• Journal of the Korean Magnetic Resonance Society
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• v.26 no.1
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• pp.1-9
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• 2022

There are two distinct approaches to improving the quality of protein NMR structures during refinement: all-atom force fields and accumulated knowledge-assisted methods that include Rosetta. Mao et al. reported that, for 40 proteins, Rosetta increased the accuracies of their NMR-determined structures with respect to the X-ray crystal structures (Mao et al., J. Am. Chem. Soc. 136, 1893 (2014)). In this study, we calculated 32 structures of those studied by Mao et al. using all-atom force field and implicit solvent model, and we compared the results with those obtained from Rosetta. For a single protein, using only the experimental NOE-derived distances and backbone torsion angle restraints, 20 of the lowest energy structures were extracted as an ensemble from 100 generated structures. Restrained simulated annealing by molecular dynamics simulation searched conformational spaces with a total time step of 1-ns. The use of GPU-accelerated AMBER code allowed the calculations to be completed in hours using a single GPU computer-even for proteins larger than 20 kDa. Remarkably, statistical analyses indicated that the structures determined in this way showed overall higher accuracies to their X-ray structures compared to those refined by Rosetta (p-value < 0.01). Our data demonstrate the capability of sophisticated atomistic force fields in refining NMR structures, particularly when they are coupled with the latest GPU-based calculations. The straightforwardness of the protocol allows its use to be extended to all NMR structures.

• Journal of the Korean Magnetic Resonance Society
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• v.17 no.1
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• pp.11-18
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• 2013

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.

• Bulletin of the Korean Chemical Society
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• v.31 no.9
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• pp.2717-2720
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• 2010

• Korean Journal of Optics and Photonics
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• v.11 no.4
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• pp.221-226
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• 2000

We observed the spatial distributions of atom in a magneto-optical trap. These distributions include sphere, stick, ring, ring with core, sphere-sphere, sphere-ring etc. Coordinate-dependent asymmetry radiation force (CDARF) that arises due to laser beams misalignment and transverse profile of the laser beams is exerted on atoms, and the shape of trapped cloud is changed with the misalignment parameter. We use equations of motion that takes into account the Zeeman sublevels of the 87Rb atom, magnitude and direction of magnetic field, polarization of trapping lasers, and transverse profile of the laser beams. A theoretical analysis of the equation of motion for the trapped atom explained all the experimental observations.

• Bulletin of the Korean Chemical Society
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• v.35 no.6
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• pp.1713-1719
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• 2014

1FSD is a 28-residue designed protein with a ${\beta}{\beta}{\alpha}$ motif. Since this protein displays most essential features of protein structures in such a small size, this model protein can be an outstanding system for evaluating the balance in the propensity of the secondary structures and the quality of all-atom protein force fields. Particularly, this protein would be difficult to fold to its correct native structure without establishing proper balances between the secondary structure elements in all-atom energy functions. In this work, a series of the recently optimized five amber protein force fields [$ff03^*$, $f99sb^*$-ildn, ff99sb-${\phi}^{\prime}$-ildn, ff99sb-nmr1-ildn, ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn] were investigated for the simulations of 1FSD using a conventional molecular dynamics (MD) and a biased-exchange meta-dynamics (BEMD) methods. Among those tested force fields, we found that ff99sb-nmr1-ildn and ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn are promising in that both force fields can locate the native state of 1FSD with a high accuracy (backbone rmsd ${\leq}1.7{\AA}$) in the global free energy minimum basin with a reasonable energetics conforming to a previous circular dichroism (CD) experiment. Furthermore, both force fields led to a common set of two distinct folding pathways with a heterogeneous nature of the transition state to the folding. We anticipate that these force fields are reasonably well balanced, thereby transferable to many other protein folds.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.1
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• pp.24-29
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• 2014

Atomistic molecular dynamics (MD) simulation has become mature enabling close approximation of the real behaviors of biomolecules. In biomolecular NMR field, atomistic MD simulation coupled with generalized implicit solvent model (GBIS) has contributed to improving the qualities of NMR structures in the refinement stage with experimental restraints. Here all-atom force fields play important roles in defining the optimal positions between atoms and angles, resulting in more precise and accurate structures. Despite successful applications in refining NMR structure, however, the research that has studied the influence of force fields in GBIS is limited. In this study, we compared the qualities of NMR structures of two model proteins, ubiquitin and GB1, under a series of AMBER force fields-ff99SB, ff99SB-ILDN, ff99SB-NMR, ff12SB, and ff13-with experimental restraints. The root mean square deviations of backbone atoms and packing scores that reflect the apparent structural qualities were almost indistinguishable except ff13. Qualitative comparison of parameters, however, indicates that ff99SB-ILDN is more recommendable, at least in the cases of ubiquitin and GB1.

• Bulletin of the Korean Chemical Society
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• v.35 no.7
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• pp.1944-1950
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• 2014

Employment of a time consuming, sophisticated calculation using the all-atom force field and generalized-Born implicit solvent model (GBIS) for refinement of NMR structures has become practical through advances in computational methods and capacities. GBIS refinement improves the qualities of the resulting NMR structures with reduced computational times. However, the contribution of GBIS to NMR structures has not been sufficiently studied in a quantitative way. In this paper, we report the effects of GBIS on the refined NMR structures of ubiquitin (UBQ) and GB1 with subsets of distance restraints derived from experimental data. Random omission prepared a series of distance restraints 0.05, 0.1, 0.3, 0.5, and 0.7 times smaller. For each number, we produced five different restraints for statistical analysis. We then recalculated the NMR structures using CYANA software, followed by GBIS refinements using the AMBER package. GBIS improved both the precision and accuracy of all the structures, but to varied levels. The degrees of improvement were significant when the input restraints were insufficient. In particular, GBIS enabled GB1 to form an accurate structure even with distance restraints of 5%, revealing that the root-mean-square deviation was less than 1 ${\AA}$ from the X-ray backbone structure. We also showed that the efficiency of searching the conformational space was more important for finding accurate structures with the calculation of UBQ with 5% distance restraints than the number of conformations generated. Our data will provide a meaningful guideline to judge and compare the structural improvements by GBIS.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.221-233
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• 2004

Molecular docking falls into the general category of global optimization problems since its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor-ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native -like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems.