to extract valuable information from protein sequences, which can be used for the systematic analysis of small or medium size protein sequences. The computer programs used in this paper are available on request. 相似文献
15.
A G Fincham 《The Biochemical journal》1979,181(1):171-175
A simple, reproducible gel-filtration procedure for the isolation of one of the major 'J-Group' polypeptides of the bovine foetal dental-enamel matrix is described. The purified polypeptide was characterized by amino acid analysis, electrophoresis, cleavage with CNBr and N-terminal analyses. The isolated component is shown to be closely similar to an amelogenin component described by other workers. 相似文献
16.
Y Sasaki-Yagi S Kimura Y Imanishi 《International journal of peptide and protein research》1991,38(4):378-384
The opioid receptor binding of [Leu]enkephalin derivatives with extended address segment to the C-terminal was studied. The extension peptide is designed to take an amphiphilic helical structure in order to evaluate effects of helical conformation and membrane affinity of enkephalin moiety of the derivatives on receptor binding. In the delta-receptor-selective binding assay, Tyr-Gly-Gly-Phe-Leu-Lys-Aib-Leu-Aib-OH (1) showed the same affinity as enkephalinamide, whereas in the mu-receptor-selective binding assay, a 7-fold reduction in affinity was observed. On the other hand, Tyr-Gly-Gly-Phe-Leu-(Lys-Aib-Leu-Aib)2-OH (2) showed 51- and 96-fold decreases in affinities for delta- and mu-receptors, respectively, compared with enkephalinamide. The low receptor affinity of derivative 2 is considered due to alpha-helical conformation, which might not be compatible with topological requirements of delta- and mu-receptors. A dimer, Tyr-Gly-Gly-Leu-Phe-(Lys-Aib-Leu-Aib)2-Lys(X)-Aib-OCH3 (X = Tyr-Gly-Gly-Phe-Leu-, (4], showed 2.5- and 3.0-fold increases in affinities respectively for delta- and mu-receptors compared with the monovalent derivative 2, possibly due to cross-linking of neighboring receptors. The Hill plot of the binding of the dimer to bovine brain membranes was composed of two phases, although such a heterogeneity of receptors was not observed in the presence of naloxone or in the binding to NG108-15 cell membranes. These findings indicate the presence of the bivalent-ligand-induced interactions between delta- and mu-receptors in bovine brain membranes. 相似文献
17.
A V Finkel'shte?n 《Molekuliarnaia biologiia》1976,10(2):507-513
For all the 20 natural amino acid residues the conformations, permitted by taking into account steric interactions (a small variation of valent angles was admitted) and interactions with the solvent (water) were singled out. 相似文献
18.
Formulations of conformational weights for helix-coil transitions can be extended to substantially more complex situations than are usually pursued. General rules for matrix multiplication that depend parametrically on the interaction ranges and numbers of rotamers of residues are presented. The orders of the matrices of statistical weights can be increased with chain length, so that an individual matrix element can represent any specified single conformation, as needed. By the appropriate choice of interaction ranges and numbers of available conformers, approximations can be introduced in which: (1) an average of the conformations of any chain segment is obtained, (2) specific residue-residue interactions are excluded, or (3) the conformation of a part of the chain is restricted or fixed. The method is appropriate for treating specific interactions in peptides and could be used together with available experimental information to develop models of conformational transitions. As such, the methods represent a class of calculations aimed at more rigorous calculations built around known features of a molecule. The aim is to facilitate calculations that bridge the gap between nonquantitative molecular model building and more rigorous but less directed molecular mechanics calculations. The method can directly include any desired longer range of interactions, if the interaction range is not too long to make impossible the manipulation of the requisite matrices. An outline is presented of an application to treat salt bridges in the C peptide of ribonuclease A. 相似文献
19.
L I Larsson 《The journal of histochemistry and cytochemistry》1979,27(9):1283-1284
Immunocytochemical studies habe shown that many peptides which profoundly affect the endocrine and exocrine functions of the pancreas are localized to neurons. In the cat, such peptidergic nerves appear to innervate ganglia, islets and blood vessels of the pancreas, whereas their contributions to exocrine cells are minor. Our studies suggest that pancreatic ganglia represent one major site of action of the peptides and that, in addition, nerves containing the vasoactive intestinal polypeptide and gastrin/CCK-related peptides profoundly affect pancreatic blood flow and insulin secretion, respectively. 相似文献
20.