Nucleic acid base-pairing and N-methylacetamide self-association in chloroform:: affinity and conformation

被引:37
作者
Luo, R
Head, MS
Given, JA
Gilson, MK
机构
[1] Ctr Adv Res Biotechnol, Rockville, MD 20850 USA
[2] Natl Inst Stand & Technol, Gaithersburg, MD 20899 USA
关键词
D O I
10.1016/S0301-4622(98)00229-4
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
A recently developed computational method, 'mining minima', is used to examine the hydrogen-bonding interactions of nucleic acid base-pairs and of the N-methylacetamide homodimer in chloroform. The mining minima algorithm aggressively samples molecular conformations, identifies the most important local minima, and computes their contributions to the overall free energy of the system. Here, the CHARMM 98 parameter set is used for the potential energy and the generalized Born/surface area solvent model is used to account for the influence of the solvent. Good agreement with experiment is obtained for the non-covalent binding affinities of a series of complexes. The computational approach used here is applicable to a range of molecular systems. (C) 1999 Elsevier Science B.V. All rights reserved.
引用
收藏
页码:183 / 193
页数:11
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