• Bulletin of the Korean Chemical Society
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• 제27권4호
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• pp.529-534
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• 2006

Chemical modification of the S. cerevisiae farnesyl protein transferase (FPT) with CMC, phenylglyoxal and DEPC resulted in enzyme inactivation, depending upon the reagent concentration. The peptide substrate GST-PEP-I, a GST-fused undecapeptide mimicking the C-terminus of $p21^{Ki-ras}$, protected the enzyme against inactivation by CMC which is specific to either aspartate or glutamate, while the other substrate farnesyl pyrophosphate (FPP) showed protection against phenylglyoxal which is the specific modifier of arginine residues, dependent on the substrate concentrations. Neither of the two substrates protected the enzyme against histidine inactivation by DEPC. It is suggested that there is at least one aspartate or glutamate residue at the peptide substrate binding site, and that at least one arginine residue is located at the binding site of FPP. There also seems to be at least one histidine residue which is critical for enzymic activity and is exposed toward the bulk solution, excluded from the substrate binding sites.

• Bulletin of the Korean Chemical Society
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• 제12권3호
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• pp.286-289
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• 1991

The changed isotropic absolute Raman intensities of the phosphate residue in the complexes of positive charge oligopeptides, lys-lys, arg-arg, lys-aromat-lys, negative charge diethyl phosphoric acid (DEP) and polyriboadenylic acid{poly(rA)} were reported and discussed. Our measurements showed that the absolute intensities of phosphate stretch vibration in complexes were different according to the reaction partners. Due to the partial electrical charge and molecular structure of oligopeptides for the complex formation lysine can interact more strongly than arginine when the reaction partners have short chain and no steric hindrance. Owing to these reasons the intensity of phosphate stretching vibration is very sensitive according to the circumstance of reaction. From our results we could suggest that we can discriminate any one of the the lysine and arginine in the complicated biological molecule during interaction between nucleotides and proteins. The activity of reaction of two basical oligopeptides is not quite similar for complex formation in aqueous solution. The activity of dipeptides depends upon the structure of molecule and environment for complex formation. Aromatic ring contributes to electrostatic interaction in complexes. The amount of the absolute intensity for pure stacking interaction is smaller than electrostatic interaction in macromolecular complexes.

• Molecules and Cells
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• 제39권4호
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• pp.316-321
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• 2016

The receptor activator of nuclear factor ${\kappa}B$ (RANK) and its ligand RANKL are key regulators of osteoclastogenesis and well-recognized targets in developing treatments for bone disorders associated with excessive bone resorption, such as osteoporosis. Our previous work on the structure of the RANK-RANKL complex revealed that Loop3 of RANK, specifically the non-canonical disulfide bond at the tip, performs a crucial role in specific recognition of RANKL. It also demonstrated that peptide mimics of Loop3 were capable of interfering with the function of RANKL in osteoclastogenesis. Here, we reported the structure-based design of a smaller peptide with enhanced inhibitory efficiency. The kinetic analysis and osteoclast differentiation assay showed that in addition to the sharp turn induced by the disulfide bond, two consecutive arginine residues were also important for binding to RANKL and inhibiting osteoclastogenesis. Docking and molecular dynamics simulations proposed the binding mode of the peptide to the RANKL trimer, showing that the arginine residues provide electrostatic interactions with RANKL and contribute to stabilizing the complex. These findings provided useful information for the rational design of therapeutics for bone diseases associated with RANK/RANKL function.

• 한국패류학회지
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• 제29권3호
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• pp.171-179
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• 2013

