• 한국식품과학회지
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• 제31권6호
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• pp.1488-1494
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• 1999

감마선 조사가 상업적 등급의 SPI와 WPC의 SDS-PAGE 헝태와 이차구조 함량, 용해도 등 이화학적 변화에 미치는 영향을 조사하였다. 감마선이 조사된 SPI와 WPC의 SDS-PAGE 형태은 SPI 용액의 경우 5 kGy 이상 조사에서 단백질의 degraded pattern과 아울러 중합이 나타난 반면에 WPC 용액에서는 단백질이 절단된 형태로 나타났다. 반면에 감마선이 조사된 SPI와 WPC 분말의 경우 분자량 분포에는 큰 변화가 없었다. Circular dichroism 연구에서 감마선이 조사된 SPI와 WPC용액의 이차구조의 변화는 감마선 조사에 의하여 단백질의 구조 변화를 나타내는 random coil함량이 증가하였다. 또한, SPI와 WPC 분말의 경우에는 감마선 조사에 의한 용해도의 차이가 있었다.

• Journal of the Korean Society for Industrial and Applied Mathematics
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• 제15권3호
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• pp.191-199
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• 2011

In this paper, we adopt a position specific scoring matrix as an abstraction of amino acid type to derive two new statistical potentials for protein structure prediction, and investigated its effect on the quality of the potentials compared to that derived using residue specific amino acid identity. For stringent test of the potential quality, we carried out folding simulations of 91 residue A chain of protein 2gpi, and found unexpectedly that the abstract amino acid type improved the quality of the one-body type statistical potential, but not for the two-body type statistical potential which describes long range interactions. This observation could be effectively used when one develops more accurate potentials for structure prediction, which are usually involved in merging various one-body and many-body potentials.

• 한국자기공명학회논문지
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• 제10권1호
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• pp.96-104
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• 2006

The gene coding for APG8a (At4g21980), a protein from Arabidopsis thaliana, is involved in the autophagy process. The protein is an interesting candidate for structure determination by NMR spectroscopy. Toward this end, APG8a has been produced recombinantly in Escherichia coli and typical NMR experiments such as $^{15}N-HSQC$, HNCA, HN(CO)CA, CBCA(CO)NH, HCCH-TOCSY, HNCO were performed. The backbone resonances, HN, N, CA, CB, and C' were sequence-specifically assigned, and the secondary structures including 3 $\alpha$ helices and $4\beta$ strands were deduced based on the assignments. Due to the intrinsic flexibility or the effect of the denaturant, the backbone resonances were not fully observed. Since the structure calculation by NMR data was not possible, the 3-dimensional model was built based on the sequence homology, and compared with the NMR results. The overall structure of the model could explain and complement the NMR derived secondary structures.

• 한국자기공명학회논문지
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• 제2권2호
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• pp.131-140
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• 1998

The calcium-induced structural changes in the skeletal muscle regulatory protein troponin C (NTnC) involve a transition from a ‘closed’to an ‘open’structure with the concomitant exposure of a large hydrophobic interaction site for target proteins. Structural studies have served to define this conformational change and elucidate the mechanism of the linkage between calcium binding and the induced structural changes. There are now several structures of NTnC available from both NMR and X-ray crystallography. Comparison of the calcium bound structures reveals differences in the level of opening. We have considered the concept of a flexible open state of NTnC as a possible explanation for this apparent discrepancy. We also present simulations of the closed-to-open transition which are in agreement with the flexibility concept and with experimental energetics data.

• Journal of Microbiology and Biotechnology
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• 제9권5호
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• pp.562-567
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• 1999

Single-stranded DNA binding protein (SSB) is well-characterized as having a helix-destabilizing activity. The helix-destabilizing capability of SSB has been re-examined in this study. The results of restriction endonuclease protection assays and titration experiments suggest that the stimulatory effect of SSB on strand exchange acts by melting out the secondary structure which is inaccessible to RecA protein binding; however, SSB is excluded from regions of secondary structure present in native single-stranded DNA. Complexes of SSB and RecA protein are required for eliminating the secondary structure barriers under optimal conditions for strand exchange.

