• BMB Reports
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• v.28 no.4
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• pp.363-367
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• 1995

E. coli methionyl-tRNA synthetase is one of the class I tRNA synthetases. The Tryptophane residue at the position 461 located in the C-terminal domain of the enzyme is a key amino acid for the interaction with the anticodon of $tRNA^{Met}$. W461 was replaced with other amino acids to determine the chemical requirement for the interaction with the anticodon of $tRNA^{Met}$. Saturation mutagenesis at the position 461 generated a total of 12 substitution mutants of methionyl-tRNA synthetase. All the mutants showed the same in vivo stability as the wild-type enzyme, suggesting that the amino acid substitutions did not cause severe conformational change of the protein The mutants containing tyrosine, phenylalanine, histidine and cysteine substitutions showed in vivo activity while all the other mutants did not. The comparison of the in vitro aminoacylation activities of these mutants showed that aromatic ring structure, Van der Waals volume and hydrogen bond potential of the amino acid residue at the position 461 are the major determinants for the interaction with the anticodon of $tRNA^{Met}$.

• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.90-95
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• 2016

Heat Shock 70kDa Protein 1-Like(HSPA1L)는 Heat-shock protein70(HSP70) family에 속하는 chaperone protein으로 polypeptide folding, assembly, protein degradation 등 다양한 biological processes에 관여하고 있다. HSPA1L은 human methyltransferase-like protein 21A(METTL21A)에 의해 lysine residue에 methylation이 일어나게 되는데, 암세포에서 일반적인 HSPA1L은 주로 세포질에서 발견되는 반면 methylated HSPA1L의 경우 주로 핵에서 발견이 됨으로써 HSPA1L methylation이 암 세포 성장에 중요할 역할을 할 것이라 추측되며 anti-cancer drug target으로 주목 받고 있다. 하지만 현재 HSPA1L의 구조가 부분적으로만 밝혀져 있어 HSPA1L와 METTL21A가 어떤 residue들이 interaction 하여 binding을 하는지에 대해서 아직 밝혀 지지 않았다. 이로 인해 anti-cancer drug target으로서의 연구에 제한이 있다. 이번 연구에서는 homology modeling(Galaxy-TBM, Galaxy-refine)을 통해 HSPA1L 전체 구조를 밝혀 낸 후, HSPA1L 와 METTL21A를 protein-protein docking을 통해 binding pose 예측을 하였다. 이러한 binding pose를 protein interaction analysis하여 HSPA1L과 METTL21A binding에 관여하는 중요 residue들을 밝혀 냈다. 이러한 structural information은 methylated HSPA1L와 암 세포 성장간의 연관성, 더 나아가 anti-cancer drug 개발로 까지도 이어 질 수 있을 것이라 생각한다.

• Proceedings of the Korean Biophysical Society Conference
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• 1999.06a
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• pp.40-40
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• 1999

We propose a method where interaction energies and force components are calculated separately for each residue of biomolecules. It is found that the correlation factors obtained from the analysis of five types of force terms and one interaction energy term (main chain self-energy) can be used to predict a mutants free energy difference relative to wild type.(omitted)

• Journal of applied mathematics & informatics
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• v.27 no.5_6
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• pp.1017-1031
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• 2009

The problem of interaction of surface water waves by small undulation at the bottom of a laterally unbounded sea is treated on the basis of linear water wave theory for both normal and oblique incidences. Perturbation analysis is employed to obtain the first order corrections to the reflection and transmission coefficients in terms of integrals involving the shape function c(x) representing the bottom undulation. Fourier transform method and residue theorem are applied to obtain these coefficients. As an example, a patch of sinusoidal ripples is considered in both the cases as the shape function. The principal conclusion is that the reflection coefficient is oscillatory in the ratio of twice the surface wave number to the wave number of the ripples. In particular, there is a Bragg resonance between the surface waves and the ripples, which is associated with high reflection of incident wave energy. The theoretical observations are validated computationally.

• Genomics & Informatics
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• v.21 no.3
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• pp.41.1-41.11
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• 2023

The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.

• Animal cells and systems
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• v.15 no.2
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• pp.95-106
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• 2011

The transient receptor potential vanilloid 4 (TRPV4) cation channel, a member of the TRP vanilloid subfamily, is expressed in a broad range of tissues. Nitric oxide (NO) as a gaseous signal mediator shows a variety of important biological effects. In many instances, NO has been shown to exhibit its activities via a protein S-nitrosylation mechanism in order to regulate its protein functions. With functional assays via site-directed mutagenesis, we demonstrate herein that NO induces the S-nitrosylation of TRPV4 $Ca^{2+}$ channel on the $Cys^{853}$ residue, and the S-nitrosylation of $Cys^{853}$ reduced its channel sensitivity to 4-${\alpha}$ phorbol 12,13-didecanoate and the interaction between TRPV4 and calmodulin. A patch clamp experiment and $Ca^{2+}$ image analysis show that the S-nitrosylation of $Cys^{853}$ modulates the TRPV4 channel as an inhibitor. Thus, our data suggest a novel regulatory mechanism of TRPV4 via NO-mediated S-nitrosylation on its $Cys^{853}$ residue.

