On achieving better than 1-A accuracy in a simulation of a large protein: Streptomyces griseus protease A.

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TitleOn achieving better than 1-A accuracy in a simulation of a large protein: Streptomyces griseus protease A.
Publication TypeJournal Article
Year of Publication1993
AuthorsKitson, DH, Avbelj, F, Moult, J, Nguyen, DT, Mertz, JE, Hadzi, D, Hagler, AT
JournalProc Natl Acad Sci U S A
Volume90
Issue19
Pagination8920-4
Date Published1993 Oct 1
ISSN0027-8424
KeywordsBacterial Proteins, Computer Simulation, Kinetics, Models, Molecular, Protein Structure, Secondary, Serine Endopeptidases, Software, Streptomyces griseus, Time Factors, X-Ray Diffraction
Abstract

Computational methods are frequently used to simulate the properties of proteins. In these studies accuracy is clearly important, and the improvement of accuracy of protein simulation methodology is one of the major challenges in the application of theoretical methods, such as molecular dynamics, to structural studies of biological molecules. Much effort is being devoted to such improvements. Here, we present an analysis of a 187-ps molecular dynamics simulation of the serine protease Streptomyces griseus protease A in its crystal environment. The reproduction of the experimental structure is considerably better than has been achieved in earlier simulations--the root mean square deviation of the simulated structure from the x-ray structure being less than 1 A, a significant step toward the goal of simulating proteins to within experimental error. The use of a longer cutoff with truncation rather than a switching function, inclusion of all crystalline water and the counterions in the crystallization medium, and use of the consistent valence force field characterize the differences in this calculation.

Alternate JournalProc. Natl. Acad. Sci. U.S.A.
PubMed ID8415632
PubMed Central IDPMC47472
Grant ListGM30564 / GM / NIGMS NIH HHS / United States
GM30793 / GM / NIGMS NIH HHS / United States