Biophysical Society Thematic Meeting | Hamburg 2022

Biophysics at the Dawn of Exascale Computers

Thursday Speaker Abstracts

DECIPHERING THE ENERGETICS OF PERIPHERAL PROTEIN-MEMBRANE INTERACTIONS Emmanuel E Moutoussamy 1 ; Hanif M Khan 1 ; Qaiser Waheed 1 ; Anne Gershenson 4 ; Mary F Roberts 3 ; Chris Chipot 2 ; Nathalie Reuter 1 ; 1 University of Bergen, Department of Chemistry & Computational Biology Unit, Bergen, Norway 2 Université de Lorraine, Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n 7019, Vandœuvre-lès-Nancy, France 3 Boston College, Department of chemistry, Chestnut Hill, MA, USA 4 University of Massachusetts Amherst, Department of Biochemistry and Molecular Biology, Amherst, MA, USA Peripheral membrane proteins (PMPs) bind temporarily to cellular membranes and play important roles in signalling, lipid metabolism and membrane trafficking. Obtaining accurate membrane-PMP affinities using experimental techniques is more challenging than for protein- ligand affinities in aqueous solution, and molecular dynamics (MD) simulations have the potential to fill that gap. The phosphatidylinositol-specific phospholipase C from Bacillus thurigiensis (BtPI-PLC), reduces host innate immunity by catalyzing the cleavage of GPI- anchored proteins at the surface of the cell, thereby contributing to bacterial virulence. The availability of detailed experimental data for BtPI-PLC binding to lipid vesicles makes it a convenient choice to evaluate computational approaches. Apparent dissociation constants (K D ) for BtPI-PLC on small unilamellar POPC vesicles have been determined experimentally for an array of membrane compositions and protein variants. Using free energy perturbation calculations, we computed the energetic cost of alanine substitution for five interfacial aromatics. The obtained values were in good agreement with experimental data (Waheed et al, J Phys Chem Lett, 2019) showing that FEP calculations provide a computationally inexpensive way to dissect the roles of interfacial amino acids. Calculation of standard protein-membrane binding free energy using MD simulations remains a daunting challenge owing to the size of the biological objects at play, the slow lipid diffusion and the large variation in configurational entropy that accompanies the binding process. To overcome these challenges, we used a computational framework relying on a series of potential-of-mean-force (PMF) calculations including a set of geometrical restraints on collective variables (Gumbart et al., JCTC, 2013). We computed a standard binding free energy of -8.2±1.4 kcal/mol, in reasonable agreement with the reported experimental values (-6.6±0.2 kcal/mol). In light of the 2.3- μs separation PMF calculation, we could gain insights into the mechanism whereby BtPI-PLC disengages from interactions with the lipid bilayer during separation (Moutoussamy et al, ChemRxiv, 2022).

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