Molecular mechanics calculations of proteins. Comparison of different energy minimization strategies

Journal of Biomolecular Structure & Dynamics
I T Christensen, F S Jørgensen

Abstract

A general strategy for performing energy minimization of proteins using the SYBYL molecular modelling program has been developed. The influence of several variables including energy minimization procedure, solvation, dielectric function and dielectric constant have been investigated in order to develop a general method, which is capable of producing high quality protein structures. Avian pancreatic polypeptide (APP) and bovine pancreatic phospholipase A2 (BP PLA2) were selected for the calculations, because high quality X-ray structures exist and because all classes of secondary structure are represented in the structures. The energy minimized structures were evaluated relative to the corresponding X-ray structures. The overall similarity was checked by calculating RMS distances for all atom positions. Backbone conformation was checked by Ramachandran plots and secondary structure elements evaluated by the length on hydrogen bonds. The dimensions of active site in BP PLA2 is very dependent on electrostatic interactions, due to the presence of the positively charged calcium ion. Thus, the distances between calcium and the calcium-coordinating groups were used as a quality index for this protein. Energy minimized structures of th...Continue Reading

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Citations

Apr 3, 2001·European Journal of Pharmacology·I SylteS G Dahl
Jul 28, 2004·Xenobiotica; the Fate of Foreign Compounds in Biological Systems·D F V LewisP S Goldfarb
Oct 3, 2008·Journal of Enzyme Inhibition and Medicinal Chemistry·Simonetta Oliaro-BossoGianni Balliano
May 4, 2005·Journal of Computer-aided Molecular Design·Giuseppe ErmondiDario Longo
May 15, 2003·Journal of Biomolecular Structure & Dynamics·Knut Teigen, Aurora Martinez
Mar 26, 2003·Biochemistry·Matthías ThórólfssonAurora Martínez
Mar 3, 2004·Biochemistry·Zhiling ZhangDouglas D Root

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