• 한국자기공명학회논문지
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• 제19권3호
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• pp.132-136
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• 2015

Nuclear magnetic resonance (NMR) spectroscopy, owing to its ability to provide atomic level information on molecular structure, dynamics and interaction, has become one of the most powerful methods in early drug discovery where hit finding and hit-to-lead generation are mainly pursued. In recent years, drug discovery programs originating from the fragment-based drug discovery (FBDD) strategies have been widely incorporated into academia and industry in which a wide variety of NMR methods become an indispensable arsenal to elucidate the binding of small molecules onto bimolecular targets. In this review, I briefly describe FBDD and introduce NMR methods mainly used in FBDD campaigns of my company. In addition, quality control of fragment library and practical NMR methods in industrial aspect are discussed shortly.

• 한국자기공명학회:학술대회논문집
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• 한국자기공명학회 2001년도 제18회 학술발표회
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• pp.17-17
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• 2001

• 한국자기공명학회:학술대회논문집
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• 한국자기공명학회 1999년도 하계총회 및 제15회 자기공명 학술발표회
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• pp.9-9
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• 1999

• 한국자기공명학회:학술대회논문집
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• 한국자기공명학회 2000년도 동계총회 및 제16회 자기공명 학술발표회
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• pp.12-13
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• 2000

• 한국자기공명학회:학술대회논문집
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• 한국자기공명학회 2002년도 International Symposium on Magnetic Resonance
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• pp.29-29
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• 2002

• 한국자기공명학회:학술대회논문집
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• 한국자기공명학회 2002년도 International Symposium on Magnetic Resonance
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• pp.42-42
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• 2002

• Bulletin of the Korean Chemical Society
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• 제17권2호
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• pp.109-112
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• 1996

• Bulletin of the Korean Chemical Society
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• 제28권4호
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• pp.662-666
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• 2007

Poly(vinyl butyral) (PVB) with different wt% water was studied gravimetrically as well as with 1H magic angle spinning (MAS) nuclear magnetic resonance (NMR). The composition of PVB samples changes during MAS NMR because of the centrifugal force. As MAS time progresses, initially free water was removed fast but bound water also was gradually depleted. More water was diminished at faster spinning speeds, longer spinning time, higher temperatures, and higher initial water contents. As water in PVB was reduced, the chemical shifts and line widths of different types of water and also those of PVB changed. Our results demonstrate that 1H MAS NMR carried out at 10 kHz in less than about 5 minutes is a convenient and sensitive technique to measure: (a) the content variations of different types of water in polymers, (b) the degree of the interaction of water and polymer, and (c) the molecular dynamics of the polymer. Our study can be extended to different soft polymers with other small molecules than water in them.

• 한국자기공명학회논문지
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• 제19권2호
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• pp.83-87
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• 2015

Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain ($Syn4^{cyto}$) in focal contacts, interacts with various cell adhesion adaptor proteins including $Syn4^{cyto}$ to control cell signaling. Syndesmos consists of 211 amino acids and it exists as a dimer (44kDa) in solution. Recently, we have determined the structure of syndesmos by x-ray crystallography, however, dynamics related to syndecan binding still remain elusive. In this report, we performed NMR experiments to acquire biochemical and structural information of syndesmos. Based on a series of three-dimensional triple resonance experiments on a $^{13}C/^{15}N/^2H$ labeled protein, NMR spectra were obtained with well dispersed and homogeneous NMR data. We present the sequence specific backbone assignment of syndesmos and assigned NMR data with combination structural information can be directly used for the studies on interaction with $Syn4^{cyto}$ and other binding molecules.

• 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.