A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins

Abstract

The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the effects of solvation and electrostatics, because explicit atomic representation of the solvent and lipid molecules is computationally expensive and impractical for routine NMR-restrained calculations that start from completely extended polypeptide templates. Here, we describe the extension of a previously described implicit solvation potential, eefxPot, to include a membrane model for NMR-restrained calculations of membrane protein structures in XPLOR-NIH. The key components of eefxPot are an energy term for solvation free energy that works together with other nonbonded energy functions, a dedicated force field for conformational and nonbonded protein interaction parameters, and a membrane function that modulates the solvation free energy and dielectric screening as a function of the atomic distance from the membrane center, relative to the membrane thickness. Initial results obtained for membrane proteins with structures determined experimentally in lipid bilayer membranes show that eefxPot affords significant improvements in structural quality, accuracy, and precision. Calculations with eefxPot are straightforward to implement and can be used to both fold and refine structures, as well as to run unrestrained molecular-dynamics simulations. The potential is entirely compatible with the full range of experimental restraints measured by various techniques. Overall, it provides a useful and practical way to calculate membrane protein structures in a physically realistic environment.

Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation

“…2B, Table 1). Taken together, these results reflect the ability of eefxPot to effectively guide the conformation of Ail towards native fold, as observed for other soluble and membrane proteins (Tian et al 2014, 2015). …”

“…It is also important to note that since the lipid bilayer membrane of eefxPot is modeled implicitly, its ability to reflect the structural and physical properties of natural membranes is limited (Tian et al 2015). The principal limitations of the model are related to its inadequate representation of the hydrophobic matching phenomenon.…”

“…In all cases of soluble and membrane proteins tested so far (Tian et al 2014, 2015), eefxPot outperforms the standard REPEL force field: it yields structures with higher accuracy, precision and conformational quality and is very effective at guiding proteins towards their native fold, even in the absence of large numbers of experimental restraints. Furthermore, as eefxPot is developed for XPLOR-NIH, it is fully compatible with all the experimental restraining terms available in the program, as well as with the full range of molecular parameters and topologies relevant for NMR, such as paramagnetic spin labels, for example.…”

“…The potential is based on the CHARMM effective energy function for implicit water and membrane solvation (Lazaridis and Karplus 1999; Lazaridis 2003). While the first version of eefxPot was limited to bulk water solvation (Tian et al 2014), the most recent development includes the membrane and supports structure calculations of membrane proteins in an implicit membrane environment (Tian et al 2015). …”

“…Two structures were calculated with XPLOR-NIH (Schwieters et al 2003; Schwieters et al 2006), one using the standard, purely repulsive form of the Van der Waals function (REPEL), with the default protein topology and parameter files ( protein.par and protein.top ), and the other using the implicit membrane function of the potential, eefxPot , with its dedicated protein topology and parameter files ( protein_eef.par and protein_eef.top ) (Tian et al 2014, 2015). The structural coordinates and experimental restraints have been deposited in the Protein Data Bank (PDB: 2N2L, 2N2M).…”