Conformational Study of Man(β1,4)Man using Molecular Dynamics Simulation

Issanin,Alexander N.,Kim,Yangmee 建國大學校基礎科學硏究所 1999 理學論集 Vol.24 No.-

분자동력학 시뮬레이션과 단열에너지 계산을 이용하여 Man(β1,4)Man의 구조적 유동성을 연구하였다. 용매효과를 고려하기 위해 유전율 50을 이용하였다. 이때 단열에너지 지도는 A (ψ=-70˚, Φ=-48)˚, B(ψ=69˚, Φ=-13˚), C(ψ=32˚, Φ=-49˚)의 세 안정한 구조를 보여주었다. 분자동력학 계산동안 A구조는 다른 두 구조로의 전이를 전혀 일으키지 않음에 반해, 12 psec후에 C구조는 B구조로의 전이를 보여 주었다. Man(β1,4)Man 은 실제 수용액중에서 두 개의 안정한 A, B 구조간의 동적 평형상태이거나 A, B 두 구조의 독립적인 상태로 존재할것으로 보인다. 단열에너지 지도나 분자동력학 계산은 Man(β1,4)Man의 구조에 대한 많은 정보를 주었으며 핵자기공명분광법에 의한 구조나 결정구조가 얻어질 수 없는 경우에 좋은 구조연구방법으로 사려된다. Conformational flexibilities of Man(β1,4)Man are investigated through molecular dynamics simulation in conjunction with the adiabatic energy map. Effect of solvent was studied using the simulation with a dielectric constant of 50. Adiabatic energy map with a dielectric constant of 50 contains three local minima, A at ψ=-70˚, Φ=-48˚, B at ψ=69˚, Φ=-13˚, and C at ψ=32˚, Φ=-49˚. While transition between A and other two low energy structures was not observed during the molecular dynamics simulation, C structure underwent transition to B structure after 12 psec. It may be possible that Man(β1,4)Man exists either in dynamic equilibrium of two states or as discrete two states in real solution. Adiabatic energy maps and molecular dynamics simulations revealed the information about the internal flexibilities of Man(β1,4)Man and can be good alternatives when structure can not be solved by NMR experiment or x-ray crystallography.

NMR Assignment of des [40-93] Mutant of Bovine Angiogenin

Yangmee Kim,Woonghee Kim,Sun-Hee Back,Dong-Il Kang,신항철 대한화학회 2008 Bulletin of the Korean Chemical Society Vol.29 No.11

Angiogenin is a potent inducer of blood vessel formation and is overexpressed in many cancers. It is a member of the pancreatic RNase superfamily. Angiogenin has 33% sequence identity with RNase A. All RNases family proteins except angiogenin and turtle RNase have four disulfide bonds. Angiogenin has three disulfide bonds, [C27-C82], [C40-C93] and [C58-C108], respectively. To examine the role of disulfide bond [C40-C93] near the nuclear localization site, recombinant des [40-93] mutant by replacement of cysteines at positions 40 and 93 with serines was cloned, expressed, and purified. CD spectrum of des [40-93] was similar to that of wild type and implies that the overall folding of two forms is similar. 2D and 3D NMR experiments for 15N and/or 13C-isotope labeled des [40-93] were performed and the backbone resonance assignment was done. Based on the result of backbone assignment and chemical shift index (CSI), we confirmed that deletion of [C40-C93] disulfide bond affected the local structural stability of bovine angiogenin near the nuclear localization site and ribonucleolytic active site. Based on this assignment, studies on structure and dynamics of des [40-93] mutant will be performed.

