Thermodynamic and kinetic characterization of transmembrane helix association

Abstract

The transient dimerization of transmembrane proteins is an important event in several cellular processes and computational methods are being increasingly used to quantify their underlying energetics. Here, we probe the thermodynamics and kinetics of a simple transmembrane dimer to understand membrane protein association. A multi-step framework has been developed in which the dimerization profiles are calculated from coarse-grain molecular dynamics simulations, followed by meso-scale simulations using parameters calculated from the coarse-grain model. The calculated value of DG assoc is approx. À20 kJ mol À1 and is consistent between three methods. Interestingly, the meso-scale stochastic model reveals low dimer percentages at physiologically-relevant concentrations, despite a favorable DG assoc . We identify generic driving forces arising from the protein backbone and lipid bilayer and complementary factors, such as protein density, that govern self-interactions in membranes. Our results provide an important contribution in understanding membrane protein organization and linking molecular, nano-scale computational studies to meso-scale experimental data.

Effect of Lipid Bilayer Composition on Membrane Protein Association

“…The dimerization free energy, ΔG dimer has been found to range between À20 kJ/mol to À40 kJ/mol and was calculated to be most favorable in the case of glycophorin A, followed by ErbB2 transmembrane helices and the least for polyalanine peptides. Although, the free energy estimate for glycophorin A and ErbB2 appeared to be higher than in vivo measurements, in the case of polyalanine, ΔG dimer was found to be consistent with in vitro estimates [48]. Interestingly, oncogenic mutants of ErbB2 were estimated to have a lower ΔG dimer than the wild type ErbB2, confirming the presence of a stable dimer state in these mutants.…”

“…Thus, a few pathways of association can be easily obtained, but it remains difficult to access the complete free energy surface from unbiased simulations. We recently performed a millisecond time-scale coarse-grain simulation of a model peptide in which several association/dissociation events were sampled [48]. A dimerization profile could be calculated from the density of states and shown to correspond well to profiles calculated from biased methods.…”

“…To overcome the limitation of reduced sampling and statistical significance of most unbiased simulation approaches, we are testing a new framework to perform multiple independent unbiased simulations starting from random conformations [48]. In the absence of large barriers, the ensemble of simulations progresses according to the underlying energy landscape and allows for a comprehensive sampling of the phase space.…”

“…To estimate the free energy of dimerization, the underlying energy landscape and the driving forces governing association, the PMF profiles of several transmembrane helices, such as glycophorin A [51], ErbB2 [56] and polyalanine peptides [48] have been estimated by computational methods. For glycophorin A and ErbB2 transmembrane helices, the profiles were calculated from biased umbrella sampling calculations.…”

Interplay between Membrane Curvature and Cholesterol: Role of Palmitoylated Caveolin-1

“…A control protein (a-construct) was modeled to test the effect of the secondary structure with an a-helical CSD. The CSD was modeled using the Martini DAFT protocol to generate coordinates for an ideal helix using a backbone dihedral force constant of 400 kJ mol À1 (41,42). The different fragments were combined by modeling them in visual molecular dynamics, and standard Martini backbone bonds were defined between them.…”