• EDISON SW 활용 경진대회 논문집
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• 제5회(2016년)
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• pp.62-66
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• 2016

Tumor suppressor protein p53 loses its function upon binding with the HDM2 protein, and inhibiting the p53-HDM2 interaction is critical to suppress tumor cell growth. Recently, the cyclized helix-loop-helix peptide (cHLH) mimicking the ${\alpha}-helix$ part of the p53 protein has been designed and found to exhibit high binding affinity with HDM2. Here, we report the structural and thermodynamic characteristics of the bound complex of the cHLH peptide with the HDM2 protein. We performed molecular dynamics simulations to investigate the structural features of the cHLH peptide as well as its complex with the HDM2. The binding free energy calculation based on the integral equation theory was also executed to quantify the binding affinity for the cHLH/HDM2 complex and to understand the factors contributing to the binding affinity. We found a variety of factors for the helix stability of the cHLH peptide as well as in the complexation with the HDM2, which may provide an insight into the development of anti-cancer drug designs.

• BMB Reports
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• 제35권2호
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• pp.194-198
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• 2002

Eukaryotic replication protein A (RPA) is a single-stranded(ss) DNA binding protein with multiple functions in DNA replication, repair, and genetic recombination. The 70-kDa subunit of eukaryotic RPA contains a conserved four cysteine-type zinc-finger motif that has been implicated in the regulation of DNA replication and repair. Recently, we described a novel function for the zinc-finger motif in the regulation of human RPA's ssDNA binding activity through reduction-oxidation (redox). Here, we show that yeast RPA's ssDNA binding activity is regulated by redox potential through its RPA32 and/or RPA14 subunits. Yeast RPA requires a reducing agent, such as dithiothreitol (DTT), for its ssDNA binding activity. Also, under non-reducing conditions, its DNA binding activity decreases 20 fold. In contrast, the RPA 70 subunit does not require DTT for its DNA binding activity and is not affected by the redox condition. These results suggest that all three subunits are required for the regulation of RPA's DNA binding activity through redox potential.

• 대한약학회:학술대회논문집
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• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.1
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• pp.317.1-317.1
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• 2003

Carbohydrate-binding proteins have been isolated from various sources, including plants, animals, fungi, and bacteria, and they have been used extensively in the detection, localization, and isolation of glycoconjugates. Many carbohydrate-binding proteins are purified from mushrooms, however, only a few proteins with sialic acid-binding specificity have been reported. In the present study, a novel sialic acid-binding protein, designated PJA, has been purified from the mushroom Paecilomyces japonica. followed by extraction and affinity chromatography. (omitted)

• Journal of Microbiology
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• 제33권2호
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• pp.165-170
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• 1995

The 356 amino acid long lambda integrase protein of bacteriophage .lambda. constains two autonomous DNA binding domains with distinct sequence specificities. The amino terminal domain of integrase is implicated to bind to the arm-type sequences and the carboxyl domain interacts with the coretype sequencess. As a first step to understand the molecular mechanism of the integrase-DNA interaction at the arm-type site, the int(am)94 gene carrying an amber mutation at the 94th codon of the int was cloned under the control of the P$\_$tac/ promoter and the lacI$\_$q/ gene. The Int(am)94 mutant protein of amino terminal 93 amino acid residues can be produced at high level from a suppressor free strain harboring the plasmid pInt(am)94. The arm-type binding activity of Int(am)94 were measured in vivo and in vitro. A comparison of the arm-type binding properties of the wild-type integrase and the truncated Int(am)94 mutant indicated that the truncated fragment containing 93 amino acid residues carry all the determinants for DNA binding at the arm-type sites.

• Interdisciplinary Bio Central
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• 제2권2호
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• pp.6.1-6.5
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• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• Molecules and Cells
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• 제20권2호
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• pp.297-302
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• 2005

The integrity and proper functioning of telomeres require association of telomeric DNA sequences with specific binding proteins. We have characterized PLP-1, a $PUR{\alpha}$ homolog encoded by F45E4.2, which we previously identified as a candidate double stranded telomere binding protein, by affinity chromatography followed by mass spectrometry. PLP-1 bound double-stranded telomeric DNA in vitro as shown by competition assays. Core binding was provided by the third and fourth nucleotides of the TTAGGC telomeric repeat. This is quite different from the binding sequence of CEH-37, another C. elegans telomere binding protein, suggesting that multiple proteins may bind nematode telomeric DNA simultaneously in vivo.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 1996년도 정기총회 및 학술발표회
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• pp.9-9
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• 1996

