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Implicit model to capture electrostatic features of membrane environment.

Rituparna SamantaJeffrey J Gray
Published in: bioRxiv : the preprint server for biology (2023)
Membrane proteins participate in many life processes. They constitute 30% of the human proteome and are targets for over 60% pharmaceuticals. Accurate and accessible computational tools to design membrane proteins will transform the platform to engineer membrane proteins for therapeutic, sensor, and separation processes. While soluble protein design has advanced, membrane protein design remains challenging due to the difficulties in modeling the lipid bilayer. Electrostatics plays an intimate role in the physics of membrane protein structure and function. However, accurately capturing electrostatic energies in the low-dielectric membrane often requires expensive calculations that are not scalable. In this work, we contribute a fast-to-compute electrostatic model that considers different lipid bilayers and their features, making design calculations tractable. We demonstrate that the updated energy function improves the calculation of the tilt angle of membrane proteins, stability, and confidence in designing charged residues.
Keyphrases
  • molecular dynamics simulations
  • density functional theory
  • high resolution
  • high throughput
  • fatty acid
  • small molecule
  • amino acid