• Bulletin of the Korean Chemical Society
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• 제30권5호
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• pp.1139-1142
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• 2009

Refinement of NMR structures by molecular dynamics (MD) simulations with a solvent model has improved the structural quality. In this study, we applied MD refinement with the generalized Born (GB) implicit solvent model to protein structure determined under membrane-like environments. Despite popularity of the GB model, its applications to the refinement of NMR structures of hydrophobic proteins, in which detergents or organic solvents enclose proteins, are limited, and there is little information on the use of another GB parameter for these cases. We carried out MD refinement of crambin NMR structure in dodecylphosphocholine (DPC) micelles (Ahn et al., J. Am. Chem. Soc. 2006, 128, 4398-4404) with GB/Surface area model and two different surface tension coefficients, one for aquatic and the other for hydrophobic conditions. Our data show that, of two structures by MD refinement with GB model, the one refined with the parameter to consider hydrophobic condition had the better qualities in terms of precision and solvent accessibility.

• 한국자기공명학회논문지
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• 제26권1호
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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.

• Bulletin of the Korean Chemical Society
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• 제31권9호
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• pp.2717-2720
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• 2010

• Bulletin of the Korean Chemical Society
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• 제35권7호
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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.

• 한국자기공명학회논문지
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• 제18권1호
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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.

• 한국자기공명학회논문지
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• 제17권1호
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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.

• Korean Chemical Engineering Research
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• 제43권1호
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• pp.71-75
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• 2005

초거대 자기 저항 물질인 $La_{0.5}Ca_{0.5}MnO_3$의 분말과 pellet을 졸-겔 법으로 제조하였다. 열처리 온도를 변화시켜 얻은 시료에 대해 FT-IR과 CP/MAS $^{13}C$ solid state NMR spectroscopy 그리고 XRD 등을 이용해 구조변화를 관찰하였다. 양이온 조성 비율을 알아보기 위해 ICP-AES를 이용하였으며, 입자크기와 균일도를 FE-SEM/EDS로, 미세구조와 격자 패턴은 TEM으로 관찰하였다. VSM을 이용하여 자기적 특성을 살펴보았으며 큐리온도($T_c$)는 236 K에서 측정되었다.

• 한국결정학회지
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• 제6권2호
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• pp.93-97
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• 1995

Re(≡NC6H5)(PPh3)2CI3 화합물이 1,2-bis(diphenylphosphino)ethane (DPPE)와 반응하여 fac-Re(≡NC6H5)(DPPE)CI3이 되었다. 이 생성물의 구조를 1H-NMR, 원소분석, 그리고 X-ray 회절법으로 규명하였다. 이 생성물은 단사정계로 (Pc, a=11.083(3)Å, b=10.930(1)Å, c=14.081(2)Å, β=108.37(2)°, Z=2) 결정화되었다. 최소자승법으로 구조를 정밀화한 결과 신뢰도는 R(wR2)=0.0254(0.0607)이였다.

• 한국결정학회지
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• 제7권2호
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• pp.113-119
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• 1996

Re(O)(PPh3)2Cl3과 2,3,4,5,6-pentafluoroaniline (C6F5NH2)의 반응으로 Re(NC6F5)(PPh3)2Cl3 생성물을 얻었다. 이 화합물의 구조를 1H-NMR, 원소분석, 그리고 X-ray 회절법으로 규명하였다. 화합물을 사방정계로 (Pna21, a=18.763Å, b=14.737(2)Å, c=16.707(3)Å, Z=4) 결정화되었다. 최소자승법으로 구조를 정밀화한 결과 신뢰도는 R(wR2) = 0.0455(0.1148)였다.

• 한국자기공명학회논문지
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• 제2권2호
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• pp.85-105
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• 1998

Prions cause neurodegenerative diseases in animals and humans. The scrapie prion protein (PrPSc) is the major-possibly only-component of the infectious prion and is generated from the cellular isoform (PrPC) by a conformational change. Limited proteolysis of PrPSc produces an polypeptide comprised primarily of residues 90 to 231, which retains infectivity. The three-dimensional structure of rPrP(90-231), a recombinant protein resembling PrPC with the Syrian hamster (SHa) sequence, was solved using multidimensional NMR. Low-resolution structures of rPrP(90-231), synthetic peptides up to 56 residues, a longer (29-231, full-length) protein with SHa sequence, and a short here further structure refinement of rPrP(90-231) and dynamic features of the protein. Consideration of these features in the context of published data suggests regions of conformational heterogeneity, structural elements involved in the PrPC\longrightarrowPrPSc transformation, and possible structural features related to a species barrier to transmission of prion diseases.