Paper Citing NAMD - Abstract
Catte, Andrea; Patterson, James C.; Bashtovyy, Denys; Jones, Martin K.; Gu, Feifei; Li, Ling; Rampioni, Aldo; Sengupta, Durba; Vuorela, Timo; Niemela, Perttu; Karttunen, Mikko; Marrink, Siewert Jan; Vattulainen, Ilpo; Segrest, Jere P.
Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations
BIOPHYSICAL JOURNAL, 94:2306-2319, MAR 15 2008
Spheroidal high-density lipoprotein (HDL) particles circulating in the blood are formed through an enzymatic process activated by apoA-1, leading to the esterification of cholesterol, which creates a hydrophobic core of cholesteryl ester molecules in the middle of the discoidal phospholipid bilayer. In this study, we investigated the conformation of apoA-1 in model spheroidal HDL (ms-HDL) particles using both atomistic and coarse-grained molecular dynamics simulations, which are found to provide consistent results for all HDL properties we studied. The observed small contribution of cholesteryl oleate molecules to the solvent-accessible surface area of the entire ms-HDL particle indicates that palmitoyloleoylphosphatidylcholines and apoA-1 molecules cover the hydrophobic core comprised of cholesteryl esters particularly well. The ms-HDL particles are found to form a prolate ellipsoidal shape, with sizes consistent with experimental results. Large rigid domains and low mobility of the protein are seen in all the simulations. Additionally, the average number of contacts of cholesteryl ester molecules with apoA-1 residues indicates that cholesteryl esters interact with protein residues mainly through their cholesterol moiety. We propose that the interaction of annular cholesteryl oleate molecules contributes to apoA-1 rigidity stabilizing and regulating the structure and function of the ms-HDL particle.
