STRUCTURE REFINEMENT USING TIME-AVERAGED J-COUPLING CONSTANT RESTRAINTS

被引:108
作者
TORDA, AE [1 ]
BRUNNE, RM [1 ]
HUBER, T [1 ]
KESSLER, H [1 ]
VANGUNSTEREN, WF [1 ]
机构
[1] TECH UNIV MUNICH,INST ORGAN CHEM,W-8046 GARCHING,GERMANY
关键词
J-COUPLING; TIME AVERAGING; STRUCTURE REFINEMENT; COMPUTER SIMULATION; MOLECULAR DYNAMICS;
D O I
10.1007/BF00242475
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
We describe a new penalty function for use in restrained molecular dynamics simulations which allows experimental J-coupling information to be enforced as a time-averaged, rather than instantaneous, quantity. The pseudo-energy term has been formulated in terms of a calculated J value (a measured quantity) rather than the relevant dihedral angle (a derived quantity). This accounts for the distinct non-linearity of the coupling constant with respect to either Cartesian coordinates or dihedral angles. Example simulations of the cyclic decapeptide antamanide show the procedure's ability to enforce experimental restraints while exploring a large region of conformational space and producing a relatively small disturbance of the physical force field.
引用
收藏
页码:55 / 66
页数:12
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