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A Comparative Study on the Ability of Two Implicit Solvent Lipid Models to Predict Transmembrane Helix Tilt Angles
- Source :
- The Journal of Membrane Biology, Frank, Aaron; & Andricioaei, Ioan. (2011). A Comparative Study on the Ability of Two Implicit Solvent Lipid Models to Predict Transmembrane Helix Tilt Angles. The Journal of Membrane Biology, 239(1), pp 57-62. doi: 10.1007/s00232-010-9325-7. Retrieved from: http://www.escholarship.org/uc/item/6414n1v8
- Publication Year :
- 2010
- Publisher :
- Springer Science and Business Media LLC, 2010.
-
Abstract
- Free-energy profiles describing the relative orientation of membrane proteins along predefined coordinates can be efficiently calculated by means of umbrella simulations. Such simulations generate reliable orientational distributions but are difficult to converge because of the very long equilibration times of the solvent and the lipid bilayer in explicit representation. Two implicit lipid membrane models are here applied in combination with the umbrella sampling strategy to the simulation of the transmembrane (TM) helical segment from virus protein U (Vpu). The models are used to study both orientation and energetics of this α-helical peptide as a function of hydrophobic mismatch. We observe that increasing the degree of positive hydrophobic mismatch increased the tilt angle of Vpu. These findings agree well with experimental data and as such validate the solvation models used in this study.
- Subjects :
- Tilt angle
Physiology
Lipid Bilayers
Biophysics
Models, Biological
01 natural sciences
Article
Umbrella sampling
Quantitative Biology::Subcellular Processes
Hydrophobic effect
03 medical and health sciences
Hydrophobic mismatch
0103 physical sciences
Computer Simulation
Lipid bilayer
Implicit solvent model
030304 developmental biology
Physics::Biological Physics
Quantitative Biology::Biomolecules
0303 health sciences
010304 chemical physics
Chemistry
Cell Membrane
Solvation
Life Sciences
Membrane Proteins
Cell Biology
Hydrophobic interaction
Lipids
Transmembrane protein
Biochemistry, general
Crystallography
Transmembrane domain
Tilt (optics)
Human Physiology
Chemical physics
Solvents
Molecular simulations
Hydrophobic and Hydrophilic Interactions
Subjects
Details
- ISSN :
- 14321424 and 00222631
- Volume :
- 239
- Database :
- OpenAIRE
- Journal :
- The Journal of Membrane Biology
- Accession number :
- edsair.doi.dedup.....2a63d6cae44f55510db0cfdb9850aeb8