ArticleBiophysical journal1997
Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics.
Article in Biophysical journal, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Dynamic Coupling of Tyrosine 185 with the Bacteriorhodopsin Photocycle, as Revealed by Chemical Shifts, Assisted AF-QM/MM Calculations and Molecular Dynamic Simulations.International journal of molecular sciences · 2021Article
- Phase behavior and domain size in sphingomyelin-containing lipid bilayers.Biochimica et biophysica acta · 2013Article
- Local Lipid Reorganization by a Transmembrane Protein Domain.The journal of physical chemistry letters · 2012Article
- 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
- 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
- Dynamics of water molecules in the bacteriorhodopsin trimer in explicit lipid/water environment.Biophysical journal · 2004Article
- Molecular dynamics simulations of the E1/E2 transmembrane domain of the Semliki Forest virus.Biophysical journal · 2003Article
- Backbone dynamics of bacteriorhodopsin as studied by (13)C solid-state NMR spectroscopy.European biophysics journal : EBJ · 2003Article
- Mapping the energy surface of transmembrane helix-helix interactions.Biophysical journal · 2001Article
- Molecular dynamics simulations predict a tilted orientation for the helical region of dynorphin A(1-17) in dimyristoylphosphatidylcholine bilayers.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
- Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer.Biophysical journal · 2000Article
- Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer.Biophysical journal · 1999Article
- Alamethicin helices in a bilayer and in solution: molecular dynamics simulations.Biophysical journal · 1999Article
- Molecular dynamics simulations of individual alpha-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. II. Interaction energy analysis.Biophysical journal · 1998Article
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1 author.
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Abstract
Understanding the role of the lipid bilayer in membrane protein structure and dynamics is needed for tertiary structure determination methods. However, the molecular details are not well understood. Molecular dynamics computer calculations can provide insight into these molecular details of protein:lipid interactions. This paper reports on 10 simulations of individual alpha-helices in explicit lipid bilayers. The 10 helices were selected from the bacteriorhodopsin structure as representative alpha-helical membrane folding components. The bilayer is constructed of dimyristoyl phosphatidylcholine molecules. The only major difference between simulations is the primary sequence of the alpha-helix. The results show dramatic differences in motional behavior between alpha-helices. For example, helix A has much smaller root-mean-squared deviations than does helix D. This can be understood in terms of the presence of aromatic residues at the interface for helix A that are not present in helix D. Additional motions are possible for the helices that contain proline side chains relative to other amino acids. The results thus provide insight into the types of motion and the average structures possible for helices within the bilayer setting and demonstrate the strength of molecular simulations in providing molecular details that are not directly visualized in experiments.
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