ATOMIC-LEVEL ACCURACY IN SIMULATIONS OF LARGE PROTEIN CRYSTALS

被引:178
作者
YORK, DM
WLODAWER, A
PEDERSEN, LG
DARDEN, TA
机构
[1] NIEHS,RES TRIANGLE PK,NC 27709
[2] DUKE UNIV,DEPT CHEM,DURHAM,NC 27706
[3] MICROELECTR CTR N CAROLINA,N CAROLINA SUPERCOMP CTR,RES TRIANGLE PK,NC 27709
[4] NCI,MACROMOLEC STRUCT LAB,FREDERICK,MD 21702
[5] UNIV N CAROLINA,DEPT CHEM,CHAPEL HILL,NC 27599
关键词
D O I
10.1073/pnas.91.18.8715
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Proper treatment of long-range Coulombic forces presents a major obstacle to providing realistic molecular dynamics simulations of macromolecules. Traditional approximations made to lessen computational cost ultimately lead to unrealistic behavior, The particle mesh Ewald method accommodates long-range Coulombic forces accurately and efficiently by use of fast Fourier transform techniques. We report a 1-ns simulation of bovine pancreatic trypsin inhibitor in a crystal unit cell using the particle mesh Ewald methodology. We iind an rms backbone deviation from the x-ray structure (0.33 Angstrom) that is lower than that observed between bovine pancreatic trypsin inhibitor in different crystal forms and much lower than those of previous simulations. These results bridge the gap between structures obtained from molecular simulation and those from experiment.
引用
收藏
页码:8715 / 8718
页数:4
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