Paper Citing NAMD - Abstract
Tsai, Hui-Hsu Gavin; Lee, Jian-Bin; Li, Hung-Sheng; Hou, Tsai-Yi; Chu, Wen-Yuan; Shen, Po-Chuan; Chen, Ying-Yu; Tan, Chun-Jui; Hu, Jia-Cheng; Chiu, Chih-Chiang
Geometrical effects of phospholipid olefinic bonds on the structure and dynamics of membranes: A molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:1234-1247, MAY 2015
The trans isomers of fatty acids are found in human adipose tissue. These isomers have been linked with deleterious health effects (e.g., coronary artery disease). In this study, we performed molecular dynamics simulations to investigate the structures and dynamic properties of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) and 1-palmitoyl-2-elaidoyl sn-glycero-3-phosphatidylcholine (PEPC) lipid bilayers. The geometry of the olefinic bond and membrane packing effects significantly influenced the conformations and dynamics of the two C-C single bonds adjacent to the olefinic bond. For the PEPC lipid, the two C-C single bonds adjacent to the olefinic bond adopted mainly nonplanar skew-trans and planar cis-trans motifs; although the cis conformation featured relatively strong steric repulsion, it was stabilized through membrane packing because its planar structure is more suitable for membrane packing. Moreover, membrane packing effects stabilized the planar transition state for conformational conversion to a greater extent than they did with the nonplanar transition state, thereby affecting the dynamics of conformational conversion. The rotational motions of the first neighboring C-C single bonds were much faster than those of typical saturated C-C single bonds; in contrast, the rotational motions of the second neighboring C-C single bonds were significantly slower than those of typical saturated torsion angles. The packing of PEPC lipids is superior to that of POPC lipids, leading to a smaller area per lipid, a higher order parameter and a smaller diffusion coefficient. The distinct properties of POPC and PEPC lipids result in PEPC lipids forming microdomains within a POPC matrix. (C) 2015 Elsevier B.V. All rights reserved.
