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Ryu, Hyojung,Lim, GyuTae,Sung, Bong Hyun,Lee, Jinhyuk Oxford University Press 2016 Bioinformatics Vol. No.
<P><B>Summary:</B> Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores.</P><P><B>Availability and implementation:</B> NMRe is available at http://psb.kobic.re.kr/nmre/</P><P><B>Contact:</B> jinhyuk@kribb.re.kr</P><P><B>Supplementary information:</B> Supplementary data are available at <I>Bioinformatics</I> online.</P>
NMR Structure Determination by Conformational Space Annealing
Jinhyuk Lee,Jinwoo Lee,Jooyoung Lee 한국산업응용수학회 2009 한국산업응용수학회 학술대회 논문집 Vol.4 No.2
We have carried out numerical experiments to investigate the applicability of global optimization method to the NMR structure determination. Since the number of NMR observables is relatively small in the early stage of NMR structure determination process and long range NOE observables are difficult to obtain, advanced sampling techniques are greatly in need to generate valid NMR structures from a small number of experimental restraints. By utilizing conformational space annealing method, we have determined solution NMR structures from NOE distance and backbone dihedral restraints. Several solution NMR structures are determined starting from fully randomized conformations. We have evaluated them by measuring the qualities of determined structures, such as structure convergence of ensemble, Ramachandran preferences, clash scores, and the total NOE violation. These qualities are compared to those from the corresponding PDB structures.
Sulfuretin, a natural Src family kinases inhibitor for suppressing solar UV-induced skin aging
Han, Ahram,Lee, Jinhyuk,Lee, Myung-hee,Lee, Sung-Young,Shin, Eun Ju,Song, Young-Ran,Lee, Kwang Min,Lee, Ki Won,Lim, Tae-Gyu Elsevier 2019 Journal of Functional Foods Vol.52 No.-
<P><B>Abstract</B></P> <P>This study suggests sulfuretin as an ant-skin aging agent. Sulfuretin significantly reduces solar UV (sUV)-increased matrix metalloproteinase-1 (MMP-1) expression and c-Jun phosphorylation in human dermal fibroblasts as well as skin tissue. An examination of the underlying mechanisms showed that sUV-activated MAPK signaling pathways are blocked by sulfuretin. Interestingly, sulfuretin directly inhibits the kinase activity of selected Src family. Because the amino acid sequence of Hck kinase which used kinase array is 230–497, it was assumed that sulfuretin interacts with this conserved domain of Src family kinase. It was also found that sulfuretin directly binds to sulfuretin with the lowest binding energy of −8.9 kcal/mol and free energy of −10.07 kcal/mol. Additionally, Hck protein was precipitated with sulfuretin-conjugated Sepharose 4B beads in HDFs cell lysate. Overall, present findings indicated that sulfuretin plays the role of anti-skin aging agent by acting as a general Src family kinase inhibitor in human skin.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The anti-wrinkle formation activity of sulfuretin was suggested. </LI> <LI> Sulfuretin acts as general Src family kinase inhibitor. </LI> <LI> The expected interaction was assumed using computer modeling. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
Understanding β-Hairpin Formation: Computational Studies for Three Different Hairpins
Jinhyuk Lee,신석민 대한화학회 2008 Bulletin of the Korean Chemical Society Vol.29 No.4
We have studied the folding mechanism of β-hairpins in the proteins 1GB1, 3AIT and 1A2P by conducting unfolding simulations at moderately high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the positions of the hydrophobic core residues lead to subtle differences in the details of folding dynamics. However, the folding of three different hairpins can be explained by a unified mechanism that is a blend of the hydrogen-bond-centric and the hydrophobic-centric models. The initial stage of β-hairpin folding involves various partially folded intermediate structures which are stabilized by both the van der Waals interactions of hydrophobic core residues and the electrostatic interactions of non-native hydrogen bonds. The native structure is obtained by forming native contacts in the final tune-up process. Depending on the relative positions of the hydrophobic residues, the actual mechanism of hairpin folding may or may not exhibit well-defined intermediates.
Lee, Su Ui,Lee, Seoghyun,Ro, Hyunju,Choi, Ji-Hee,Ryu, Hyung Won,Kim, Mun-Ock,Yuk, Heung Joo,Lee, Jinhyuk,Hong, Sung-Tae,Oh, Sei-Ryang Elsevier 2018 Phytomedicine Vol.40 No.-
<P>Conclusion: We propose that piscroside C is a promising therapeutic constituent of YPL-001 through its inhibition of PKC delta activity in the TNF-RSC/IKK/NF-kappa B/MUC5AC signaling cascade.</P>
Implementation and application of helix–helix distance and crossing angle restraint potentials
Lee, Jinhyuk,Im, Wonpil Wiley Subscription Services, Inc., A Wiley Company 2007 Journal of computational chemistry Vol. No.
<P>Based on the definition of helix–helix distance and crossing angle introduced by Chothia et al. (J Mol Biol 1981, 145, 215), we have developed the restraint potentials by which the distance and crossing angle of two selected helices can be maintained around target values during molecular dynamics simulations. A series of assessments show that calculated restraint forces are numerically accurate. Since the restraint forces are only exerted on atoms which define the helical principal axes, each helix can rotate along its helical axis, depending on the helix–helix intermolecular interactions. Such a restraint potential enables us to characterize the helix–helix interactions at atomic details by sampling their conformational space around specific distance and crossing angle with (restraint) force-dependent fluctuations. Its efficacy is illustrated by calculating the potential of mean force as a function of helix–helix distance between two transmembrane helical peptides in an implicit membrane model. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 669–680, 2007</P> <B>Graphic Abstract</B> <P> <img src='wiley_img/01928651-2007-28-3-JCC20614-gra001.gif' alt='wiley_img/01928651-2007-28-3-JCC20614-gra001'> </P>