Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations

• Published in: Proteins, structure, function, and bioinformatics Vol. 57; no. 4; pp. 783 - 791
• Main Authors: Faraldo-Gómez, José D., Forrest, Lucy R., Baaden, Marc, Bond, Peter J., Domene, Carmen, Patargias, George, Cuthbertson, Jonathan, Sansom, Mark S.P.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.12.2004; Wiley
• Subjects: Chemical Sciences; Computer Simulation; conformational space; convergence; covariance analysis; Debye-Waller B-factors; ergodicity; essential dynamics; Membrane Proteins; Membrane Proteins - chemistry; molecular dynamics; or physical chemistry; phase space; Principal Component Analysis; Protein Conformation; Theoretical and
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.20257

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 β‐barrels such as OmpT, to larger and more complex structures such as rhodopsin and FepA. Principal component analysis of the Cα‐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. Proteins 2004. © 2004 Wiley‐Liss, Inc.