Conversion Shift of D-Fructoseto D-Psicose for the Enzyme-Catalyzed Epimerization by Adding Borate

Nam-Hee Kim,Hye-Jung Kim,Dong-Il Kang,Ki-Woong Jeong,Jung-Kul Lee,Yangmee Kim,Deok-Kun Oh 한국생물공학회 2008 한국생물공학회 학술대회 Vol.2008 No.4

Comparative Homology Modeling and Ligand Docking Study of Human Catechol-O-Methyltransferase for Antiparkinson Drug Design

Yangmee Kim,이지영 대한화학회 2005 Bulletin of the Korean Chemical Society Vol.26 No.11

Catechol-O-methyltransferase (COMT, EC 2.1.1.6) is an S-adenosylmethionine (SAM, AdoMet) dependent methyltransferase, and is related to the functions of the neurotransmitters in various mental processes, such as Parkinson’s disease. COMT inhibitors represent a new class of antiparkinson drugs, when they are coadministered with levodopa. Based on x-ray structure of rat COMT (rCOMT), the three dimensional structure of human COMT (hCOMT) was constructed by comparative homology modeling using MODELLER. The catalytic site of these two proteins showed subtle differences, but these differences are important to determine the characterization of COMT inhibitor. Ligand docking study is carried out for complex of hCOMT and COMT inhibitors using AutoDock. Among fifteen inhibitors chosen from world patent, nine models were energetically favorable. The average value of heavy atomic RMSD was 1.5 Å. Analysis of ligand-protein binding model implies that Arg201 on hCOMT plays important roles in the interactions with COMT inhibitors. This study may give insight to develop new ways of antiparkinson drug.

NMR spin relaxation approaches for characterizing protein motions

Yangmee Kim 한국구조생물학회 2015 Biodesign Vol.3 No.1

Flexibilities in protein conformations are essential for their functions, playing key roles in molecular recognition, ratelimiting conformational transitions, and catalysis. Information on the structure of proteins should be complemented by the information on their motion, both to characterize the protein and to understand its function. The relationship between protein structure, dynamics, and function is very challenging to study because the conformational space available to a protein is extensive and the time scales of conformational motions range widely, from picoseconds to seconds. These time scales are accessible by solution NMR making it a suitable technique for investigating the motions in proteins. In this review, an introduction to NMR spin relaxation approaches is provided to investigate protein dynamics on picosecondto- second time scales, showing the recent NMR techniques as well as case studies on protein motions. The importance of dynamic features of proteins for their molecular recognition processes and the catalytic activities of enzymes is demonstrated using spin relaxation approaches, showing that solution NMR spectroscopy is a unique tool for studying protein dynamics.

Inhibitor Design for Human Heat Shock Protein 70 ATPase Domain by Pharmacophore-based in silico Screening

Yangmee Kim,Jee-Young Lee,Ki-Woong Jung 대한화학회 2008 Bulletin of the Korean Chemical Society Vol.29 No.9

translocation and degradation, regulates apoptosis in cancer cells. Recently, it has been reported that the green tea flavonoid (−)-epigallocatechin 3-gallate (EGCG) induces apoptosis in numerous cancer cell lines and could inhibit the anti-apoptotic effect of human Hsp70 ATPase domain (hATPase). In the present study, docking model between EGCG and hATPase was determined using automated docking study. Epi-gallo moiety in EGCG participated in hydrogen bonds with side chain of K71 and T204, and has metal chelating interaction with hATPase. Hydroxyl group of catechin moiety also participated in metal chelating hydrogen bond. Gallate moiety had two hydrogen bondings with side chains of E268 and K271, and hydrophobic interaction with Y15. Based on this docking model, we determined two pharmacophore maps consisted of six or seven features, including three or four hydrogen bonding acceptors, two hydrogen bonding donors, and one lipophilic. We searched a flavonoid database including 23 naturally occurring flavonoids and 10 polyphenolic flavonoids with two maps, and myricetin and GC were hit by map I. Three hydroxyl groups of B-ring in myricetin and gallo moiety of GC formed important hydrogen bonds with hATPase. 7-OH of A-ring in myricetin and OH group of catechin moiety in GC are hydrogen bond donors similar to gallate moiety in EGCG. From these results, it can be proposed that myricetin and GC can be potent inhibitors of hATPase. This study will be helpful to understand the mechanism of inhibition of hATPase by EGCG and give insights to develop potent inhibitors of hATPase.