• 한국식품저장유통학회:학술대회논문집
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• 한국식품저장유통학회 2003년도 제23차 추계총회 및 국제학술심포지움
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• pp.135.1-135
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• 2003

To elucidate the effect of gamma-irradiation on the molecular properties of hemoglobin, the secondary, tertiary structure, and the molecular weight size of the protein were examined after irradiation at 0.5, 1, 5, and 10 kGy. Gamma-irradiation of hemoglobin solutions caused the disruption of the ordered structure of the protein molecules, as well as degradation, cross-linking, and aggregation of the polypeptide chains. A SDS-PAGE study indicated that irradiation caused initial fragmentation of the proteins and subsequent aggregation due to cross-linking of the protein molecules. The effect of irradiation on the protein was more significant at lower protein concentrations. Ascorbic acid decreased the degradation and aggregation of proteins by scavenging oxygen radicals that were produced by irradiation. A circular dichroism study showed that irradiation decreased the helical content of hemoglobin with a concurrent increase of the aperiodic structure content. Fluorescence spectroscopy indicated that irradiation decreased the emission intensity that was excited at 280 nm.

• Bulletin of the Korean Chemical Society
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• 제25권11호
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• pp.1676-1680
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• 2004

We demonstrate that wide-angle X-ray scattering pattern from photoactive yellow protein (PYP) in solution using a high flux third generation synchrotron X-ray source reflects not only the overall structure, but also fine structures of the protein. X-ray scattering data from PYP in solution have been collected in q ranges from 0.02 ${\AA}^{-1}$ to 2.8 ${\AA}^{-1}$. These data are sensitive to the protein structure and consistent with the calculation based on known crystallographic atomic coordinates. Theoretical scattering patterns were also calculated for the intermediates during the photocycle of PYP to estimate the feasibility of time-resolved wide-angle X-ray scattering experiments on such proteins. These results demonstrate the possibility of using the wide-angle solution X-ray scattering as a quantitative monitor of photo-induced structural changes in PYP.

• Genomics & Informatics
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• 제1권1호
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• pp.7-19
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• 2003

The latest measure of the relative evolutionary age of protein structure families was applied (based on taxonomic diversity) using the protein structural interactome map (PSIMAP). It confirms that, in general, protein domains, which are hubs in this interaction network, are older than protein domains with fewer interaction partners. We apply a hypothesis of 'biological network evolution' to explain the positive correlation between interaction and age. It agrees to the previous suggestions that proteins have acquired an increasing number of interaction partners over time via the stepwise addition of new interactions. This hypothesis is shown to be consistent with the scale-free interaction network topologies proposed by other groups. Closely co-evolved structural interaction and the dynamics of network evolution are used to explain the highly conserved core of protein interaction pathways, which exist across all divisions of life.

• 통합자연과학논문집
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• 제11권2호
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• pp.101-106
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• 2018

Corticotropin - releasing hormone receptor 1 (CRHR1) forms an integral part of the pathophysiology of disorders like post-traumatic stress disorder, stress, anxiety, addiction, and depression. Hence it is essential to look for new, potent and structure-specific inhibitors of CRHR1. We have analysed the protein-protein interaction complexes of the CRHR1 receptor with its native ligand CRF and full agonist Sauvagine. The structure of Sauvagine was predicted using homology modelling. We have identified that the residues TYR253, ASP254, GLU256, GLY265, ARG1014 and LY1060 are important in the formation of protein-protein complex formation. Future studies on these residues could throw light on the crucial structural features required for the formation of CRHR1-inhibitor complex and in studies that try to solve the structural complexities of CRHR1.

• 정보처리학회논문지D
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• 제11D권7호
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• pp.1517-1526
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• 2004

공공 데이터베이스의 이용 가능한 단백질 데이터의 양적 증가와 함께 포스트지놈 시대가 도래되면서, 단백질의 3차 구조에 대한 연구가 활발하게 진행되고 있다. 단백질의 구조를 효과적으로 파악하기 위해서 단백질의 3차 구조를 시각화할 필요가 있다. 최근 많은 시각화 도구들이 이미 그 구조가 알려진 단백질을 시각화하기 위해 Java 기술을 이용하여 개발되었다. 본 논문에서는 새로운 단백질 시각화 도구인 JProtein 시스템은 Java3D 기법을 이용하여 개발되었다. Java3D 3D 표현을 위한 프로그래밍 인터페이스를 제공하는 APIdl다. JProtein 시스템은 시각화된 아미노산 내의 원자들간의 각도 및 거리 정보를 제공하며, 단백질 분자구조에 대해 여러 가지 3차원 표현 모델을 지원한다. 특히, JProtein 시스템은 비동기식 스테레오 뷰와 함께 동기식 스테레오 뷰를 지원한다.