• 대한화학회지
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• 제58권6호
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• pp.560-568
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• 2014

단백질 폴딩 반응에서 정전기적 상호작용의 역할을 라이신 29를 알라닌으로 치환한 변이 유비퀴틴을 사용하여 탐색하였다. 유비퀴틴의 입체구조에서 라이신 29의 곁사슬은 글루탐산 16과 아스파르산 21의 곁사슬과 근접한 거리에 있어서 곁사슬끼리 정전기적 상호작용을 통하여서 삼차원 입체구조를 안정화시킬 것으로 예측되었다. 라이신을 알라닌으로 치환하여 정전기적 상호작용을 제거하였을 때 유비퀴틴의 native state의 구조적 안정성이 ~20% 감소한 점은 라이신 29에 의한 정전기적 상호작용이 단백질 삼차구조의 안정성에 상당히 기여하고 있다는 점을 시사하였다. 폴딩 반응의 진행 과정을 stopped-flow 장치로 측정한 folding kinetics 실험은 이전에 관찰된 것과 마찬가지로 unfolded state에서 native state로 진행하는 과정에 중간단계를 거치는 three-state on-pathway 메커니즘을 따르는 것으로 나타났다. 더욱이 라이신 29에 의한 정전기적 상호작용이 중간단계의 구조적 안정성에 기여하는 정도가 native state의 구조적 안정성에 기여하는 정도의 ~55%인 것으로 나타났다. 이는 유비퀴틴 폴딩의 중간단계의 구조도 라이신 29에 의한 정전기적 상호작용에 의하여 상당히 안정화 된다는 것을 의미하며 따라서 정전기적 상호작용이 단백질 삼차원 입체구조의 골격이 완성된 폴딩의 마지막 단계에 형성되어 단백질 native state의 안정성에만 기여하는 것이 아니라 중간단계가 형성되는 폴딩 반응의 초기에도 형성되어 폴딩 반응을 이끌어가는데도 기여한다는 것을 의미한다.

• 정보처리학회논문지B
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• 제13B권7호
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• pp.679-688
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• 2006

대용량 실험으로부터 산출된 단백질 상호작용 데이터는 위양성(false positive) 데이터의 비율이 높다는 단점을 가지고 있다. 본 논문에서는 오류가 섞여있는 단백질 상호작용 데이터를 입력으로 받아 각 단백질 상호작용의 신뢰도를 검증하는 시스템을 제안하고 구현하였다. 제안 시스템은 단백질 상호작용 데이터에 상호작용의 근거로서 사용될 수 있는 다양한 생물학적 특징들에 관한 데이터를 통합하고 특징 선택 방법을 사용하여 통합된 속성들 중 위양성 여부를 판별하는데 가장 적합한 특징들을 선택한 후 데이터 마이닝 분류 알고리즘을 적용하여 대용량 실험으로부터 산출된 단백질 상호작용 데이터의 신뢰도를 평가한다. 특징 선택의 결과와 분류 기법의 성능은 데이터 특성에 매우 의존하므로, 제안시스템에 가장 적합한 속성 부분집합과 가장 좋은 성능을 내는 분류 알고리즘을 찾기 위해 다양한 특징 선택 방법과 데이터 마이닝 분류 알고리즘들을 적용하고 그 성능을 다각적으로 비교분석 하였다. 실험 결과, 특징 선택 방법과 분류 알고리즘을 결합시킨 제안 시스템은 오류 데이터가 섞여있는 단백질 상호작용 데이터에서 실제로 상호작용하는 단백질 쌍을 골라내는 작업에 있어 기존 연구들에 비해 매우 뛰어난 성능을 보여줬다. 또한 본 연구를 통해 단백질 상호작용 데이터의 신뢰도를 검증함에 있어서 다양한 특징 선택 방법들과 분류 알고리즘들이 성능에 미치는 영향에 관해서도 정리할 수 있었다.

• 셀메드
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• 제4권1호
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• pp.6.1-6.12
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• 2014

Anthrax is the deadly disease for human being caused by Bacillus anthracis. Instantaneous research work on the mode of infection of the organism revealed that different proteases are involved in different steps of pathogenesis. Present study reports the in silico characterization and the detection of pathogenic proteases involved in anthrax infection through protein-protein interaction. A total of 13 acid, 9 neutral, and 1 alkaline protease of Bacillus anthracis were selected for analysing the physicochemical parameter, the protein superfamily and family search, multiple sequence alignment, phylogenetic tree construction, protein-protein interactions and motif finding. Among the 13 acid proteases, 10 were found as extracellular enzymes that interact with immune inhibitor A (InhA) and help the organism to cross the blood brain barrier during the process of infection. Multiple sequence alignment of above acid proteases revealed the position 368, 489, and 498-contained 100% conserved amino acids which could be used to deactivate the protease. Among the groups analyzed, only acid protease were found to interact with InhA, which indicated that metalloproteases of acid protease group have the capability to develop pathogenesis during B. anthracis infection. Deactivation of conserved amino acid position of germination protease can stop the sporulation and germination of B anthracis cell. The detailed interaction study of neutral and alkaline proteases could also be helpful to design the interaction network for the better understanding of anthrax disease.

