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Characterization of the conformational and orientational dynamics of ganglioside GM1 in a dipalmitoylphosphatidylcholine bilayer by molecular dynamics simulations

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Title Characterization of the conformational and orientational dynamics of ganglioside GM1 in a dipalmitoylphosphatidylcholine bilayer by molecular dynamics simulations
 
Creator PATEL, RONAK Y
BALAJI, PETETY V
 
Subject molecular dynamics
cell membranes
monolayers
electrochemistry
 
Description The structure and dynamics of a single GM1 (Gal5-β1,3-GalNAc4-β1,4-(NeuAc3-α2,3)-Gal2-β1,4-Glc1-β1,1-Cer) embedded in a DPPC bilayer have been studied by MD simulations. Eleven simulations, each of 10 ns productive run, were performed with different initial conformations of GM1. Simulations of GM1-Os in water and of a DPPC bilayer were also performed to delineate the effects of the bilayer and GM1 on the conformational and orientational dynamics of each other. The conformation of the GM1 headgroup observed in the simulations is in agreement with those reported in literature; but the headgroup is restricted when embedded in the bilayer. NeuAc3 is the outermost saccharide towards the water phase. Glc1 and Gal2 prefer a parallel, and NeuAc3, GalNac4 and Gal5 prefer a perpendicular, orientation with respect to the bilayer normal. The overall characteristics of the bilayer are not affected by the presence of GM1; however, GM1 does influence the DPPC molecules in its immediate vicinity. The implications of these observations on the specific recognition and binding of GM1 embedded in a lipid bilayer by exogenous proteins as well as proteins embedded in lipids have been discussed.
 
Publisher Elsevier
 
Date 2009-04-23T11:40:41Z
2011-12-08T06:25:21Z
2011-12-26T13:01:31Z
2011-12-27T05:45:04Z
2009-04-23T11:40:41Z
2011-12-08T06:25:21Z
2011-12-26T13:01:31Z
2011-12-27T05:45:04Z
2007
 
Type Article
 
Identifier Biochimica et Biophysica Acta (BBA) - Biomembranes 1768(6), 1628-1640
0005-2736
10.1016/j.bbamem.2007.02.020
http://hdl.handle.net/10054/1214
http://dspace.library.iitb.ac.in/xmlui/handle/10054/1214
 
Language en