Docking Study of Biflavonoids, Allosteric Inhibitors of Protein Tyrosine Phosphatase 1B

Yangmee Kim,Jee-Young Lee,Ki-Woong Jung,Eun-Rhan Woo 대한화학회 2008 Bulletin of the Korean Chemical Society Vol.29 No.8

tyrosine kinases (RTKs). Inhibition of protein tyrosine phosphatase 1B (PTP1B) has been proposed as a strategy for the treatment of type 2 diabetes and obesity. Recently, it has been reported that amentoflavone, a biflavonoid extracted from Selaginella tamariscina, inhibited PTP1B. In the present study, docking model between amentoflavone and PTP1B was determined using automated docking study. Based on this docking model and the interactions between the known inhibitors and PTP1B, we determined multiple pharmacophore maps which consisted of five features, two hydrogen bonding acceptors, two hydrogen bonding donors, and one lipophilic. Using receptor-oriented pharmacophore-based in silico screening, we searched the biflavonoid database including 40 naturally occurring biflavonoids. From these results, it can be proposed that two biflavonoids, sumaflavone and tetrahydroamentoflavone can be potent allosteric inhibitors, and the linkage at 5',8''-position of two flavones and a hydroxyl group at 4'-position are the critical factors for their allosteric inhibition. This study will be helpful to understand the mechanism of allosteric inhibition of PTP1B by biflavonoids and give insights to develop potent inhibitors of PTP1B.

Antiseptic Effect of Ps-K18: Mechanism of Its Antibacterial and Anti-Inflammatory Activities

Jang, Mihee,Kim, Jieun,Choi, Yujin,Bang, JeongKyu,Kim, Yangmee MDPI AG 2019 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.20 No.19

<P>Recently, bioactive peptides have attracted attention for their therapeutic applications in the pharmaceutical industry. Among them, antimicrobial peptides are candidates for new antibiotic drugs. Since pseudin-2 (Ps), isolated from the skin of the paradoxical frog Pseudis paradoxa, shows broad-spectrum antibacterial activity with high cytotoxicity, we previously designed Ps-K18 with a Lys substitution for Leu18 in Ps, which showed high antibacterial activity and low toxicity. Here, we examined the potency of Ps-K18, aiming to develop antibiotics derived from bioactive peptides for the treatment of Gram-negative sepsis. We first investigated the antibacterial mechanism of Ps-K18 based on confocal micrographs and field emission scanning electron microscopy, confirming that Ps-K18 targets the bacterial membrane. Anti-inflammatory mechanism of Ps-K18 was investigated by secreted alkaline phosphatase reporter gene assays and RT-PCR, which revealed that Ps-K18 activates innate defense via Toll-like receptor 4-mediated nuclear factor-kappa B signaling pathways. Moreover, we investigated the antiseptic effect of Ps-K18 using a lipopolysaccharide or Escherichia coli K1-induced septic shock mouse model. Ps-K18 significantly reduced bacterial growth and inflammatory responses in the septic shock model. Ps-K18 showed low renal and liver toxicity and attenuated lung damage effectively. This study suggests that Ps-K18 is a potent peptide antibiotic that could be applied therapeutically to Gram-negative sepsis.</P>

Design of potent 9-mer antimicrobial peptide analogs of protaetiamycine and investigation of mechanism of antimicrobial action

Shin, Soyoung,Kim, Jin-Kyoung,Lee, Jee-Young,Jung, Ki-Woong,Hwang, Jae-Sam,Lee, Juneyoung,Lee, Dong Gun,Kim, Iksoo,Shin, Song Yub,Kim, Yangmee John Wiley Sons, Ltd. 2009 Journal of Peptide Science Vol.15 No.9

