• 약학회지
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• 제49권5호
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• pp.428-436
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• 2005

DNA topoisomerase I(TOP1) helps the control of DNA replication, transcription and recombination by assist­ing breaking and rejoining of DNA double strand. Camptothecin (CPT) and its derivative, topotecan, are known to inhibit TOP1 by intercalating into TOP1-DNA complex. Recently various non-CPT intercalators are synthesized for a new class of TOP1 inhibitors. In this study, six compounds isolated from Poria cocos were investigated for their interaction with TOP1­DNA complex using the flexible docking program, FlexiDock. The binding modes were analyzed and compared with the TOP1 inhibition activities. The compounds that showed potent activity were intercalated between the + 1/-1 base pairs of DNA, located near the active site phosphotyrosine723 and formed hydrogen bonds with active site residues. On the other hand, compounds with no activity were not docked at all. The binding modes were well correlated with the inhibition activity, suggesting the possibility that potent inhibitors can be designed from the information presented by the docking study.

• 산업기술연구
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• 제26권B호
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• pp.163-171
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• 2006

Human immunodeficiency virus type 1 (HIV-1) integrase plays a critical role in the life cycle of the HIV virus. An ability to accurately map its electrostatic potential, and then use this information to predict the manner in which DNA will bind to the active site of the catalytic domain could provide a foundation for inhibitory design. Attempts to discern the crystal structure of HIV-1 integrase have proven problematic, especially in the region of enzymatic activity, that being those residues involved in the catalysis of the integration of viral DNA into the host cell. However, there is a structural correlation in to the region of interest with avian sarcoma virus (ASV), so a homology model utilizing this similarity was constructed to approximate the behavior/structure of the undetermined portions of the HIV-1 integrase crystal. After this model was constructed and its energy minimized, electrostatic calculations were carried out on the substance, so that an electrostatic potential map was constructed. Using this information, it was determined that DNA binding was oriented so as to exploit the regions of positive potential nearby the active site, as well as the positive potential of the magnesium cofactors.

• BMB Reports
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• 제29권4호
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• pp.321-326
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• 1996

Spinach glycolate oxidase was subjected to a series of chemical modifications aimed at identifying amino acid residues essential for catalytic activity. The oxidase was reversibly inactivated by treatment with pyridoxal 5'-phosphate (PLP). The inactivation by PLP was accompanied by the appearance of an absorption peak of around 430 nm, which was shifted to 325 nm upon reduction with $NaBH_4$. After reduction, the PLP-treated oxidase showed a fluorescence spectrum with a maximum of around 395 nm by exciting at 325 nm. The substrate-competitive inhibitors oxalate and oxaloacetate provided protection against inactivation of the oxidase by PLP. These results suggest that PLP inactivates the enzyme by fonning a Schiff base with lysyl residue(s) at an active site of the oxidase. The enzyme was also inactivated by tryptophan-specific reagent N-bromosuccinimide (NBS). However, competitive inhibitors oxalate and oxaloacetate could not protect the oxidase significantly against inactivation of the enzyme by NBS. The results implicate that the inactivation of the oxidase by NBS is not directly related to modification of the tryptophanyl residue at an active site of the enzyme. Treatments of the oxidase with cysteine-specific reagents iodoacetate, silver nitrate, and 5,5'-dithiobis-2-nitrobenzoic acid did not affect significantly the activity of the enzyme.

