The Free Energy Landscape of Dimerization of a Membrane Protein, NanC

Abstract

Membrane proteins are frequently present in crowded environments, which favour lateral association and, on occasions, two-dimensional crystallization. To better understand the non-specific lateral association of a membrane protein we have characterized the free energy landscape for the dimerization of a bacterial outer membrane protein, NanC, in a phospholipid bilayer membrane. NanC is a member of the KdgM-family of bacterial outer membrane proteins and is responsible for sialic acid transport in E. coli. Umbrella sampling and coarse-grained molecular dynamics were employed to calculate the potentials of mean force (PMF) for a variety of restrained relative orientations of two NanC proteins as the separation of their centres of mass was varied. We found the free energy of dimerization for NanC to be in the range of to . Differences in the depths of the PMFs for the various orientations are related to the shape of the proteins. This was quantified by calculating the lipid-inaccessible buried surface area of the proteins in the region around the minimum of each PMF. The depth of the potential well of the PMF was shown to depend approximately linearly on the buried surface area. We were able to resolve local minima in the restrained PMFs that would not be revealed using conventional umbrella sampling. In particular, these features reflected the local organization of the intervening lipids between the two interacting proteins. Through a comparison with the distribution of lipids around a single freely-diffusing NanC, we were able to predict the location of these restrained local minima for the orientational configuration in which they were most pronounced. Our ability to make this prediction highlights the important role that lipid organization plays in the association of two NanCs in a bilayer.

Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: Difference between atomistic and coarse-grained simulations

“…71,72 There are several interaction modes, stabilized by energies in the order of 30-60 kJ/mol. 71 Although analysis of β-barrel proteins was not within the scope of this study, in the case of NanC, the free energy of dimerization was estimated to be in the range of −66 to −45 kJ/mol using a modified version of MARTINI, 73 and the free energy for association of two OmpF trimers was estimated to be about −150 kJ/mol by MARTINI. 74 The importance of these studies lies in the analysis of association interfaces rather than the accuracy with which the free energies of association can be estimated.…”

In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality

“…Trimeric structures of Class 5C (OprP) and Class 6B (ScrY and maltoporins) porins have also been solved. Several publications have shown that the classic monomeric non-specific porins and specific diffusion channels actually oligomerized in the right conditions (e.g., lower temperatures or less detergents) [ 44 , 70 , 74 , 88 , 94 , 95 , 96 , 97 ]. Thus, unconventional methods might be necessary to detect protein oligomerization of non-specific porins and/or specific diffusion channels.…”

Excessive aggregation of membrane proteins in the Martini model

“…[ 32 ] showed that it can be reproduced if the Lennard-Jones interaction strength between protein beads is drastically weakened [ 32 ]. In the same spirit, dimerization free energies calculated for membrane proteins and peptides indicate a very strong tendency for dimerization [ 11 , 12 , 33 – 38 ] as exemplified by the dimerization free energies of about −150 kJ/mol and −160 kJ/mol reported for outer membrane protein F (OmpF) [ 38 ] and κ -opioid receptor (KOPr) [ 11 ], respectively. Even though free energies cannot be directly linked to dimerization kinetics, it is obvious that such strong affinities indicate irreversible binding.…”