동양달팽이의 arginine kinase 유전자는 염기서열 1065개로 이루어져있으며 355개의 아미노산으로 이루어져 있으며, BLAST 결과를 토대로 유사도가 높은 25개의 참고 서열과 동양달팽이의 arginine kinase의 아미노산 서열을 MEGA5 프로그램의 clustalW 모듈을 이용하여 multiple sequence alignment 를 수행한 결과, 연체동물문에 속하는 복족강 (5종), 두족강 (5종), 이매패강 (4종) 등에 속하는 생물들이 같은 군으로 묶였으며, 절지동물문 곤충강 에 속하는 나비목 (2종), 벌목 (1종), 노린재목 (2종) 등에 속하는 생물들이 같은 군으로 묶이고, 갑각강 (5종), 거미강 (1종) 에 속하는 생물들이 묶이는 것을 알 수 있었다. Psipred 소프트웨어를 통해 2D 구조를 비교 분석한 결과도 multiple align 및 phylodendrogram 결과와 밀접한 관계가 있음을 알 수 있었다. 시간에 따른 arginine kinase의 발현양상을 확인한 결과 control에 비하여 6시간에서 약 1.2배 정도 발현이 증가하는 것을 확인할 수 있었으며, 12시간이 지나면 점차 감소하는 것을 확인할 수 있었다. EST를 통해 밝혀진 N. samarangae 의 Ark 서열은 근연종들의 서열과 일치함을 알 수 있었으며, 본 연구 결과를 통해 무척추동물에서의 선천성 면역 관련 유전자 연구에 동양달팽이가 좋은 모델이 될 수 있음을 제시하고 있다.

• Bulletin of the Korean Chemical Society
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• 제28권8호
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• pp.1317-1321
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• 2007

Arginine conjugated PAMAM dendrimer, PAMAM-R was modified with propylene oxide via hydroxylation of primary amines of arginine residues. About 49 amines were detected to be converted to amino alcohols by 1H NMR. The newly synthesized polymer, PAMAM-R-PO was able to completely retard pDNA from a charge ratio of 2. The average diameter of PAMAM-R-PO polyplex was found to be 242 nm at a charge ratio of 30. The Zeta-potential value of PAMAM-R-PO polyplex was able to reach 20-30 mV over a charge ratio of 10. PAMAM-R-PO indicated higher cell viability than unmodified PAMAM-R on HeLa and 293 cells because of its hydroxylated amines. Transfection experiments on 293 cells showed that the transfection efficiency of PAMAM-R-PO was found to be 1.5-1.9 times higher than that of PEI25kDa at a charge ratio of 30. The polymer eventually displayed about 2 times greater transfection efficiency than PAMAM-R at the same charge ratio in the absence of serum. Therefore, we concluded that the modification of primary amines of PAMAMR to amino alcohols gives positive effects such as reduced cytotoxicity and enhanced transfection efficiency on 293 cells for gene delivery potency of PAMAM-R.

• BMB Reports
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• 제29권6호
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• pp.507-512
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• 1996

The NADPH oxidase of phagocytes catalyzes the reduction of oxygen to $O_{2}^{-}$ at the expense of NADPH The enzyme is dormant in resting neutrophils and hecomes activated on stimulation. During activation. $p47^{phox}$ (phagocyte oxidase factor), a cytosolic oxidase subunit, becomes extensively phosphorylated on a number of serines located between S303-S379. Although the biochemical role of phosphorylation is speculative, it has been suggested that phosphorylation could neutralize the strongly cationic C-terminal which may result in the change of conformation of $p47^{phox}$ and subsequent translocation of this protein and other cytosolic components to the membrane. In order to mimic the effect of phosphorylation in terms of neutralizing the positive charges, recombinant $p47^{phox}$ was treated with phenylglyoxal, which removes positive charges of arginine residues. Modification of recombinant $p47^{phox}$ resulted in the activation of oxidase in a cell-free translocation system as well as a conformational change in recombinant $p47^{phox}$ which may be responsible for the activation of the enzyme.

• 한국미생물·생명공학회지
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• 제51권3호
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• pp.243-249
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• 2023

We recently found that the insect-derived antimicrobial peptide CopA3 (LLCIALRKK) directly binds to and inhibits the proteolytic activation of caspases, which play essential roles in apoptotic processes. However, the mechanism of CopA3 binding to caspases remained unknown. Here, using recombinant GST-caspase-3 and -6 proteins, we investigated the mechanism by which CopA3 binds to caspases. We showed that replacement of cysteine in CopA3 with alanine caused a marked loss in its binding activity towards caspase-3 and -6. Exposure to DTT, a reducing agent, also diminished their interaction, suggesting that this cysteine plays an essential role in caspase binding. Experiments using deletion mutants of CopA3 showed that the last N-terminal leucine residue of CopA3 peptide is required for binding of CopA3 to caspases, and that C-terminal lysine and arginine residues also contribute to their interaction. These conclusions are supported by binding experiments employing direct addition of CopA3 deletion mutants to human colonocyte (HT29) extracts containing endogenous caspase-3 and -6 proteins. In summary, binding of CopA3 to caspases is dependent on a cysteine in the intermediate region of the CopA3 peptide and a leucine in the N-terminal region, but that both an arginine and two adjacent lysines in the C-terminal region of CopA3 also contribute. Collectively, these results provide insight into the interaction mechanism and the high selectivity of CopA3 for caspases.