• Journal of Sericultural and Entomological Science
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• v.39 no.2
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• pp.169-173
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• 1997

The behavior of tyrosine(Tyr.) residue of Bombyx mori silk fiber from yellow fluorescent cocoon has been examined for the dependence of pH in aqueous silk solution under the presence of orange II salt. Through the peak separation of angular dependence of spectral pattern of 15N-Tyr. and [1-13C]-Tyr. between the fiber axis and the molecular bond direction, N-H bond in fiber as well as the orientation distribution around the fiber axis were analyzed. Also, and sericin component was obtained from these angular dependence of oriented spectral pattern. The pH dependence of the 13C NMR chemical shift of B. mori silk fibroin was examined in aqueous solution in the presince of orange II are broad at pH$\geq$7.0. However, these become sharper at pH$\geq$8.0 and remain sharp at higher pH. In these higher pH range, a chemical shift change occurs due to the deprotonation of the Tyr. side group of fibroin. At higher pH. such a hydrophobic cluster is destroyed because of the electrostatic interaction according to the deprotonation of the Tyr-OH group.

• Animal cells and systems
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• v.11 no.1
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• pp.39-50
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• 2007

Tau plays a role in numerous neuronal processes, such as vesicle transport, microtubule-plasma membrane interaction and intracellular localization of proteins. SUMO (Small Ubiquitin-like Modifier) modification (SUMOylation) appears to regulate diverse cellular processes including nuclear transport, signal transduction, apoptosis, autophagy, cell cycle control, ubiquitin-dependent degradation, as well as gene transcription. We noticed that putative SUMOylation site is localized at $^{340}K$ of $Tau(^{339}VKSE^{342})$ with the consensus sequence information (${\Phi}KxE$ ; where ${\Phi}$ represents L, I, V or F and x is any amino acid). In this report, we demonstrated that $^{340}K$ of Tau is the SUMOylation site and that a point mutant of Tau S214E (an analog of the phospho $^{214}S$ Tau) promotes its SUMOylation at $^{340}K$ and its nuclear or nuclear vicinity localization, by co-immunoprecipitation and confocal microscopy analysis. Further, we demonstrate that the Tau S214E (neither Tau S214A nor Tau K340R) mutant increases its protein stability. However, the SUMOylation at $^{340}K$ of Tau did not influence cell survival, as determined by FACS analysis. Therefore, our results suggested that the phosphorylation of Tau on $^{214}S$ residue promotes its SUMOylation on $^{340}K$ residue and nuclear vicinity localization, and increases its stability, without influencing cell survival.

• Journal of Photoscience
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• v.11 no.1
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• pp.29-33
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• 2004

The mechanism of interaction of cyanocobalamin (CB) with bovine serum albumin (BSA) has been investigated by spectrofluorometric and circular dichroism methods. Association constant for the CB-BSA system showed that the interaction is non-covalent in nature. Binding studies in the presence of an hydrophobic probe, 8-anilino-l-naphthalene sulphonic acid, sodium salt (ANS) showed that there is hydrophobic interaction between CB and ANS and they do not share common sites in BSA. Stern-Volmer analysis of fluorescence quenching data showed that the fraction of fluorophore (protein) accessible to the quencher (CB) was close to unity indicating thereby that both tryptophan residues of BSA are involved in drug-protein interaction. The rate constant for quenching, greater than $10^{10}$ $M^{-1}$ $s^{-1}$, indicated that the drug binding site is in close proximity to tryptophan residue of BSA. Thermodynamic parameters obtained from data at different temperatures showed that the binding of CB to BSA involves hydrophobic bonds predominantly. Significant increase in concentration of free drug was observed for CB in presence of paracetamol. Circular dichroism studies revealed the change in helicity of BSA due to binding of CB to BSA.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.17-25
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• 2003

Determining the binding sites in protein-nucleic acid complexes is essential to the complete understanding of protein-nucleic acid interactions and to the development of new drugs. We have developed a set of algorithms for analyzing protein-nucleic acid interactions and for predicting potential binding sites in protein-nucleic acid complexes. The algorithms were used to analyze the hydrogen-bonding interactions in protein-RNA and protein-DNA complexes. The analysis was done both at the atomic and residue level, and discovered several interesting interaction patterns and differences between the two types of nucleic acids. The interaction patterns were used for predicting potential binding sites in new protein-RNA complexes.