• Journal of the Korean Chemical Society
• /
• v.50 no.5
• /
• pp.362-368
• /
• 2006

SH group modifying chemicals were used to characterize the eight cysteine residues of cabbage PLD. 5,5-dithiobis(2-nitrobenzoate)(DTNB) was used to titrate the SH group of cysteine residues . Based on the optical density at 412nm due to the reduced DTNB, 4 SH groups are found to be present in a native PLD while 8 SH groups in the denatured PLD whose tertiary structure was perturbed by 8M urea. The results imply that among the 8 cysteine residues of PLD, the half(4) are exposed on the surface whereas the other half are present at the interior of the enzyme tertiary structure. The PLD was inactivated by SH modifying reagents such as p-chloromercuribenzoate(PCMB), iodoacetate, iodoacetamide, and N-ethylmaleimide. At the addition of dithiothreitol(DTT) only the PCMB inhibited PLD activity was recovered reversibly. The micro-environment of the exposed SH group of cysteine residues was examined with various disulfide compounds with different functional groups and we found that anionic or neutral disulfides appear to be more effective than the positively charged cystamine for inactivating the PLD activity. The effect of redox state of cysteine residues on the PLD activity was further explored with H2O2. The oxidation of SH groups by H2O2 inhibited the PLD activity more than 70%, which was mostly recovered by DTT. From these results, we could confirm chemically that all the cysteine residues of PLD are present as in their reduced SH forms and the 4 SH groups exposed on the surface of the enzyme may play important roles in the regulation of PLD activity.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2003.10a
• /
• pp.277-287
• /
• 2003

Acetolactate synthase (ALS, EC 4.1.3.18; also referred to as acetohydroxy acid synthase) catalyzes the first common step in the biosynthesis of valine, leucine, and isoleucine in microorganisms and plants. Recently X-ray structure of yeast ALS was available. Pair-wise alignment of yeast and tobacco ALS sequences revealed 63% sequence similarity. Using Deep View and automatic modeling on Swiss model server, we have generated reliable models of tobacco ALS based on yeast ALS template with a calculated pair-wise RMSD of 0.86 Angstrom. Functional roles of four residues located on the subunit interface (H142, El43, M350, and R376) were examined by site-directed mutagenesis. Seven mutants were generated and purified, of which three mutants (H142T, M350V, and R376F) were found to be inactivated under various assay conditions. The H142k mutant showed moderately altered kinetic properties. The E143A mutant increased 10-fold in K$_m$ value while other parameters remained unchanged. The M350C mutant was strongly resistant to three tested herbicides, while the R376k mutant can bind with herbicide carder at similar affinity to that of wild type enzyme, as determined by tryptophan quenching study. Except M350V mutant, all other mutants were ate to bind with cofactor FAD. Taken together, it is likely that residues H142 and E143 are located at the active site, while residues M350 and R376 are possibly located at the overlapping region of active site and herbicide binding site of the enzyme. Our data also allows us to hypothesize that the interaction between side chains of residues M350 and R376 are probably essential for the correct conformation of the active site. It remains to be elucidated that, whether the herbicide, upon binding with enzyme, inactivates the enzyme by causing change in the active site allosterically, which is unfavorable for catalytic activity.

• Journal of Life Science
• /
• v.17 no.1 s.81
• /
• pp.6-11
• /
• 2007

[ $\beta$ ]-Fructofuranosidases, a family 32 of glycoside hydrolases (GH32), share three conserved domains including the W(L/M)(C/N)DP(Q/N), FRDPK, and ECP(D/G) motifs. The functional role of the conserved acidic residues within three domains of levan fructotransferase, one of the $\beta-fructofuranosidases$, from Microbacterium sp. AL-210 was studied by site-directed mutagenesis. Each mutant was overexpressed in E. coli BL21(DE3) and purified by using Hi-Trap chelating affinity chromatography and fast performance liquid chromatography. Substitution of Asp-63 by Ala, Asp-195 by Asn, and Glu-245 by Ala and Asp decreased the enzyme activity by approximately 100-fold compared to the wild-type enzyme. This result indicates that three acidic residues Asp-63, Asp-195, and Glu-245 play a major role in catalysis. Since the three acidic residues are present in a conserved position in inulinase, levanase, levanfructotransferase, and invertase, they are likely to have a common functional role as nucleophile, transition state stabilizer, and general acid in $\beta-fructofuranosidases$.

• Molecules and Cells
• /
• v.27 no.3
• /
• pp.359-363
• /
• 2009

Chfr, a checkpoint with FHA and RING finger domains, plays an important role in cell cycle progression and tumor suppression. Chfr possesses the E3 ubiquitin ligase activity and stimulates the formation of polyubiquitin chains by Ub-conjugating enzymes, and induces the proteasome-dependent degradation of a number of cellular proteins, including Plk1 and Aurora A. While Chfr is a nuclear protein that functions within the cell nucleus, how Chfr is localized in the nucleus has not been clearly demonstrated. Here, we show that nuclear localization of Chfr is mediated by nuclear localization signal (NLS) sequences. To reveal the signal sequences responsible for nuclear localization, a short lysine-rich stretch (KKK) at amino acid residues 257-259 was replaced with alanine, which completely abolished nuclear localization. Moreover, we show that nuclear localization of Chfr is essential for its checkpoint function but not for its stability. Thus, our results suggest that NLS-mediated nuclear localization of Chfr leads to its accumulation within the nucleus, which may be important in the regulation of Chfr activation and Chfr-mediated cellular processes, including cell cycle progression and tumor suppression.

• Journal of IKEEE
• /
• v.13 no.3
• /
• pp.18-23
• /
• 2009

FEATURE is a computational method to recognize functional and structural sites for automatic protein function prediction. By profiling physicochemical properties around residues, FEATURE can characterize and predict functional and structural sites in 3D protein structures in a high-throughput manner. Despite its effectiveness, it has been challenging to apply FEATURE to novel protein data due to limited customization support. To address this problem, we thoroughly analyze the internal modules of FEATURE and propose a methodology to customize FEATURE so that it can be used for new protein data for automatic functional annotations.

• Journal of Integrative Natural Science
• /
• v.15 no.4
• /
• pp.179-186
• /
• 2022

The c-Jun N-terminal kinase (JNK3) play major role in neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, cerebral ischemia and other Central Nervous System disorders. Since JNK3 is primarily stated in the brain and stimulated by stress-stimuli, this situation is conceivable that inhibiting JNK3 could be a possible treatment for the mechanisms underlying neurodegenerative diseases. In this study drugs from Zinc15 database were screened to identify the JNK3 inhibitors by Molecular docking and Density functional theory approach. Molecular docking was done by Autodock vina and the ligands were selected based on the binding affinity. Our results identified top ten novel ligands as potential inhibitors against JNK3. Molecular docking revealed that Venetoclax, Fosaprepitant and Avapritinib exhibited better binding affinity and interacting with proposed binding site residues of JNK3. Density functional theory was used to compute the values for energy gap, lowest unoccupied molecular orbital (LUMO), and highest occupied molecular orbital (HOMO). The results of Density functional theory study showed that Venetoclax, Fosaprepitant and Avapritinib serves as a lead compound for the development of JNK3 small molecule inhibitors.

• BMB Reports
• /
• v.32 no.3
• /
• pp.306-310
• /
• 1999

The partial cDNA of the MT-c clone encoding snake venom metalloprotease was subcloned and expressed in E. coli. The expressed metalloprotease was purified by affinity chromatography in the presence of urea, and then successfully refolded into its functional form, retaining metalloprotease activity that hydrolyzes fibrinogen. The simple and convenient refolding strategy established in this work was highly efficient in recovering the recombinant enzyme activity. Experimental evidence suggests that the C-terminal amino acid stretch of 16 residues is a critical sequence for proper folding of the metalloprotease domain.

• Proceedings of the Korean Biophysical Society Conference
• /
• 1998.06a
• /
• pp.33-33
• /
• 1998

Oxidation and reduction of amino acid residues in proteins affect their functional properties. Especially, redox modulation of ion channel activities has been reported in number of ion channel proteins. In this study, we investigated the effects of tertiary-butyl hydrogen peroxide (tBHP) on the large-conductance Ca$\^$2＋/ -activated K$\^$+/(Maxi-K) channel of rat brain using lipid bilayer reconstitution technique.(omitted)

• Food Science and Industry
• /
• v.43 no.2
• /
• pp.67-78
• /
• 2010

• Mass Spectrometry Letters
• /
• v.7 no.4
• /
• pp.85-90
• /
• 2016

Post-translational modifications (PTMs) of proteins regulate self-renewal and differentiation in embryonic stem cells (ESCs). Nitration of tyrosine residues of proteins in ESCs modulates their downstream pathways, which can affect self-renewal and differentiation. However, protein tyrosine nitration (PTN) in ESCs has been rarely studied. We reviewed 23 nitrated sites in stem cell proteins. Functional enrichment analysis showed that these nitrated proteins are involved in signal transduction, cell adhesion and migration, and cell proliferation in ESCs. Comparison between the nitrated and known phosphorylated sites revealed that 7 nitrated sites had overlapping phosphorylated sites, indicating functional links of PTNs to their associated signaling pathways in ESCs. Therefore, nitrated proteome provides a basis for understanding potential roles of PTN in self-renewal and differentiation of ESCs.