Current time in Korea 11:08 Oct 19 (Thu) Year 2017 KCS KCS Publications
KCS Publications
My Journal Log In Register
HOME > Search > Browsing(BKCS) > Archives

Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 30, Number 5
BKCSDE 30(5)
May 20, 2009 

 
Title
Refinement of Protein NMR Structure under Membrane-like Environments with an Implicit Solvent Model
Author
JunGoo Jee*, Hee Chul Ahn
Keywords
NMR, Implicit solvent, Molecular dynamics simulation, Generalized Born model, Force field
Abstract
Refinement of NMR structures by molecular dynamics (MD) simulations with a solvent model has improved the structural quality. In this study, we applied MD refinement with the generalized Born (GB) implicit solvent model to protein structure determined under membrane-like environments. Despite popularity of the GB model, its applications to the refinement of NMR structures of hydrophobic proteins, in which detergents or organic solvents enclose proteins, are limited, and there is little information on the use of another GB parameter for these cases. We carried out MD refinement of crambin NMR structure in dodecylphosphocholine (DPC) micelles (Ahn et al., J. Am. Chem. Soc. 2006, 128, 4398-4404) with GB/Surface area model and two different surface tension coefficients, one for aquatic and the other for hydrophobic conditions. Our data show that, of two structures by MD refinement with GB model, the one refined with the parameter to consider hydrophobic condition had the better qualities in terms of precision and solvent accessibility.
Page
1139 - 1142
Full Text
PDF