ISSN:
0006-3525
Keywords:
Chemistry
;
Polymer and Materials Science
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
Notes:
We developed an efficient Monte Carlo Simulated Annealing (MCSA) program for modeling protein loops with high speed. The total conformational energy in each step of MCSA simulation consists of two parts: the nonbonded atomic interaction represented by a simple soft-sphere potential and the harmonic distance constraint to ensure the smooth connection of the loop segment to the rest of the protein structure. The soft-sphere potential was a simplified potential that has been successfully used by the authors in modeling the carbohydrate part of glycoprotein systems [H. Zhang, Y. Yang, L. Lai, and Y. Tang (1996), Carbohydrate Research, Vol. 284, pp. 25-34]. It only considers the purely repulsive steric interactions to avoid artificial attractive forces between atoms in the absence of solvent molecules. The N-terminal of the loop segment was connected to the bulk protein part, and two dummy main-chain atoms N and Cα immediately following the C-terminal of the loop segment were constrained to their real positions in the protein structure, which not only assures the correct geometry of loop-protein connection but also is more rigorous than the previous work. To improve the speed, two strategies, the local region method and grid-mapping method, were devised to accelerate the computation of environmental interaction that is responsible for the major part of the computing consumption. The grid-mapping method can reduce computational time dramatically. Conformations with rational steric packing and smooth connection to the rest of the protein structure were generated by the MCSA program, and then were refined by the empirical force field CHARMm [B. R. Brook, R. E. Braccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus (1983), Journal of Computational Chemistry, Vol. 4, pp. 187-217]. Bovine pancreatic trypsin inhibitor (BPTI) was used as an example to test the ability of loop modeling of the method, and five loops in BPTI were calculated. Conformations close to the crystal structure were generated for all of them. With the criteria of CHARMm energy, near-native conformations can be selected, for example, the backbone rms deviation 0.93 A from the crystal structure was gotten for the longest 9-residue loop. © 1997 John Wiley & Sons, Inc.
Additional Material:
6 Ill.
Type of Medium:
Electronic Resource
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