A Simple Protocol for Identification of Helical and Mobile Residues in Membrane Proteins

Abstract

A simple molecular dynamics (MD) simulations is shown to predict protocol whether a residue is in a structured α-helical segment or in a mobile loop or terminal segment of a membrane protein. The results are verified by comparisons with experimental NMR data. The protocol consists of performing several independent MD simulations on a polypeptide sequence of interest in a dielectric continuum with a relative permittivity ϵ = 2. The time histories of the individual angles between NH bond vectors at time 0 and time tlater are calculated, and then Gaussian smoothing of typically 50 ps is applied.The smoothed data are subtracted from the original data to yield the short time fluctuations of the NH bond vectors, and then the rms deviations of the angles are calculated and compared to experimental NMR results. Pf1 coat protein and the c subunit of the E. coliF 1F 0ATP synthase are used as examples of membrane proteins. The calculated NH bond rms fluctuations are in qualitative agreement with experimental NMR data in showing that each of these proteins has a mobile segment connecting two helices, as well as mobile N and C-terminal regions. This MD simulations protocol can demonstrate the presence of both the amphipathic and hydrophobic helices while hydropathy plots are able to detect only the hydrophobic helices present in membrane proteins.