NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores

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>

The effect of support in deoxygenation of stearic acid over tungsten-platinum catalyst

Jinhyuk Lee,Ilho Choi,Hyeyoung Choi,Jeongsik Han,Jinsuk Lee,Kyungran Hwang,Kwanyoung Lee 한국신재생에너지학회 2016 한국신재생에너지학회 학술대회논문집 Vol.2016 No.5

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.

KINGS: A Preliminary Result of the Fornax cluster

JaeHyung Lee,Myung Gyoon Lee,Sungsoon lim,Jubee Sohn,In Sung Jang,Jinhyuk Ryu,wang-Ho Lee,Youkyung Ko,Jung Hwan Lee 한국천문학회 2016 天文學會報 Vol.41 No.1

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>

<i>De novo</i> protein structure prediction by dynamic fragment assembly and conformational space annealing

Lee, Juyong,Lee, Jinhyuk,Sasaki, Takeshi N.,Sasai, Masaki,Seok, Chaok,Lee, Jooyoung Wiley Subscription Services, Inc., A Wiley Company 2011 Proteins Vol.79 No.8

<P><B>Abstract</B></P><P><I>Ab initio</I> protein structure prediction is a challenging problem that requires both an accurate energetic representation of a protein structure and an efficient conformational sampling method for successful protein modeling. In this article, we present an <I>ab initio</I> structure prediction method which combines a recently suggested novel way of fragment assembly, dynamic fragment assembly (DFA) and conformational space annealing (CSA) algorithm. In DFA, model structures are scored by continuous functions constructed based on short‐ and long‐range structural restraint information from a fragment library. Here, DFA is represented by the full‐atom model by CHARMM with the addition of the empirical potential of DFIRE. The relative contributions between various energy terms are optimized using linear programming. The conformational sampling was carried out with CSA algorithm, which can find low energy conformations more efficiently than simulated annealing used in the existing DFA study. The newly introduced DFA energy function and CSA sampling algorithm are implemented into CHARMM. Test results on 30 small single‐domain proteins and 13 template‐free modeling targets of the 8th Critical Assessment of protein Structure Prediction show that the current method provides comparable and complementary prediction results to existing top methods. Proteins 2011; © 2011 Wiley‐Liss, Inc.</P>

Finding Hidden Star Clusters Using the WISE

Jinhyuk Ryu,Jaehyung Lee,Myung Gyoon Lee 한국천문학회 2012 天文學會報 Vol.37 No.1

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>

Vision-based Tactile Sensor using Random Pattern

Jinhyuk Lee,Suwoong Lee,Minyoung Kim 제어로봇시스템학회 2022 제어로봇시스템학회 국제학술대회 논문집 Vol.2022 No.11

Tactile sensors are being used in various fields such as automated factories and human collaboration, and have been developed in various technological ways. Most contact discrimination methods are performed through sensing of the physical aspect. On the other hand, in recent years, a vision-based tactile sensor that can obtain more information by replacing the existing method with only visual data of an image using a camera sensor has been proposed. Existing visionbased tactile sensors have markers as a standard to detect changes or have a pattern of a certain shape and arrangement. We propose a vision-based tactile sensor that can estimate the position of a contact with an easy design and compact hardware size. As a vision-based tactile sensor is a sensor that acquires various information about contact through image processing of visual data, it is possible to update the function of a tactile sensor by making good use of the fact that it is possible only through algorithm development without a separate hardware reconfiguration. We plan to continue our research to obtain more detailed contact information such as accuracy, force, and direction of force.

Fisetin inhibits TNF-α/NF-κB-induced IL-8 expression by targeting PKCδ in human airway epithelial cells

Lee, Seoghyun,Ro, Hyunju,In, Hyun Ju,Choi, Ji-Hee,Kim, Mun-Ock,Lee, Jinhyuk,Hong, Sung-Tae,Lee, Su Ui Elsevier 2018 Cytokine Vol.108 No.-

<P><B>Abstract</B></P> <P>Fisetin (3,7,3′,4′-tetrahydroxyflavone), a natural flavonoid, is a therapeutic agent for respiratory inflammatory diseases such as chronic obstructive pulmonary disease (COPD). However, detailed molecular mechanisms regarding the target protein of fisetin remain unknown.</P> <P>Fisetin significantly reduces tumour necrosis factor alpha (TNF-α)-induced interleukin (IL)-8 levels by inhibiting both nuclear factor kappa B (NF-κB) transcriptional activity and the phosphorylation of its upstream effectors. We show that fisetin prevents interactions between protein kinase C (PKC)δ and TNF receptor-associated factor 2 (TRAF2), thereby inhibiting the inhibitor of kappa B kinase (IKK)/NF-κB downstream signalling cascade. Furthermore, we found that fisetin directly binds to PKCδ <I>in vitro</I>. Our findings provide evidence that fisetin inhibits the TNF-α-activated IKK/NF-κB cascade by targeting PKCδ, thereby mediating inflammatory diseases such as COPD.</P> <P>These data suggest that fisetin is a good therapeutic drug for the treatment of inflammatory lung diseases, such as COPD, by inhibiting the TNF-α/NF-κB signalling pathway.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Fisetin inhibits TNF-α-increased <I>IL-8</I> gene expression by blocking NF-κB activity. </LI> <LI> Fisetin inhibits TNF-α-mediated interactions between PKCδ and TRAF2. </LI> <LI> Fisetin inhibits PKCδ activity. </LI> </UL> </P>