• Journal of Applied Biological Chemistry
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• 제54권1호
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• pp.56-62
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• 2011

Tyrosinase 저해활성화 반응에 대한 polyhydroxy 치환된 flavone 유도체(1-25) 중, hydroxyl-치환기($R_1-R_9$)들의 역할을 이해하기 위하여 Free-Wilson 분석과 tyrosinase (PDB ID: Deoxyform (2ZMX) 및 Oxy-form; 1WX2)의 활성화 지점에 대한 분자도킹이 연구되었다. Free-Wilson 분석으로부터 $R_1-R_9$ 치환기중에서 $R_1$=hydroxyl 치환기가 tyrosinase 저해활성에 가장 큰 영향을 미치고 있음을 알았다. 기질분자의 hydroxyl 치환기들과 tyrosinase의 반응점 내 아미노산 잔기들 사이의 수소결합들은 안정한 기질-수용체 착 화합물을 형성하는데 기여하였다. 특히, 수소결합성에 기초한 비경쟁적 저해활성화 반응은 기질분자의 hydroxyl 치환기들과 tyrosinase의 반응점 내 peroxide 산소원자(Per404) 사이의 수소결합을 경유하여 일어날 것임을 제안하였다.

• 한국산학기술학회:학술대회논문집
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• 한국산학기술학회 2012년도 춘계학술논문집 1부
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• pp.182-186
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• 2012

human tyrosinase (hTyr) catalyzes first and the rate limiting step in the synthesis of polymerized pigment, melanin which determines skin, hair and eye colors. Mutation of hTyr often brings about decrease of melanin production and further albinism. Meanwhile, a number of cosmetic companies providing skincare products for woman in Asia-Pacific region have tried to develop inhibitors to bright skin color for several decades. In this study, we built a 3D structure by comparative modeling technique based on the crystal structure of tyrosinase from bacillus megaterium as a template to serve structural information of hTyr. According to our model and sequence analysis of type 3 copper protein family proteins, two copper atoms of active site located deep inside are coordinated with six strictly conserved histidine residues coming from four-helix-bundle. Cavity which accommodates substrates was like funnel shape of which entrance was wide and expose to solvent. In addition, protein-substrate and protein-inhibitor complex were modeled with the guide of van der waals surface generated by in house software. Our model suggested that only phenol group or its analogs can fill the binding site near nuclear copper center because inside of binding site has narrow shape relatively. In conclusion, the results of this study may provide helpful information for designing and screening new anti-melanogensis agents.

• Bulletin of the Korean Chemical Society
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• 제24권12호
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• pp.1799-1804
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• 2003

Acetolatate synthase(ALS) catalyzes the first common step in the biosynthesis of valine, leucine, isoleucine in plants and microorganisms. ALS is the target of several classes of herbicides, including the sulfonylureas, the imidazolinones, and the triazolopyrimidines. To elucidate the roles of arginine residues in tobacco ALS, chemical modification and site-directed mutagenesis were performed. Recombinant tobacco ALS was expressed in E. coli and purified to homogeneity. The ALS was inactivated by arginine specific reagents, phenylglyoxal and 2,3-butanedione. The rate of inactivation was a function of the concentration of modifier. The inactivation by butanedione was enhanced by borate, and the inactivation was reversible on removal of excess butanedione and borate. The substrate pyruvate and competitive inhibitors fluoropyruvate and phenylpyruvate protected the enzyme against inactivation by both modifiers. The mutation of well-conserved Arg198 of the ALS by Gln abolished the enzymatic activity as well as the binding affinity for cofactor FAD. However, the mutation of R198K did not affect significantly the binding of FAD to the enzyme. Taken together, the results imply that Arg198 is essential for the catalytic activity of the ALS and involved in the binding of FAD, and that the positive charge of the Arg is crucial for the interaction with negatively charged FAD.

• Journal of Microbiology and Biotechnology
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• 제8권6호
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• pp.581-587
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• 1998

Essential amino acids involved in the catalytic role of the extracellular cytosine deaminase from Chromobacterium violaceum YK 391 were determined by chemical modification studies. The enzyme activity required the reduced form of Fe (II) ion, since the enzyme was inhibited by ο-phenanthroline. The enzyme activity was completely inhibited by the chemical modifiers, such as p-chloromercuribenzoate (p-CMB), p-hydroxymercuribenzoate, and chloramine-T at 1 mM each. The enzyme activity was also markedly inhibited by pyridoxal-5'-phosphate, diethyl pyrocarbonate, and phenylmethylsulfonyl fluroride at 1 mM each. The inactivation of the enzyme activity with p-CMB was reversed by a high concentration of cytosine. Furthermore, the inactivation of the enzyme activity with p-CMB was also reactivated by 1 mM dithiothreitol, 1 mM 2-mercaptoethanol, 1 mM cysteine-HCI, 10% ethyl alcohol, and 10% methyl alcohol. These results suggested that cysteine and methionine residues might be located in or near the active site of the enzyme, while lysine, histidine, and serine residues might be indirectly involved in the enzyme activity.

