Biophysical Society Thematic Meeting | Trieste 2024

Emerging Theoretical Approaches to Complement Single-Particle Cryo-EM

Friday Speaker Abstracts

WHAT DETERMINES THE DWELL-TIME OF A BOUND LIPID? INTERPRETING LIPID DENSITIES IN STRUCTURAL DATA USING MOLECULAR DYNAMICS SIMULATIONS AND SPECIALIZED TOOLS FOR THEIR ANALYSIS Nathan Bernhardt 1 ; Shan Zhang 1 ; Robyn Stix 2 ; José D Faraldo-Gómez 1 ; 1 Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA 2 Molecular and Cell Biology Graduate Program, Johns Hopkins University, Baltimore, MD, USA Structural studies of membrane proteins often report detection of phospholipid molecules, but in many cases of interest, it is unclear how to discriminate between bona-fide regulatory sites and non-specific densities, as the lipid headgroups that should be conferring specificity are often unresolved. This lack of detail implies that the stabilization of these lipids on the protein surface owes to other factors. In this study, we show that the dynamics of phospholipids at the protein membrane interface is primarily dictated by the protein topography and its influence on the lipid chains. That is, long-lasting complexes form at sites where the features of this topography protect individual lipids from being displaced by their neighbors. This conclusion stems from a novel framework for identifying important interactions stabilizing bound lipids based on molecular dynamics simulations and a suite of specialized analysis tools. We apply this methodology to both the Kv2.1 and KcsA potassium channels, whose mechanisms are known to be modulated by specific lipid types. In both cases, structural data reveals lipid densities, clearly resolved for the chains but not for the headgroups. Our simulations closely replicate the experimental data, and reveal it largely reflects the topographical features of the protein surface within the hydrophobic span of the membrane, rather than the potential for interactions between polar protein sidechains and lipid headgroups. We conclude with a discussion of the broader implications of these findings and the origins of specificity in lipid regulatory mechanisms.

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