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Lipid-protein interactions of integral membrane proteins: a comparative simulation study.
- Source :
-
Biophysical journal [Biophys J] 2004 Dec; Vol. 87 (6), pp. 3737-49. Date of Electronic Publication: 2004 Oct 01. - Publication Year :
- 2004
-
Abstract
- The interactions between membrane proteins and their lipid bilayer environment play important roles in the stability and function of such proteins. Extended (15-20 ns) molecular dynamics simulations have been used to explore the interactions of two membrane proteins with phosphatidylcholine bilayers. One protein (KcsA) is an alpha-helix bundle and embedded in a palmitoyl oleoyl phosphatidylcholine bilayer; the other (OmpA) is a beta-barrel outer-membrane protein and is in a dimyristoyl phosphatidylcholine bilayer. The simulations enable analysis in detail of a number of aspects of lipid-protein interactions. In particular, the interactions of aromatic amphipathic side chains (i.e., Trp, Tyr) with lipid headgroups, and "snorkeling" interactions of basic side chains (i.e., Lys, Arg) with phosphate groups are explored. Analysis of the number of contacts and of H-bonds reveal fluctuations on an approximately 1- to 5-ns timescale. There are two clear bands of interacting residues on the surface of KcsA, whereas there are three such bands on OmpA. A large number of Arg-phosphate interactions are seen for KcsA; for OmpA, the number of basic-phosphate interactions is smaller and shows more marked fluctuations with respect to time. Both classes of interaction occur in clearly defined interfacial regions of width approximately 1 nm. Analysis of lateral diffusion of lipid molecules reveals that "boundary" lipid molecules diffuse at about half the rate of bulk lipid. Overall, these simulations present a dynamic picture of lipid-protein interactions: there are a number of more specific interactions but even these fluctuate on an approximately 1- to 5-ns timescale.
- Subjects :
- Computer Simulation
Diffusion
Membrane Fluidity
Membrane Proteins chemistry
Membranes, Artificial
Motion
Protein Binding
Protein Conformation
Bacterial Outer Membrane Proteins chemistry
Bacterial Proteins chemistry
Dimyristoylphosphatidylcholine chemistry
Lipid Bilayers chemistry
Models, Chemical
Models, Molecular
Phosphatidylcholines chemistry
Potassium Channels chemistry
Subjects
Details
- Language :
- English
- ISSN :
- 0006-3495
- Volume :
- 87
- Issue :
- 6
- Database :
- MEDLINE
- Journal :
- Biophysical journal
- Publication Type :
- Academic Journal
- Accession number :
- 15465855
- Full Text :
- https://doi.org/10.1529/biophysj.104.048397