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JKMRS Volume 17, No 1 11-18;Effects of generalized-Born implic...
2013년 06월 20일 / 조회수: 487

Effects of generalized-Born implicit solvent models

in NMR structure refinement

 

Jun-Goo Jee*

 

Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University,

80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea

 

 

Received May 13, 2013; Revised June 04, 2013; Accepted June 10, 2013

 


Abstract   Rapid advances of computational power and method have made it practical to apply the time-consuming calculations with all-atom force fields and sophisticated potential energies into refining NMR structure. Added to the all-atom force field, generalized-Born implicit solvent model (GBIS) contributes substantially to improving the qualities of the resulting NMR structures. GBIS approximates the effects that explicit solvents bring about even with fairly reduced computational times. Although GBIS is employed in the final stage of NMR structure calculation with experimental restraints, the effects by GBIS on structures have been reported notable. However, the detailed effect is little studied in a quantitative way. In this study, we report GBIS refinements of ubiquitin and GB1 structures by six GBIS models of AMBER package with experimental distance and backbone torsion angle restraints. Of GBIS models tested, the calculations with igb=7 option generated the closest structures to those determined by X-ray both in ubiquitin and GB1 from the viewpoints of root-mean-square deviations. Those with igb=5 yielded the second best results. Our data suggest that the degrees of improvements vary under different GBIS models and the proper selection of GBIS model can lead to better results.

 

Keywords NMR, all-atom force field, generalized-Born implict solvent model

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