ArticleBiophysical journal2008
Distribution of amino acids in a lipid bilayer from computer simulations.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 236 papers.
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Who cites it
236 citing papers in PubMed, 544 citations in OpenAlex.
- Article
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- Impact of Lipid Composition on Membrane Partitioning and Permeability of Gas Molecules.Membranes · 2026Article
- Water at Lipid Interfaces: Domains and Defects.Sub-cellular biochemistry · 2026Review
- Amino acid-based surfactants: sustainable synthesis and antimicrobial mechanisms.Beilstein journal of organic chemistry · 2026Review
- The polybasic puzzle: how N-terminal charges modulate GαiCell communication and signaling : CCS · 2025Article
- Thermodynamics of arginine interactions with organic phosphates.Biophysical journal · 2025Article
- Identifying and quantifying membrane interactions of the protein human cis-prenyltransferase.Protein science : a publication of the Protein Society · 2025Article
- Ergosterol depletion by fish AMP analogs likely enhances fungal membrane permeability.Biophysical journal · 2025Article
- A quantitative analysis of ligand binding at the protein-lipid bilayer interface.Communications chemistry · 2025Article
- Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3.Communications chemistry · 2025Article
- Molecular dynamics simulations unveil the aggregation patterns and salting out of polyarginines at zwitterionic POPC bilayers in solutions of various ionic strengths.Computational and structural biotechnology journal · 2024Article
- Water in peripheral TM-interfaces of Orai1-channels triggers pore opening.Communications biology · 2024Article
- Elucidating Antibiotic Permeation through theJournal of chemical information and modeling · 2024Article
176 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have calculated the distribution in a lipid bilayer of small molecules mimicking 17 natural amino acids in atomistic detail by molecular dynamics simulation. We considered both charged and uncharged forms for Lys, Arg, Glu, and Asp. The results give detailed insight in the molecular basis of the preferred location and orientation of each side chain as well the preferred charge state for ionizable residues. Partitioning of charged and polar side chains is accompanied by water defects connecting the side chains to bulk water. These water defects dominate the energetic of partitioning, rather than simple partitioning between water and a hydrophobic phase. Lys, Glu, and Asp become uncharged well before reaching the center of the membrane, but Arg may be either charged or uncharged at the center of the membrane. Phe has a broad distribution in the membrane but Trp and Tyr localize strongly to the interfacial region. The distributions are useful for the development of coarse-grained and implicit membrane potentials for simulation and structure prediction. We discuss the relationship between the distribution in membranes, bulk partitioning to cyclohexane, and several amino acid hydrophobicity scales.
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