<P>Protaetiamycine is an insect defensin, a naturally occurring 43-amino-acid-residue antimicrobial peptide derived from the larvae of the beetle Protaetia brevitarsis. In a previous work that aimed at developing short antibiotic peptides, we designed 9-mer peptide analogs of protaetiamycine. Among them, RLWLAIGRG-NH<SUB>2</SUB> showed good antifungal activity against Candida albicans. In this study, we designed four 9-mer peptide analogs based on the sequence of RLWLAIGRG-NH<SUB>2</SUB>, in which Gly or Ile was substituted with Arg, Lys, or Trp to optimize the balance between the hydrophobicity and cationicity of the peptides and to increase bacterial cell selectivity. We measured their toxicity to bacteria and mammalian cells as well as their ability to permeabilize model phospholipid membranes. Substitution of Arg for Gly9 at the C-terminus (9Pbw1) resulted in two- to fourfold improvement in antibacterial activity. Further substitution of Gly7 with Lys (9Pbw2 and 9Pbw4) caused four- to eightfold improvement in the antibacterial activity without increase in cytotoxocity, while substitution of Gly7 with Trp (9Pbw3) increased cytotoxicity as well as antibacterial activity. The peptides 9Pbw2 and 9Pbw4 with the highest bacterial cell selectivity were not effective in depolarizing the membrane of Staphylococcus aureus cytoplasmic membranes and showed almost no leakage of a fluorescent dye entrapped within the vesicles. Gel-retardation experiments indicated that 9Pbw2 and 9Pbw4 inhibited the migration of DNA at concentrations >20 µM. Three positively charged residues at the C-terminus in 9Pbw2 and 9Pbw4 may facilitate effective penetration into the negatively charged phospholipid membrane of bacteria. The results obtained in this study suggest that the bactericidal action of our potent antibacterial peptides, namely 9Pbw2 and 9Pbw4, may be attributed to the inhibition of the functions of intracellular components after penetration of the bacterial cell membrane. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.</P>

Effects of C-Terminal Residues of 12-Mer Peptides on Antibacterial Efficacy and Mechanism

( Kkabi Son ),( Jieun Kim ),( Mihee Jang ),( Anil Kumar Chauhan ),( Yangmee Kim ) 한국미생물 · 생명공학회 2019 Journal of microbiology and biotechnology Vol.29 No.11

The development of new antimicrobial agents is essential for the effective treatment of diseases such as sepsis. We previously developed a new short peptide, Pap12-6, using the 12 N-terminal residues of papiliocin, which showed potent and effective antimicrobial activity against multidrug-resistant Gram-negative bacteria. Here, we investigated the antimicrobial mechanism of Pap12-6 and a newly designed peptide, Pap12-7, in which the 12^th Trp residue of Pap12-6 was replaced with Val to develop a potent peptide with high bacterial selectivity and a different antibacterial mechanism. Both peptides showed high antimicrobial activity against Gram-negative bacteria, including multidrug-resistant Gram-negative bacteria. In addition, the two peptides showed similar anti-inflammatory activity against lipopolysaccharidestimulated RAW 264.7 cells, but Pap12-7 showed very low toxicities against sheep red blood cells and mammalian cells compared to that showed by Pap12-6. A calcein dye leakage assay, membrane depolarization, and confocal microscopy observations revealed that the two peptides with one single amino acid change have different mechanisms of antibacterial action: Pap12-6 directly targets the bacterial cell membrane, whereas Pap12-7 appears to penetrate the bacterial cell membrane and exert its activities in the cell. The therapeutic efficacy of Pap12-7 was further examined in a mouse model of sepsis, which increased the survival rate of septic mice. For the first time, we showed that both peptides showed anti-septic activity by reducing the infiltration of neutrophils and the production of inflammatory factors. Overall, these results indicate Pap12-7 as a novel non-toxic peptide with potent antibacterial and anti-septic activities via penetrating the cell membrane.