On Achieving Better than 1-Å Accuracy in a Simulation of a Large Protein: Streptomyces griseus Protease A

• Published in: Proceedings of the National Academy of Sciences - PNAS 1993-10, Vol.90 (19), p.8920-8924
• Main Authors: KITSON, D. H, AVBELJ, F, MOULT, J, NGUYEN, D. T, MERTZ, J. E, HADZI, D, HAGLER, A. T
• Format: Article
• Language: English
• Subjects: Analytical, structural and metabolic biochemistry; Atoms; Bacterial Proteins; Biological and medical sciences; Boolean functions; Computer Simulation; Crystals; Enzymes and enzyme inhibitors; Force field; Fundamental and applied biological sciences. Psychology; Hydrolases; Kinetics; Models, Molecular; Molecular biophysics; Molecular dynamics; Molecular structure; Molecules; Protein Structure, Secondary; Proteins; Serine Endopeptidases - chemistry; Simulation; Software; Streptomyces griseus; Streptomyces griseus - enzymology; Structure in molecular biology; Time Factors; Trajectories; Tridimensional structure; X-Ray Diffraction - methods
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.90.19.8920

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 Å, 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.