• 정보처리학회논문지:소프트웨어 및 데이터공학
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• 제8권10호
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• pp.421-426
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• 2019

본 논문에서는 단백질 복합체에서 단백질 사이의 접촉 영역이 갖는 기하학적 특징을 가시화하는 방법을 제안한다. 단백질 또는 리간드가 요철이 있는 곡면으로 표현될 때, 두 곡면이 서로 접하면서 교차하지 않는 성질을 형태 상보성이라 한다. 단백질-단백질 또는 단백질-리간드 도킹 연구에서 형태 상보성과 화학적인 성질, 엔트로피 등이 접촉 영역의 발견에 중요한 역할을 한다는 것을 볼 수 있다. 일반적으로 형태 상보성이 높은 영역을 발견한 뒤, 이 영역에 속한 아미노산들의 잔기 극성 및 소수성 등을 이용하여 접촉 영역을 예측한다. 접촉 영역을 예측하기 위한 연구에서는 기존에 알려진 복합체에서 접촉 영역이 갖는 기하학적인 특징을 조사하는 작업이 필요하며, 이를 위해 기하학적인 특징을 가시화하는 작업은 필수적이다. 본 논문에서는 단백질 복합체에서 접촉 영역을 발견하고, 두 개의 단백질 각각의 접촉 면에 속한 근거리의 정점들의 기하학적인 특징을 법선 벡터 및 평균 곡률로써 가시화하는 방법을 제안한다.

• 정보처리학회논문지:소프트웨어 및 데이터공학
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• 제2권12호
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• pp.899-902
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• 2013

본 논문에서는 두 개의 단백질 분자가 결합하여 복합체를 구성할 때, 두 분자 간의 접촉 영역을 발견하여 3차원 공간에서 가시화하는 방법을 제시한다. 두 분자 간의 접촉 영역은 기하학적인 측면에서 서로 상보성을 보이며, 상보적인 결합의 크기를 나타내기 위한 방법으로 접촉 영역의 면적을 계산하는 방법이 주로 사용되어 왔다. 접촉 영역의 면적을 수치화한 결과와 접촉 영역의 단순 표시는 서로 다른 접촉 영역에 대해 상대적인 결합 강도를 비교하기에는 적합하지만, 접촉 영역이 가진 기하학적인 특성을 분석하기에는 부적합하다. 본 논문에서는 접촉 영역에서 상보성을 표시하기 위해 상대 분자와의 거리 정보를 가시화하는 방법을 제시한다.

• 폴리머
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• 제36권3호
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• pp.338-343
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• 2012

콘텍트렌즈용 하이드로젤의 계면 특성의 이해를 위해 단백질 흡착 현상을 열역학을 바탕으로 연구하였다. 다른 습윤성을 갖는 $1{\times}1mm^2$ 크기의 하이드로젤을 알부민(bovine serum albumin, BSA)용액에 1시간 동안 침지시킨 후 남아있는 BSA 용액의 농도를 Bradford assay로 정량하였다. 모든 하이드로젤로의 단백질 흡착량은 단백질 농도가 증가함에 따라 계면 흡착량이 증가하며 Langmuir 곡선의 형태를 보였다. 또한 계면과 용액내의 단백질 농도비($P$), 계산된 흡착 Gibbs free energy는 하이드로젤 재료의 친수성도가 증가함에 따라 증가하였다. 표면에너지와 단백질 흡착량 상관관계를 이해하여 콘택트렌즈 재질로의 단백질 흡착현상의 물리화학적 해석이 가능함을 알 수 있었다.

• 한국농업기계학회:학술대회논문집
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• 한국농업기계학회 1993년도 Proceedings of International Conference for Agricultural Machinery and Process Engineering
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• pp.1354-1363
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• 1993

Optical methods were developed to examine their feasibility for quality evaluation of peanut with pod. Surface color and internal quality of peanut were measured without contact. The surface color of peanut was measured by light reflectance at a region of visible wavelengths. Its characteristic was high correlated with a visual grading of peanut. A trial machine for the color grading of peanut was developed using an optical sensor and it was considered to compare with the visual grading. The spectral reflectance at a region of near infrared wavelengths from 1,200 to 2,500nm was measured , and the chemical components of peanut were related to spectral reflectance at special wavelengths. The protein, fat and moisture contents of peanut were estimated by the near infrared methods. An infrared imaging method was developed to evaluate the internal quality of peanut with pod. As thermal characteristic of peanut with pod was deeply related to internal quality , the quality of peanut can be evaluated by temperature changes on the surface of peanut. Measurement of surface color, near infrared reflectance and thermal imaging were shown to be very effective in grading of peanut with pod.

• 한국자기공명학회논문지
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• 제18권1호
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• pp.30-35
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• 2014

The transcription factor CP2 regulates various biological systems at diverse tissues and cells. However, none of the four CP2 isoforms has been solved in structure yet. In particular, two different regions of the CP2b isoform have been characterized to interact with the PIAS1 in nucleus to regulate the ${\alpha}$-globin gene expression. Among them, in this study, the region encompassing residues 251-309 of CP2b was prepared as a recombinant protein and its solution structure was characterized by NMR spectroscopy. The results indicated that the CP2b(251-309) fold belongs to typical IDRs (intrinsically disordered regions), likely to facilitate promiscuous interactions with various target proteins. Unfortunately, however, its interaction with the N-terminal domain of PIAS1 (residues 1-70), which has been identified as one of the CP2b-binding sites, was not observed in the NMR-based titration experiments. Therefore, it could be postulated that the 251-309 region of CP2b would not contact with the PIAS1(1-70), but alternatively interact with another CP2b-binding region that encompasses residues 400-651 of PIAS1.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2003년도 정기총회 및 학술발표회
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• pp.68-68
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• 2003

