NDLI: Coarse-grained molecular dynamics of tetrameric transmembrane peptide bundles within a lipid bilayer.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Nguyen, Thuy Hien T. Rao, Niny Z. Schroeder, William M. Moore, Preston B.
Description	Country affiliation: United States Author Affiliation: Nguyen TH ( Department of Chemistry & Biochemistry and the West Center for Computational Chemistry and Drug Design, University of the Sciences in Philadelphia, 600 South 43rd Street, Philadelphia, PA 19104-4495, United States.)
Abstract	The conformations of model transmembrane peptides are studied to understand the structural and dynamical aspects of tetrameric bundles using a series of coarse grain (CG) molecular dynamics (MD) simulations since membrane proteins play a crucial role in cell function. In this work, two different amphipathic models have been constructed using similar hydrophobic/hydrophilic characteristics with two structurally distinct morphologies to evaluate the effect of roughness and hydrophilic topology on the structure of tetrameric bundles, one class that forms an ion-channel and one class that does not. Free energy calculations of typical amphipathic peptide topologies show that using a relatively smooth surface morphology allows for a stable conformation of the tetramer bundle in a diamond formation. However, the model with side chains attached to the core in order to roughen the surface has a stable square tetramer bundle which is consistent with experimental data and all-atom (AA) MD simulations. Comparisons of the CG simulations with AA MD simulations are in reasonable agreement with the formation of tetrameric homo-oligomers, partitioning within the lipid bilayer and tilt angle with respect to the bilayer normal. We concluded that a square or diamond shape tetrameric homo-oligomers could be stabilized by rational design of the peptide morphology and topology of the surface, thus allowing us to tune the permeability of the bundle or channel.
File Format	HTM / HTML
ISSN	00093084
e-ISSN	18732941
DOI	10.1016/j.chemphyslip.2010.04.007
Journal	Chemistry and Physics of Lipids
Issue Number	6
Volume Number	163
Language	English
Publisher	Elsevier
Publisher Date	2010-06-01
Publisher Place	Ireland
Access Restriction	Open
Subject Keyword	Discipline Biochemistry Lipid Bilayers Chemistry Membrane Proteins Molecular Dynamics Simulation Dimyristoylphosphatidylcholine Peptides Thermodynamics Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s.
Content Type	Text
Resource Type	Article
Subject	Cell Biology Organic Chemistry Molecular Biology Biochemistry

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