• Bulletin of the Korean Chemical Society
• /
• 제33권3호
• /
• pp.828-832
• /
• 2012

We performed replica exchange molecular dynamics (REMD) simulations of the tripzip2 peptide (betahairpin) using the GB implicit and TI3P explicit solvation models. By comparing the resulting free energy surfaces of these two solvation model, we found that the GB solvation model produced a distorted free energy map, but the explicit solvation model yielded a reasonable free energy landscape with a precise location of the native structure in its global free energy minimum state. Our result showed that in particular, the GB solvation model failed to describe the tryptophan packing of trpzip2, leading to a distorted free energy landscape. When the GB solvation model is replaced with the explicit solvation model, the distortion of free energy shape disappears with the native-like structure in the lowest free energy minimum state and the experimentally observed tryptophan packing is precisely recovered. This finding indicates that the main source of this problem is due to artifact of the GB solvation model. Therefore, further efforts to refine this model are needed for better predictions of various aromatic side chain packing forms in proteins.

• 대한화학회지
• /
• 제57권5호
• /
• pp.554-559
• /
• 2013

본 연구에서는 ${\beta}$-D-glucopyranose 분자의 hydroxymethyl group의 두 torsion angle의 변화에 따른 포텐셜 에너지의 변화를 진공 상태와 implicit water 상태에서 연구하였으며 이를 통해 Solvation Energy가 구조에 미치는 영향에 대해서 알아보았다. 계산에 사용한 프로그램은 AMBER package였으며, force field는 GLYCAM_06을 사용하였다. Solvation model은 Hawkins, Cramer, Truhlar 등이 제안한 generalized Born model을 사용하였다. 계산 결과, methyl hydroxyl group 내의 hydroxyl group이 고리구조의 hydroxyl group과 강한 수소결합이 가능한 영역에서 많은 변화가 일어났다. 이를 통해 solvation effect로 인해서 수소 결합의 중요성이 감소했다는 결론을 내렸다.

• Bulletin of the Korean Chemical Society
• /
• 제26권4호
• /
• pp.589-593
• /
• 2005

The solvation free energy of proton in methanol was calculated by B3LYP flavor of density functional calculations in combination with the Poisson-Boltzmann continuum solvation model. In order to check the adequacy of the computation level, the free energies of clustering in the gas phase were compared with the experimental data. The solvents were taken into account in a hybrid manner, i.e. one to five molecules of methanol were explicitly considered while other solvent molecules were represented with an implicit solvation model.

• 한국자기공명학회논문지
• /
• 제19권1호
• /
• pp.1-10
• /
• 2015

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.