HP(2-20) (AKKVFKRLEKLEKLFSKIQNDK) derived from the N-terminus of Helicobacter pylori Ribosomal Protein L1 shows potent antimicrobial activity against bacterial, fungi and cancer cells without cytotoxic effect. In order to investigate the relationships between antimicrobial activity and the structures, several analogues have been designed and synthesized. The structures of these peptides in SDS micelles have been investigated using NMR spectroscopy and they revealed that analogue 3 has the longest, well-defined alpha-helix from Val5 to Trp19. NOESY experiments performed on HP and its analogues in nondeuterated SDS micelles show that protons in the indole ring of Trp16 are in close contact with methylene protons of SDS micelles. In order to probe the position of HP and its analogues relative to the SDS micelles, spin-labeled stearate was added. Large effects are observed for the chemical shifts and the intensities of Phe5, Glu9, Phe12, and Trp16 within the helix region by 16-doxylstearate. This result implies that 16-doxylstearate is located in the center of the micelles and the hydrophobic phase of the amphiphilic ${\alpha}$-helix is located in contact with the acyl chains of the micelles. Also, Lys3 and Lys4 at N-terminus and Lys20 at C-terminus may produce an optimal arrangement for electrostatic interactions between the sulfate head groups of the SDS and the positively charged lysyl N$\sub$3/$\^$+/. Interactions between the indole ring of Trp and the membrane, as well as the amphiphilic ${\alpha}$-helical structure of HP induced by Trp at the C-terminus may allow HP to span the lipid bilayer. These structural features are crucial for their potent antibiotic activities.

• Journal of Microbiology and Biotechnology
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• 제30권8호
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• pp.1261-1271
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• 2020

Cytochrome c_L (Cytc_L) is an essential protein in the process of methanol oxidation in methylotrophs. It receives an electron from the pyrroloquinoline quinone (PQQ) cofactor of methanol dehydrogenase (MDH) to produce formaldehyde. The direct electron transfer mechanism between Cytc_L and MDH remains unknown due to the lack of structural information. To help gain a better understanding of the mechanism, we determined the first crystal structure of heme c containing Cytc_L from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MP^T at 2.13 Å resolution. The crystal structure of Ma-Cytc_L revealed its unique features compared to those of the terrestrial homologues. Apart from Fe in heme, three additional metal ion binding sites for Na⁺, Ca⁺, and Fe²⁺ were found, wherein the ions mostly formed coordination bonds with the amino acid residues on the loop (G93-Y111) that interacts with heme. Therefore, these ions seemed to enhance the stability of heme insertion by increasing the loop's steadiness. The basic N-terminal end, together with helix α4 and loop (G126 to Y136), contributed positive charge to the region. In contrast, the acidic C-terminal end provided a negatively charged surface, yielding several electrostatic contact points with partner proteins for electron transfer. These exceptional features of Ma-Cytc_L, along with the structural information of MDH, led us to hypothesize the need for an adapter protein bridging MDH to Cytc_L within appropriate proximity for electron transfer. With this knowledge in mind, the methanol oxidation complex reconstitution in vitro could be utilized to produce metabolic intermediates at the industry level.

• Maxillofacial Plastic and Reconstructive Surgery
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• 제31권6호
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• pp.461-468
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• 2009

Purpose: Platelet derived growth factor(PDGF)-BB and bone morphogenetic protein(BMP)-2 are well-known representative growth factors. The purposes of this study were to investigate the effect of rhPDGFBB and rhBMP-2 on osseointegration of titanium implants at periimplant bone defects grafted with hydroxyapatite and to evaluate the feasibility of imaging bone structures around screw-type titanium implant with micro-CT. Materials and Methods: The first molar and all premolars in the mandible region of four beagle dogs were extracted. Following a healing period of 4 months, three $8{\times}8{\times}6mm$-sized bony defects were formed and screw-type titanium implants were placed with hydroxyapatite(HA) block and growth factors; Control group, PDGF group and BMP group. Two months post-implantation, the mandible was harvested. Bone volume(BV), bone-to-implant contact(BIC) and bone mineral density(BMD) were analyzed with micro-CT and histology. Results: According to micro-CT analysis, BV and BMD measures of PDGF and BMP group were significantly higher than control group(BV; PDGF group: $p{\fallingdotseq}0.011$, BMP group: $p{\fallingdotseq}0.006$/BMD; PDGF group: $p{\fallingdotseq}0.020$, BMP group: $p{\fallingdotseq}0.011$) and BIC measures of BMP group were significantly higher than PDGF group($p{\fallingdotseq}0.015$). In histologic evaluation, BIC measures of BMP group was significantly higher than PDGF group($p{\fallingdotseq}0.048$). The values of BV in histologic sections were higher than in micro-CT images and the values of BIC in micro-CT images were higher than in histologic sections. Conclusion: The findings of this experimental study indicates that the use of rhPDGF-BB and rhBMP-2 can increase new bone formation in a large bony defect around titanium implant, and rhBMP-2 is more effective than rhPDGF-BB. Micro-CT can be considered useful for assessment as a rapid and nondestructive method for 3-dimensional measurement of bone healing around implants. Further study is necessary, however, to remove metal artifacts around titanium implant and to standardize the method.