ArticleThe journal of physical chemistry. B2015
Interactions of amino acid side-chain analogs within membrane environments.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Common synaptic phenotypes arising from diverse mutations in the human NMDA receptor subunit GluN2A.Communications biology · 2022Article
- Unusual mode of dimerization of retinitis pigmentosa-associated F220C rhodopsin.Scientific reports · 2021Article
- In Silico Prediction of the Binding, Folding, Insertion, and Overall Stability of Membrane-Active Peptides.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Generalized Born Implicit Solvent Models for Biomolecules.Annual review of biophysics · 2019Review
- Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning.Journal of chemical information and modeling · 2019Article
- Article
- Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.Journal of chemical information and modeling · 2017Article
- Computational studies of peptide-induced membrane pore formation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices.Journal of computational chemistry · 2017Article
- Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions.Journal of chemical theory and computation · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The interactions among four amino acid analog pairs (Asn, Ser, Phe, and Val) within the membrane environment were investigated using umbrella sampling molecular dynamics simulations. The results confirm generally expected qualitative trends of preferential association of polar compounds inside the membrane vs preferential interaction of hydrophobic compounds outside the membrane. Furthermore, correlations between amino acid interactions, membrane insertion, and membrane deformations are discussed and a detailed analysis of pair interaction energies is presented. A comparison of the energetics obtained from explicit lipid simulations with those from implicit membrane models reveals significant deviations and an improved parametrization of the heterogeneous dielectric generalized Born implicit model is provided that partially corrects for deficiencies in the implicit membrane model when compared with the new reference data from this study.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.