ArticleJournal of chemical information and modeling2011
Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects.
Article in Journal of chemical information and modeling, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Experimental and Theoretical Brownian Dynamics Analysis of Ion Transport During Cellular Electroporation of E. coli Bacteria.Annals of biomedical engineering · 2024Article
- Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods.Journal of chemical information and modeling · 2023Review
- Diverse Scientific Benchmarks for Implicit Membrane Energy Functions.Journal of chemical theory and computation · 2021Article
- Asymmetric opening of the homopentameric 5-HTNature communications · 2021Article
- Enhancing the Signaling of GPCRs via Orthosteric Ions.ACS central science · 2020Article
- Physics-Based Method for Modeling Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules.Journal of chemical information and modeling · 2019Article
- Exploring a new ligand binding site of G protein-coupled receptors.Chemical science · 2018Article
- A model for hydrophobic protrusions on peripheral membrane proteins.PLoS computational biology · 2018Article
- Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.Journal of chemical information and modeling · 2017Article
- The Principles of Ligand Specificity on beta-2-adrenergic receptor.Scientific reports · 2016Article
- Structure-based prediction of drug distribution across the headgroup and core strata of a phospholipid bilayer using surrogate phases.Molecular pharmaceutics · 2014Article
- Life at the border: adaptation of proteins to anisotropic membrane environment.Protein science : a publication of the Protein Society · 2014Review
- ProBLM web server: protein and membrane placement and orientation package.Computational and mathematical methods in medicine · 2014Article
- Structural adaptations of proteins to different biological membranes.Biochimica et biophysica acta · 2013Article
- Structural determinants of drug partitioning in surrogates of phosphatidylcholine bilayer strata.Molecular pharmaceutics · 2013Article
- Membrane protein native state discrimination by implicit membrane models.Journal of computational chemistry · 2013Article
- Antimicrobial action of the cyclic peptide bactenecin on Burkholderia pseudomallei correlates with efficient membrane permeabilization.PLoS neglected tropical diseases · 2013Article
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3 authors.
Funding
Abstract
A new implicit solvation model was developed for calculating free energies of transfer of molecules from water to any solvent with defined bulk properties. The transfer energy was calculated as a sum of the first solvation shell energy and the long-range electrostatic contribution. The first term was proportional to solvent accessible surface area and solvation parameters (σ(i)) for different atom types. The electrostatic term was computed as a product of group dipole moments and dipolar solvation parameter (η) for neutral molecules or using a modified Born equation for ions. The regression coefficients in linear dependencies of solvation parameters σ(i) and η on dielectric constant, solvatochromic polarizability parameter π*, and hydrogen-bonding donor and acceptor capacities of solvents were optimized using 1269 experimental transfer energies from 19 organic solvents to water. The root-mean-square errors for neutral compounds and ions were 0.82 and 1.61 kcal/mol, respectively. Quantification of energy components demonstrates the dominant roles of hydrophobic effect for nonpolar atoms and of hydrogen-bonding for polar atoms. The estimated first solvation shell energy outweighs the long-range electrostatics for most compounds including ions. The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes.
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