Computational Studies of Membrane Protein Based on NMR Observables

Abstract

Various NMR observables, such as chemical shift anisotropy (CSA) and dipolar coupling (DC) in solid-state NMR, and residual dipolar coupling (RDC) in solution NMR experiments, have been used to characterize membrane protein structures. As time- and ensemble-averaged measurements, those observables also embed protein dynamics, which provide collective motions relevant to protein function. However, most of present NMR structure determination approaches do not consider protein-lipid interactions, which are essential determinants of membrane protein structure and function. To overcome these limitations, various NMR observables are utilized as restraints to refine structure and explore dynamics in the explicit (bilayer and micelles) membranes. Restrained molecular dynamics simulations were performed for structure refinement, and ensemble dynamics techniques were implemented to investigate protein dynamics. As a representative membrane protein, Pf1 coat protein is used to as the model system. It is a single-pass transmembrane helical protein with a membrane associated periplasmic helix. The resulting structures satisfy the NMR observables and compared to the published structures. With respect to the explicit membrane, the disposition of Pf1 TM helix was identified and the dynamic nature of the periplasmic helix orientation was observed.