Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices

Bercem Dutagaci, Maryam Sayadi, Michael Feig

Research output: Contribution to journalArticle

  • 3 Citations

Abstract

The heterogeneous dielectric generalized Born (HDGB) implicit membrane formalism is extended by the addition of a van der Waals dispersion term to better describe the nonpolar components of the free energy of solvation. The new model, termed HDGBvdW, improves the energy estimates in the hydrophobic interior of the membrane, where polar and charged species are rarely found and nonpolar interactions become significant. The implicit van der Waals term for the membrane environment extends the model from Gallicchio et al. (J. Comput. Chem. 2004, 25, 479) by combining separate contributions from each of the membrane components. The HDGBvdW model is validated with a series of test cases ranging from membrane insertion and pair association profiles of amino acid side chain analogs and transmembrane helices. Overall, the HDGBvdW model leads to increased agreement with explicit membrane simulation results and experimental data.

LanguageEnglish (US)
Pages1308-1320
Number of pages13
JournalJournal of Computational Chemistry
Volume38
Issue number16
DOIs
StatePublished - Jun 15 2017

Profile

Van Der Waals
Helix
Membrane
Association reactions
Membranes
Term
Model
Energy Estimates
Solvation
Free energy
Insertion
Amino Acids
Amino acids
Free Energy
Interior
Experimental Data
Analogue
Series
Interaction
Simulation

Keywords

  • generalized Born formalism
  • implicit membrane model
  • transmembrane helix dimers

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

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