Computational simulations on membranes and a transmembrane protein

Abstract

To accurately model the transmembrane proteins, accurate descriptions of its natural environment, i.e., lipids, are critical. The all-atom CHARMM36 lipid force field (C36FF-AA) is tested with molecular dynamics (MD) simulations. Through comparison to experiments, we conclude that the C36FF-AA is accurate for use with bilayers of varying head and chain types over biologically relevant temperatures. The united-atom chain model of the C36FF (C36FF-UA) of common lipids is developed to improve simulation efficiency. It shows good agreement between the simulated bilayer properties obtained by C36FF-UA and experiments, and also between the simulated results from UA and AA lipid models. Besides the single-component membrane, multiple-components 18:2 linoleoyl-containing soybean membrane models have been developed. The structural properties of pure linoleoyl bilayers agree well with experiments, based on which the soybean membrane models also result in reasonable structural properties. Accurate lipid force field greatly facilitates the study of transmembrane proteins. Lactose permease of Escherichia coli (E. coli) belongs to major facilitator superfamily (MFS) which is the largest and most diverse family of transporters and serves as a model for secondary active transporters (SATs) in this dissertation. LacY structures of the cytoplasmic-open, occluded-like, and recently periplasmic-partially-open state have been determined, however, the crystal structure of LacY in the periplasmic-open state is still not available. The periplasmic-open LacY structure is important for understanding the complete proton/sugar transport process of LacY as well as other similar SAT proteins. MD simulations are performed to test the accuracy of the previously developed periplasmic-open LacYIM-EX model (JMB 404:506), and two other periplasmic-open LacY models, LacYSW and LacYFP models (JMB 407:698). The simulated results indicate that LacYIM-EX is the only structure that remains stable in the periplasmic-open state. The MD dummy spin label simulations (MDDS) have also been performed and the results show that the orientation of the spin labels significantly affect the distance measurement so that the proper interpretation of DEER requires the aid of MDDS simulations. Self-guided Langevin dynamics (SGLD) simulations are performed to search periplasmic-open LacY. The results show that no outward-facing is obtained with nanosecond-averaged results, but if we study individual structures, conformational sampling is obtained with certain SGLD parameters that enhance natural helical motions. This SGLD approach might hold promise for studying conformational changes of other SAT proteins