• Molecules and Cells
• /
• 제41권12호
• /
• pp.1045-1051
• /
• 2018

The developmentally regulated GTP binding protein 2 (DRG2) is involved in the control of cell growth and differentiation. Here, we demonstrate that DRG2 regulates microtubule dynamics in HeLa cells. Analysis of live imaging of the plus-ends of microtubules with EB1-EGFP showed that DRG2 deficiency (shDRG2) significantly reduced the growth rate of HeLa cells. Depletion of DRG2 increased 'slow and long-lived' subpopulations, but decreased 'fast and short-lived' subpopulations of microtubules. Microtubule polymerization inhibitor exhibited a reduced response in shDRG2 cells. Using immunoprecipitation, we show that DRG2 interacts with tau, which regulates microtubule polymerization. Collectively, these data demonstrate that DRG2 may aid in affecting microtubule dynamics in HeLa cells.

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

• BMB Reports
• /
• 제43권10호
• /
• pp.656-663
• /
• 2010

Amyloid precursor protein (APP), which is critically involved in the pathogenesis of Alzheimer's disease (AD), is cleaved by gamma/epsilon-secretase activity and results in the generation of different lengths of the APP Intracellular C-terminal Domain (AICD). In spite of its small size and short half-life, AICD has become the focus of studies on AD pathogenesis. Recently, it was demonstrated that AICD binds to different intracellular binding partners ('adaptor protein'), which regulate its stability and cellular localization. In terms of choice of adaptor protein, phosphorylation seems to play an important role. AICD and its various adaptor proteins are thought to take part in various cellular events, including regulation of gene transcription, apoptosis, calcium signaling, growth factor, and $NF-{\kappa}B$ pathway activation, as well as the production, trafficking, and processing of APP, and the modulation of cytoskeletal dynamics. This review discusses the possible roles of AICD in the pathogenesis of neurodegenerative diseases including AD.

• 한국광과학회:학술대회논문집
• /
• 한국광과학회 2001년도 학술대회지
• /
• pp.31-31
• /
• 2001

• 한국광과학회:학술대회논문집
• /
• 한국광과학회 2005년도 제12회 학술대회 논문초록
• /
• pp.97-97
• /
• 2005

• Biomolecules & Therapeutics
• /
• 제29권5호
• /
• pp.527-535
• /
• 2021

Sclerostin (SOST), a regulator of bone formation in osteocytes, inhibits the canonical Wnt signaling by interacting with low-density lipoprotein receptor-related protein 5/6 (LRP5/6) to prevent Wnt binding. Loss-of-function mutations of the SOST gene caused massive bone outgrowth and SOST-null mouse exhibited a high bone density phenotype. Therefore, SOST has been suggested as a promising therapeutic target for osteoporosis. A few previous studies with X-ray crystallography identified the binding interfaces between LRP6 and SOST, but there are limitations in these studies as they used truncated SOST protein or SOST peptide. Here, we analyzed the conformational dynamics of SOST-LRP6 E1E2 complex using hydrogen/deuterium exchange mass spectrometry (HDX-MS). We examined the effect of the C-terminal tail of SOST on LRP6 conformation upon complex formation. HDX-MS analysis suggested a new potential binding interface for the C-terminal region of SOST that was missing from the previous crystal structure of the SOST-LRP6 E1E2 complex.

• Bulletin of the Korean Chemical Society
• /
• 제35권3호
• /
• pp.858-864
• /
• 2014

Recently, many researches have shown that even photosynthetic light-harvesting pigment-protein complexes can have quantum coherence in their excitonic energy transfer at cryogenic and physiological temperatures. Because the protein supplies such noisy environment around pigments that conventional wisdom expects very short lived quantum coherence, elucidating the mechanism and searching for an applicability of the coherence have become an interesting topic in both experiment and theory. We have previously studied the quantum coherence of a phycocyanin 645 complex in a marine algae harvesting light system, using Poisson mapping bracket equation (PBME). PBME is one of the applicable methods for solving quantum-classical Liouville equation, for following the dynamics of such pigment-protein complexes. However, it may suffer from many defects mostly from mapping quantum degrees of freedom into classical ones. To make improvements against such defects, benchmarking targets with more accurately described dynamics is highly needed. Here, we fall back to reduced hierarchical equation of motion (HEOM), for such a purpose. Even though HEOM is known to applicable only to simplified system that is coupled to a set of harmonic oscillators, it can provide ultimate accuracy within the regime of quantum-classical description, thus providing perfect benchmark targets for certain systems. We compare the evolution of the density matrix of pigment excited states by HEOM against the PBME results at physiological temperature, and observe more sophisticated changes of density matrix elements from HEOM. In PBME, the population of states with intermediate energies display only monotonically increasing behaviors. Most importantly, PBME suffers a serious issue of wrong population in the long time limit, likely generated by the zero-point energy leaking problem. Future prospects for developments are briefly discussed as a concluding remark.

