Efficient Quantification of Lipid Packing Defect Sensing by Amphipathic Peptides: Comparing Martini 2 and 3 with CHARMM36

Journal of Chemical Theory and Computation, vol. 18, pp. 4503–4514

Abstract

In biological systems, proteins can be attracted to curved or stretched regions of lipid bilayers by sensing hydrophobic defects in the lipid packing on the membrane surface. Here, we present an efficient end-state free energy calculation method to quantify such sensing in molecular dynamics simulations. We illustrate that lipid packing defect sensing can be defined as the difference in mechanical work required to stretch a membrane with and without a peptide bound to the surface. We also demonstrate that a peptide's ability to concurrently induce excess leaflet area (tension) and elastic softening─a property we call the "characteristic area of sensing" (CHAOS)─and lipid packing sensing behavior are in fact two sides of the same coin. In essence, defect sensing displays a peptide's propensity to generate tension. The here-proposed mechanical pathway is equally accurate yet, computationally, about 40 times less costly than the commonly used alchemical pathway (thermodynamic integration), allowing for more feasible free energy calculations in atomistic simulations. This enabled us to directly compare the Martini 2 and 3 coarse-grained and the CHARMM36 atomistic force fields in terms of relative binding free energies for six representative peptides including the curvature sensor ALPS and two antiviral amphipathic helices (AH). We observed that Martini 3 qualitatively reproduces experimental trends while producing substantially lower (relative) binding free energies and shallower membrane insertion depths compared to atomistic simulations. In contrast, Martini 2 tends to overestimate (relative) binding free energies. Finally, we offer a glimpse into how our end-state-based free energy method can enable the inverse design of optimal lipid packing defect sensing peptides when used in conjunction with our recently developed evolutionary molecular dynamics (Evo-MD) method. We argue that these optimized defect sensors─aside from their biomedical and biophysical relevance─can provide valuable targets for the development of lipid force fields.

Authors 3

1. Niek van Hilten Aachen

   Leiden University

   Affiliation as printed

   Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands

2. Kai Steffen Stroh

   University of Göttingen · TU Dortmund University

   Affiliation as printed

   Department of Physics, Technical University Dortmund, Dortmund 44221, Germany

   Institute for Theoretical Physics, Georg-August-University Göttingen, Göttingen 37077, Germany

3. Herre Jelger Risselada corresponding Aachen

   Leiden University · University of Göttingen · TU Dortmund University

   Affiliation as printed

   Department of Physics, Technical University Dortmund, Dortmund 44221, Germany

   Institute for Theoretical Physics, Georg-August-University Göttingen, Göttingen 37077, Germany

   Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands