JKMRS Volume 19, No 1, pp 1-10;Comparison of NMR structures re... | |
---|---|
2015년 06월 20일 / 조회수: 598 | |
Comparison of NMR
structures refined under implicit and explicit solvents 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 2, 2015; Revised
May 21, 2015; Accepted May 28, 2015 Abstract Refinements with atomistic molecular dynamics (MD) simulation have
contributed to improving the qualities of NMR structures. In most cases, the
calculations with atomistic MD simulation for NMR structures employ
generalized-Born implicit solvent model (GBIS) to take into accounts solvation
effects. Developments in algorithms and computational capacities have
ameliorated GBIS to approximate solvation effects that explicit solvents bring
about. However, the quantitative comparison of NMR structures in the latest
GBIS and explicit solvents is lacking. In this study, we report the direct
comparison of NMR structures that atomistic MD simulation coupled with GBIS and
water molecules refined. Two model proteins, GB1 and ubiquitin, were
recalculated with experimental distance and torsion angle restraints, under a
series of simulated annealing time steps. Whereas the root mean square
deviations of the resulting structures were apparently similar, AMBER energies,
the most favored regions in Ramachandran plot, and MolProbity clash scores
witnessed that GBIS-refined structures had the better geometries. The outperformance
by GBIS was distinct in the structure calculations with sparse experimental
restraints. We show that the superiority stemmed, at least in parts, from the
inclusion of all the pairs of non-bonded interactions. The shorter
computational times with GBIS than those for explicit solvents makes GBIS a
powerful method for improving structural qualities particularly under the
conditions that experimental restraints are insufficient. We also propose a
method to separate the native-like folds from non-violating diverged
structures. |
|
첨부파일 | 1지준구.pdf |