• Asian Pacific Journal of Cancer Prevention
• /
• 제16권9호
• /
• pp.3817-3825
• /
• 2015

Background: The human protein methyl-transferase DOT1L catalyzes the methylation of histone H3 on lysine 79 (H3K79) at homeobox genes and is also involved in a number of significant processes ranging from gene expression to DNA-damage response and cell cycle progression. Inhibition of DOT1L activity by shRNA or small-molecule inhibitors has been established to prevent proliferation of various MLL-rearranged leukemia cells in vitro, establishing DOT1L an attractive therapeutic target for mixed lineage leukemia (MLL). Most of the drugs currently in use for the MLL treatment are reported to have low efficacy, hence this study focused on various natural compounds which exhibit minimal toxic effects and high efficacy for the target receptor. Materials and Methods: Structures of human protein methyl-transferase DOT1L and natural compound databases were downloaded from various sources. Virtual screening, molecular docking, dynamics simulation and drug likeness studies were performed for those natural compounds to evaluate and analyze their anti-cancer activity. Results: The top five screened compounds possessing good binding affinity were identified as potential high affinity inhibitors against DOT1L's active site. The top ranking molecule amongst the screened ligands had a Glide g-score of -10.940 kcal/mol and Glide e-model score of -86.011 with 5 hydrogen bonds and 12 hydrophobic contacts. This ligand's behaviour also showed consistency during the simulation of protein-ligand complex for 20000 ps, which is indicative of its stability in the receptor pocket. Conclusions: The ligand obtained out of this screening study can be considered as a potential inhibitor for DOT1L and further can be treated as a lead for the drug designing pipeline.

• International Journal of Oral Biology
• /
• 제33권4호
• /
• pp.125-129
• /
• 2008

Inositol 1,4,5-trisphosphate ($IP_3$) plays an important role in the release of $Ca^{2+}$ from intracellular stores into the cytoplasm in a variety of cell types. $IP_3$ translocation dynamics have been studied in response to many types of cell signals. However, the dynamics of cytosolic $IP_3$ in salivary acinar cells are unclear. A green fluorescent protein (GFP)-tagged pleckstrin homology domain (PHD) was constructed and introduced into a phospholipase C ${\delta}1$ (PLC ${\delta}1$) transgenic mouse, and then the salivary acinar cells were isolated. GFP-PHD was heterogeneously localized at the plasma membrane and intracellular organelles in submandibular gland and parotid gland cells. Application of trypsin, a G protein-coupled receptor activator, to the two types of cells caused an increase in GFP fluorescence in the cell cytoplasm. The observed time course of trypsin-evoked $IP_3$ movement in acinar cells was independent of cell polarity, and the fluorescent label showed an immediate increase throughout the cells. These results suggest that GFP-PHD in many tissues of transgenic mice, including non-cultured primary cells, can be used as a model for examination of $IP_3$ intracellular dynamics.

• The Korean Journal of Physiology and Pharmacology
• /
• 제26권6호
• /
• pp.469-478
• /
• 2022

WNT signaling plays an important role in cardiac development, but abnormal activity is often associated with cardiac hypertrophy, myocardial infarction, remodeling, and heart failure. The effect of WNT signaling on regulation of atrial natriuretic peptide (ANP) secretion is unclear. Therefore, the purpose of this study was to investigate the effect of Wnt agonist 1 (Wnta1) on ANP secretion and mechanical dynamics in beating rat atria. Wnta1 treatment significantly increased atrial ANP secretion and pulse pressure; these effects were blocked by U73122, an antagonist of phospholipase C. U73122 also abolished the effects of Wnta1-mediated upregulation of protein kinase C (PKC) β and γ expression, and the PKC antagonist Go 6983 eliminated Wnta1-induced secretion of ANP. In addition, Wnta1 upregulated levels of phospho-transforming growth factor-β activated kinase 1 (p-TAK1), TAK1 banding 1 (TAB1) and phospho-activating transcription factor 2 (p-ATF2); these effects were blocked by both U73122 and Go 6983. Wnta1-induced ATF2 was abrogated by inhibition of TAK1. Furthermore, Wnta1 upregulated the expression of T cell factor (TCF) 3, TCF4, and lymphoid enhancer factor 1 (LEF1), and these effects were blocked by U73122 and Go 6983. Tak1 inhibition abolished the Wnta1-induced expression of TCF3, TCF4, and LEF1 and Wnta1-mediated ANP secretion and changes in mechanical dynamics. These results suggest that Wnta1 increased the secretion of ANP and mechanical dynamics in beating rat atria by activation of PKC-TAK1-ATF2-TCF3/LEF1 and TCF4/LEF1 signaling mainly via the WNT/Ca²⁺ pathway. It is also suggested that WNT-ANP signaling is implicated in cardiac physiology and pathophysiology.