• BMB Reports
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• 제38권4호
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• pp.381-385
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• 2005

Severe acute respiratory syndrome (SARS) is an emerging infectious disease associated with a novel coronavirus (CoV) that was identified and molecularly characterized in 2003. Previous studies on various coronaviruses indicate that protein-protein interactions amongst various coronavirus proteins are critical for viral assembly and morphogenesis. It is necessary to elucidate the molecular mechanism of SARS-CoV replication and rationalize the anti-SARS therapeutic intervention. In this study, we employed an in vitro GST pull-down assay to investigate the interaction between the membrane (M) and the nucleocapsid (N) proteins. Our results show that the interaction between the M and N proteins does take place in vitro. Moreover, we provide an evidence that 12 amino acids domain (194-205) in the M protein is responsible for binding to N protein. Our work will help shed light on the molecular mechanism of the virus assembly and provide valuable information pertaining to rationalization of future anti-viral strategies.

• 한국축산식품학회지
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• 제32권5호
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• pp.627-634
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• 2012

This study was carried out to investigate the physical and thermal properties of ${\kappa}$-carrageenan (${\kappa}$-car) gel added whey protein isolate (WPI) as a cryoprotectant. The concentration of ${\kappa}$-carrageenan was fixed at 0.2 wt%. The mean ice crystal size of the WPI/${\kappa}$-car was decreased according to increasing whey protein isolate concentration. The temperature of gel-sol (Tg-s) and sol-gel (Ts-g) transition of WPI/${\kappa}$-car maxtrix was represented in the order of 3.0, 0.2, 5.0 and 1.0 wt%. In addition, the transition temperature of gel-sol of WPI in sucrose solution were showed in order of 1.0, 5.0, 0.2 and 3.0 wt% depending on whey protein isolate concentration. The shape of ice crystal was divided largely into two types, round and rectangular form. 1.0 wt% WPI/${\kappa}$-car matrix at pH 7 and 9 showed minute and rectangular formation of ice crystals and whey protein isolate in sucrose solution at a concentration of 1.0 wt% WPI/${\kappa}$-car matrix at pH 3 and 5 showed relatively large size and round ice crystals. The ice recrystallization characteristics and cryprotective effect of ${\kappa}$-carrageenan changed through the addition of different concentrations of whey protein isolate. It seems that the conformational changes induced interactions between whey protein isolate and ${\kappa}$-carrageenan affected ice recrystallization.

• Bulletin of the Korean Chemical Society
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• 제33권6호
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• pp.2005-2011
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• 2012

Nopp140 is a highly phosphorylated protein that resides in the nucleolus of mammalian cell and is involved in the biogenesis of the nucleolus. It interacts with a variety of proteins related to the synthesis and assembly of the ribosome. It also can bind to a ubiquitous protein kinase CK2 that mediates cell growth and prevents apoptosis. We found that Nopp140 is an intrinsically unfolded protein (IUP) lacking stable secondary structures over its entire sequence of 709 residues. We discovered that mitoxantrone, an anticancer agent, was able to enhance the interaction between Nopp140 and CK2 and maintain suppressed activity of CK2. Surface plasma resonance studies on different domains of Nopp140 show that the C-terminal region of Nopp140 is responsible for binding with mitoxantrone. Our results present an interesting example where a small chemical compound binds to an intrinsically unfolded protein (IUP) and enhances protein-protein interactions.

• Macromolecular Research
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• 제14권4호
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• pp.483-485
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• 2006

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 1996년도 정기총회 및 학술발표회
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• pp.21-21
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• 1996

The hyperthermostable protein, rubredoxin from Pyrococcus furiosus is 53-residue protein with a three-stranded anti-parallel $\beta$-sheet and several loops. To investigate the effect of changes of electrostatic and hydrophobic interactions on the structure and dynamic property of P. furiosus rubredoxin, molecular dynamics simulations in water were performed on three mesophilic rubredoxins, P, furiosus rubresoxin, and 5 mutants of P. furiosus rubredoxin. (omitted)

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2002년도 제9회 학술 발표회 프로그램과 논문초록
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• pp.30-30
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• 2002

The native forms of common globular proteins are in their most stable state but the native forms of plasma serpins (serine protease inhibitors) show high-energy state interactions. The high-energy state strain of a ${\alpha}$$_1$-antitrypsin, a prototype serpin, is distributed throughout the whole molecule, but the strain that regulates the function directly appears to be localized in the region where the reactive site loop is inserted during complex formation with a target protease.(omitted)

• Bulletin of the Korean Chemical Society
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• 제25권9호
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• pp.1430-1432
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• 2004