The immunosuppressive and cell cycle arrest agent rapamycin works by binding together two proteins: the FK506 binding protein (FKBP12) and the FKBP-rapamycin associated protein (FRAP). A 2.7 $\AA$ resolution crystal structure of the triple complex of human FK506 binding protein (FKBP12), rapamycin, and FKBP12-rapamycin binding domain (FRB) of FRAP, reveals two proteins bound together through rapamycin' s ability to simultaneously occupy two different hydrophobic binding pockets. (omitted)

• 한국자기공명학회논문지
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• 제20권3호
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• pp.66-70
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• 2016

The replication protein A (RPA), is a heterotrimer with 70, 32 and 14 kDa subunits and plays a crucial role in DNA replication, recombination, and repair. The largest subunit, RPA70, binds to single-stranded DNA (ssDNA) and mediates interactions with many cellular and viral proteins. In this study, we performed nuclear magnetic resonance experiments on the complex of the DNA binding domain A of human RPA70 (RPA70A) with ssDNA, d(CCCCC), at various temperatures, to understand the temperature dependency of ssDNA binding affinity of RPA70A. Essential residues for ssDNA binding were conserved while less essential parts were changed with the temperature. Our results provide valuable insights into the molecular mechanism of the ssDNA binding of human RPA.

• 생명과학회지
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• 제19권2호
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• pp.284-288
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• 2009

선천성 면역은 숙주의 물리적 방어벽을 뚫고 침입하는 감염성 질병 원인균에 대항하는 첫 번째 방어로서 아주 중요한 역할을 한다. Mannose-binding lectin (MBL 또는 mannan-binding protein, MBP)은 혈청 내에 존재하는 면역성 단백질로서 감염 후 즉시 유발되는 acute phase response의 특정 단백질이다. MBL 단백질은 세균, 바이러스, 곰팡이, 기생충 등의 탄수화합물 구조에 결합하여 식균 작용을 돕거나 보체경로를 활성화 시킨다. MBL 단백질은 C-말단이 탄수화물을 인식하는 도메인이며, 연결 목 부위와 콜라겐 부위로 구성되어 있다. 혈청 내의 MBL 농도가 낮으면 높은 빈도로 면역결핍현상이 관찰된다고 알려져 있다. MBL 단백질의 기능과 유전에 대해 많은 연구가 되어져 왔으나 아직 MBL 단백질 복합체 등에 대한 연구는 많이 이루어져 있지 않다. 따라서 MBL 연구에 필수적인 MBL cDNA 제조와 재조합 단백질의 합성, 그리고 재조합 단백질을 항원으로 사용하여 polyclonal antibody를 생산한 연구 결과를 보고하는 바이다. 본 연구결과로 획득한 MBL cDNA, 재조합 단백질과 anti-MBL 항체는 앞으로의 MBL 연구에 절대적으로 필요한 도구가 될 것으로 생각된다.

• Asian-Australasian Journal of Animal Sciences
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• 제17권10호
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• pp.1459-1464
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• 2004

The purpose of this research was to investigate the potential use of cheese whey protein (CWP), a cheese by-product. The physiological activity of calcium-binding peptides in CWP may be used as a food additive that prevents bone disorders. This research also examined the characteristics of calcium-binding peptides. After the CWP was heat treated, it was hydrolyzed by trypsin. Then calcium-binding peptides were separated and purified by ion-exchange chromatography and reverse phase HPLC, respectively. To examine the characteristics of the purified calcium-binding peptides, amino acid composition and amino acid sequence were analyzed. Calcium-binding peptides with a small molecular weight of about 1.4 to 3.4 kDa were identified in the fraction that was flowed out from 0.25 M NaCl step gradient by ion-exchange chromatography of tryptic hydrolysates. The results of the amino acid analysis revealed that glutamic acid in a calcium-binding site took up most part of the amino acids including a quantity of proline, leucine and lysine. The amino acid sequence of calcium-binding peptides showed Phe-Leu-Asp-Asp-Asp-Leu-Thr-Asp and Ile-Leu-Asp-Lys from $\alpha$-LA and Ile-Pro-Ala-Val-Phe-Lys and Val-Tyr-Val-Glu-Glu-Leu-Lys from ${\beta}$-LG.