Biochemistry 2005 Aug;44(30):10164-9
Department of Chemistry, Wabash College, 301 West Wabash Avenue, Crawfordsville, Indiana 47933, USA.
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Biochemistry 2004 Dec;43(49):15318-28
IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA.
Cholesterol's preference for specific fatty acid chains is investigated at the atomic level in a 20 ns molecular dynamics computer simulation of a lipid bilayer membrane consisting of cholesterol and 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC) in a 1:3 ratio. These simulations reproduce experimental measurements suggesting that cholesterol prefers to be solvated by saturated acyl chains and has a low affinity for polyunsaturated fatty acids. Analyses of the simulation trajectory provide a detailed picture of both the transverse and lateral structures of the lipid bilayer membrane, along with a description of lipid and cholesterol dynamics at high temporal resolution. Read More
J Am Chem Soc 2002 Jan;124(2):318-26
Department of Chemistry, Wabash College, Crawfordsville, Indiana 47933, USA.
Polyunsaturated lipids are an essential component of biological membranes, influencing order and dynamics of lipids, protein-lipid interaction, and membrane transport properties. To gain an atomic level picture of the impact of polyunsaturation on membrane properties, quantum mechanical (QM) and empirical force field based calculations have been undertaken. The QM calculations of the torsional energy surface for rotation about vinyl-methylene bonds reveal low barriers to rotation, indicating an intrinsic propensity toward flexibility. Read More
J Pept Sci 2008 Apr;14(4):374-82
Biophysics and Statistical Mechanics Group, Faculty of Electrical and Communications Engineering, Helsinki University of Technology, Finland.
A molecular dynamics simulation study of four lipid bilayers with inserted trans-membrane helical fragment of epithelial growth factor (EGF) receptor (EGF peptide) was performed. The lipid bilayers differ in their lipid composition and consist of (i) unsaturated phosphatidylcholine (palmitoyloleoylphosphatidylcholine, POPC), (ii) POPC and 20 mol% of cholesterol (Chol), (iii) sphingomyelin (SM) and 20 mol% of Chol, and (iv) SM and 50 mol% of Chol. Only 1 out of 26 residues in the EGF-peptide sequence is polar (Thr). Read More
J Am Chem Soc 2005 Apr;127(13):4576-7
IBM T. J. Watson Research Center, 1101 Kitchawan Road, P.O. Box 218, Yorktown Heights, NY 10598, USA.
We present a 118-ns molecular dynamics simulation of rhodopsin embedded in a bilayer composed of a 2:2:1 mixture of 1-stearoyl-2-docosahexaenoyl-phosphatidylcholine (SDPC), 1-stearoyl-2-docosahexaenoyl-phosphatidylethanolamine (SDPE), and cholesterol, respectively. The simulation demonstrates that the protein breaks the lateral and transverse symmetry of the bilayer. Lipids near the protein preferentially reorient such that their unsaturated chains interact with the protein, while the distribution of cholesterol in the membrane complements the variations in rhodopsin's transverse profile. Read More