[04.1] PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 57 (4): 783-791 ; DEC 1 2004
José D. Faraldo-Gómez1,*, Lucy R. Forrest 2, Marc Baaden 3,4, Peter J. Bond 4, Carmen Domene 5, George Patargias 4, Jonathan Cuthbertson 4, Mark S. P. Sansom 4
In the current report, we provide a quantitative analysis of the convergence of the sampling of conformational space accomplished in molecular dynamics simulations of membrane proteins of duration in the order of 10 nanoseconds. A set of proteins of diverse size and topology is considered, ranging from helical pores such as gramicidin and small beta-barrels such as OmpT, to larger and more complex structures such as rhodopsin and FepA. Principal component analysis of the C(alpha)-atom trajectories was employed to assess the convergence of the conformational sampling in both the transmembrane domains and the whole proteins, while the time-dependence of the average structure was analyzed to obtain single-domain information. The membrane-embedded regions, particularly those of small or structurally simple proteins, were found to achieve reasonable convergence. By contrast, extra-membranous domains lacking secondary structure are often markedly under-sampled, exhibiting a continuous structural drift. This drift results in a significant imprecision in the calculated B-factors, which detracts from any quantitative comparison to experimental data. In view of such limitations, we suggest that similar analyses may be valuable in simulation studies of membrane protein dynamics, in order to attach a level of confidence to any biologically relevant observations.
Correspondence should be addressed to José D. Faraldo-Gómez.
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York.
- Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique, 13, rue Pierre et Marie Curie, F-75005 Paris, France.
- Univ of Oxford, Lab. of Molecular Biophysics, South Parks Road, OX1 3QU Oxford, United Kingdom.
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom.