ArticleBiophysical journal1998
Molecular dynamics simulations of individual alpha-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. II. Interaction energy analysis.
Article in Biophysical journal, 1998. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 41 citations in OpenAlex.
- Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus.Journal of molecular modeling · 2010Article
- Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process.Biophysical journal · 2007Article
- Interaction of protegrin-1 with lipid bilayers: membrane thinning effect.Biophysical journal · 2006Article
- Indole localization in lipid membranes revealed by molecular simulation.Biophysical journal · 2006Article
- Lipid-protein interactions of integral membrane proteins: a comparative simulation study.Biophysical journal · 2004Article
- How environment supports a state: molecular dynamics simulations of two states in bacteriorhodopsin suggest lipid and water compensation.Biophysical journal · 2004Article
- Molecular dynamics simulations of the E1/E2 transmembrane domain of the Semliki Forest virus.Biophysical journal · 2003Article
- Investigating lipid composition effects on the mechanosensitive channel of large conductance (MscL) using molecular dynamics simulations.Biophysical journal · 2003Article
- Molecular dynamics simulations predict a tilted orientation for the helical region of dynorphin A(1-17) in dimyristoylphosphatidylcholine bilayers.Biophysical journal · 2000Article
- Atomic detail peptide-membrane interactions: molecular dynamics simulation of gramicidin S in a DMPC bilayer.Biophysical journal · 2000Article
- Protein-induced membrane disorder: a molecular dynamics study of melittin in a dipalmitoylphosphatidylcholine bilayer.Biophysical journal · 2000Article
- Structure and dynamics of K channel pore-lining helices: a comparative simulation study.Biophysical journal · 2000Article
- Molecular dynamics study of substance P peptides partitioned in a sodium dodecylsulfate micelle.Biophysical journal · 1999Article
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Authors and funding
1 author at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The concepts of hydrophobicity and hydrophobic moments have been applied in attempts to predict membrane protein secondary and tertiary structure. The current paper uses molecular dynamics computer calculations of individual bacteriorhodopsin helices in explicit dimyristoylphosphatidylcholine bilayers to examine the atomic basis of these approaches. The results suggest that the types of interactions between a particular amino acid and the surrounding bilayer depend on the position and type of the amino acid. In particular, aromatic residues are seen to interact favorably at the interface region. Analysis of the trajectories in terms of hydrophobic moments suggests the presence of a particular face that prefers lipid. The results of these simulations may be used to improve secondary structure prediction methods and to provide further insights into the two-stage model of protein folding.
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