• 한국토양비료학회지
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• 제21권4호
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• pp.416-421
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• 1988

밀과 호밀짚을 부숙(腐熟)시키면서 경시적(經時的)으로 시료(試料)를 채취(採取)하여 부식산(腐植酸)을 추출정제(抽出精製)한 후 산가수분해액중(酸加水分解液中)에 함유(含有)되어 있는 amino산(酸)을 분석(分析)한 결과(結果)는 다음과 같다. 1. 부식산(腐植酸)의 가수분해액중(加水分解液中)에 함유(含有)되고 있는 amino산(酸)의 양(量)은 밀짚과 호밀짚간(間)에는 부숙정도(腐熟程度)에 따라 차이가 있었다. 2. 두 시료(試料) 공(共)히 중성(中性) amino산(酸)이 제일 많았고 산성(酸性) amino산(酸), 염기성(鹽基性) amino산(酸)의 순(順)이었다. 3. 90 일간(日間) 부숙(腐熟)시킨 두 시료(試料)의 부식산중(腐植酸中)에 함유(含有)되고 있는 전(全)amino산양(酸量)은 밀짚이 호밀짚에 비해 훨씬 많았다. 4. Argine, histidine, tyrosine을 제외(除外)한 기타(其他) amino산(酸) 함량(含量)이 증가(增加)했는데 비해 호밀짚의 경우는 lysine, phenylalanine, tyrosine, methione 만이 증가(增加)했다. 5. 충분(充分)히 부숙(腐熟)시킨 호밀짚에서 추출(抽出)한 부식산(腐植酸)의 산가수분해액중(酸加水分解液中)에는 phenylalanine과 tyrosine이 대단(大端)히 많이 함유(含有)하고 있었다. 6. 부숙화과정(腐熟化過程)에 들어간 시료(試料)에서는 arginine은 조금도 검출(檢出)되지 않았다.

• BMB Reports
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• 제43권8호
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• pp.567-572
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• 2010

In this study, we cloned the ERF-B3 subfamily transcription factor gene BnaERF-B3-hy15 from Brassica napus L. Huyou15. This 600 bp gene encodes a 199 amino acid classic ethylene responsive factor (ERF), which shown no binding or very weak binding GCC box-binding activity by the yeast one-hybrid assay. We used gene shuffling and the yeast one-hybrid system to obtain three mutated sequences that can bind to the GCC box. Sequence analysis indicated that two residues, Gly156 in the AP2 domain and Phe62 at the N-terminal domain were mutated to arginine and serine, respectively. Changes of Gly156 to arginine and Phe62 to serine increased the GCC-binding activity of BnaERF-B3-hy15 and the alter of Gly156 to arginine changed the AP2-domain structure of BnaERF-B3-hy15.

• Archives of Pharmacal Research
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• 제12권2호
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• pp.79-87
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• 1989

Enzymatic methylation of arginine and lysine residues of several cytochrome c and lysine residue of calmodulin always resulted in lowering of their respective isoelectric points (pI). Employing cytochromes c derived from various sources, we examined a possible relationship between the degree of amino acid sequence degeneracy and the magnitude of change in the pI values by enzymatic methylation, and found that there was no correlation between these two parameters. By constructing space-filling models of oligopeptide fragments adjacent to the potential methylation sites, we have noted that not all the methylatable residues are able to form hydrogen bonds prior to the methylation. Two preparations of yeast apocytochrome c, one chemically prepared by removing heme from holocytochrome c and the other by translating yeast iso-1-cytochrome c mRNA in vitro, exhibited slightly higher Stokes radii than the homologous holocytochrome c, indicating relatively 'relaxed or open' conformation of the protein. However, when the in vitro synthesized methylated apocytochrome c was compared with the unmethylated counter-part, the Stokes radius of the latter was found to be larger.