Abstract

Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlates with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These experimental values serve as important anchor points in choosing between alternate CG models based on their observed permeation profiles, particularly for Arg, Lys and Gln residues where the all-atom OPLS solvation energy does not agree well with experiment. Available partitioning data was also used to reparameterize the representation of the peptide backbone, which needed to be made less attractive for the bilayer hydrophobic core region. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in studies of lipid-protein interactions and the conformational properties of diverse membrane protein systems.

Highlights

  • Coarse-grained (CG) simulations greatly expand the timescale of events (Kmiecik et al, 2016; Venable et al, 2017) that can be studied in physiologically realistic membrane systems (Ma et al, 2015; Van Oosten & Harroun, 2016)

  • To construct a protein force field, tabulated nonbond potentials were developed for five unique CG site types ca/p/ap/pos/neg assigned to groups of backbone and sidechain atoms based on atomistic reference simulations of peptide unfolding in water

  • The backbone unit has been made less attractive for the bilayer by assigning the polar site type for non-alanine residues and the apolar site type for alanine

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Summary

Introduction

Coarse-grained (CG) simulations greatly expand the timescale of events (Kmiecik et al, 2016; Venable et al, 2017) that can be studied in physiologically realistic membrane systems (Ma et al, 2015; Van Oosten & Harroun, 2016). A natural method for assessing the balance of energetics in a CG model is to use umbrella sampling simulations to calculate the potential of mean force (PMF) for dragging sidechain analog compounds through the bilayer (MacCallum, Bennett & Tieleman, 2008). The PMFs generated from atomistic MD of sidechains such as polar glutamine and basic arginine/lysine, have been observed to deviate from various experimental measures of solvation energy. Such studies neglect the influence of both the polypeptide backbone and the occlusion of solvent-accessible surface area by neighboring amino acid residues in a protein chain (Singh & Tieleman, 2011; Wimley, Creamer & White, 1996)

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