Paper Citing NAMD - Abstract
Shih, Amy Y.; Freddolino, Peter L.; Arkhipov, Anton; Schulten, Klaus
Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations
JOURNAL OF STRUCTURAL BIOLOGY, 157:579-592, MAR 2007
High-density lipoproteins (HDL) function as cholesterol transporters, facilitating the removal of excess cholesterol from the body. Due to the heterogeneity of native HDL particles (both in size and shape), the details on how these protein-lipid particles form and the structure they assume in their lipid-associated states are not well characterized. We report here a study of the self-assembly of discoidal HDL particles using coarse-grained (CG) molecular dynamics. The microsecond simulations reveal the self-assembly of HDL particles from disordered protein-lipid complexes to form structures containing many of the features of the generally accepted double-belt model for discoidal HDL particles. HDL assembly is found to proceed in two broad steps, aggregation of proteins and lipids driven by the hydrophobic effect which occurs on a similar to 1 mu s time scale, followed by the optimization of the protein structure driven by increasingly specific protein-protein interactions. (c) 2006 Elsevier Inc. All rights reserved.