• BMB Reports
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• 제37권5호
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• pp.597-602
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• 2004

N-terminal His-tagged recombinant $\beta$-1,4-galactosyltransferase from Neisseria meningitidis was expressed and purified to homogeneity by column chromatography using Ni-NTA resin. Mutations were introduced to investigate the roles of, Ser68, His69, Glu88, Asp90, and Tyr156, which are components of a highly conserved region in recombinant $\beta$-1,4 galactosyltransferase. Also, the functions of three other cysteine residues, Cys65, Cys139, and Cys205, were investigated using site-directed mutagenesis to determine the location of the disulfide bond and the role of the sulfhydryl groups. Purified mutant galactosyltransferases, His69Phe, Glu88Gln and Asp90Asn completely shut down wild-type galactosyltransferase activity (1-3%). Also, Ser68Ala showed much lower activity than wild-type galactosyltransferase (19%). However, only the substitution of Tyr156Phe resulted in a slight reduction in galactosyltransferase activity (90%). The enzyme was found to remain active when the cysteine residues at positions 139 and 205 were replaced separately with serine. However, enzyme reactivity was found to be markedly reduced when Cys65 was replaced with serine (27%). These results indicate that conserved amino acids such as Cys65, Ser68, His69, Glu88, and Asp90 may be involved in the binding of substrates or in the catalysis of the galactosyltransferase reaction.

• BMB Reports
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• 제42권3호
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• pp.172-177
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• 2009

Phosphoglucose isomerase (PGI) is involved in synthesizing extracellular polysaccharide (EPS). The gene encoding PGI in Sphingomonas chungbukensis DJ77 was cloned and expressed in E. coli, and the protein was characterized. The pgi gene from DJ77 is 1,503 nucleotides long with 62% GC content and the deduced amino acid sequence shows strong homology with PGIs from other sources. The molecular masses of PGI subunit and native form were estimated to be 50 kDa and 97 kDa, respectively. Four potentially important residues (H361, R245, E330 and K472) were identified by homology modeling. The mutations, H361A, R245A, E330A, R245K and E330D resulted in decrease in Vmax by hundreds fold, however no significant change in Km was observed. These data suggest that the three residues (H361, R245Aand E330) are likely located in the active site and the size as well as the spatial position of side chains of R245 and E330 are crucial for catalysis.

• Archives of Pharmacal Research
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• 제28권5호
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• pp.561-565
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• 2005

Bacterial arylsulfate sulfotransferase (ASST) catalyzes the transfer of sulfate group from a phenyl sulfate ester to a phenolic acceptor. The promoter region and the transcripti on start sites of Enterobacter amnigenus astA have been determined by primer extension analysis. Northern blot analysis resolved two mRNA species with lengths of 3.3 and 2.0 kb, which correspond to the distances between the transcriptional initiation sites and the two inverted repeat sequences (IRSs). By length, the 3.3 kb RNA could comprise the three-gene (astA with dsbA and dsbB) operon. ASST has three highly conserved cysteine residues. Reducing and non-reducing SDS-PAGE and activity staining showed that disulfide bond is needed for the activity of the enzyme. To identify the cysteine residues responsible for the disulfide bond formation, a series of Cys to Ser mutants has been constructed and the enzymatic activity was measured. Based on the results, we assumed that the first cysteine (Cys349) might be involved in disulfide bond mainly with the second cysteine (Cys445) and result in active conformation.