• BMB Reports
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• 제37권1호
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• pp.28-34
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• 2004

The discovery of biochemical and cellular functions of unannotated gene products begins with a database search of proteins with structure/sequence homologues based on known genes. Very recently, a number of frontier groups in structural biology proposed a new paradigm to predict biological functions of an unknown protein on the basis of its three-dimensional structure on a genomic scale. Structural proteomics (genomics), a research area for structure-based functional discovery, aims to complete the protein-folding universe of all gene products in a cell. It would lead us to a complete understanding of a living organism from protein structure. Two major complementary experimental techniques, X-ray crystallography and NMR spectroscopy, combined with recently developed high throughput methods have played a central role in structural proteomics research; however, an integration of these methodologies together with comparative modeling and electron microscopy would speed up the goal for completing a full dictionary of protein folding space in the near future.

• 응용통계연구
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• 제22권3호
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• pp.627-634
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• 2009

Recently, the general contour Monte Carlo has been proposed by Liang (2004) as a space annealing version(ACMC) for optimization problems. The algorithm can be applied successfully to determine the ground configurations for the prediction of protein folding. In this approach, we use the distances between the consecutive $C_{\alpha}$ atoms along the peptide chain and the mapping sequences between the 20-letter amino acids and a coarse-grained three-letter code. The algorithm was tested on the real proteins. The comparison showed that the algorithm made a significant improvement over the simulated annealing(SA) and the Metropolis Monte Carlo method in determining the ground configurations.

• Molecules and Cells
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• 제38권8호
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• pp.715-722
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• 2015

In Gram-negative bacteria in the periplasmic space, the dimeric thioredoxin-fold protein DsbC isomerizes and reduces incorrect disulfide bonds of unfolded proteins, while the monomeric thioredoxin-fold protein DsbA introduces disulfide bonds in folding proteins. In the Gram-negative bacteria Salmonella enterica serovar Typhimurium, the reduced form of CueP scavenges the production of hydroxyl radicals in the copper-mediated Fenton reaction, and DsbC is responsible for keeping CueP in the reduced, active form. Some DsbA proteins fulfill the functions of DsbCs, which are not present in Gram-positive bacteria. In this study, we identified a DsbA homologous protein (CdDsbA) in the Corynebacterium diphtheriae genome and determined its crystal structure in the reduced condition at $1.5{\AA}$ resolution. CdDsbA consists of a monomeric thioredoxin-like fold with an inserted helical domain and unique N-terminal extended region. We confirmed that CdDsbA has disulfide bond somerase/reductase activity, and we present evidence that the N-terminal extended region is not required for this activity and folding of the core DsbA-like domain. Furthermore, we found that CdDsbA could reduce CueP from C. diphtheriae.

• 자연과학논문집
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• 제18권1호
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• pp.1-8
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• 2007

컴퓨터 시뮬레이션의 효율적인 한 방법을 재조명하였다. 이 방법을 이용하면, 여러 열역학적 상태들을 단 한 번의 시뮬레이션으로 조사할 수 있다. 그렇게 할 수 있는 것은, 조사하고자 하는 모든 상태들에 대해 관련 배열공간을 골고루 탐사하는 방법의 능력에 기인한다. 이 방법은 아직도 다중최소 문제가 여전히 큰 장애로 남아 있는 생체고분자와 같은 복잡계의 시뮬레이션에도 이용할 수 있다. 이 논문에서 방법의 이론을 간단히 재검토하고 어떻게 시뮬레이션으로 실현하는지 예를 들어 설명하겠다.

• 미생물학회지
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• 제31권4호
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• pp.274-278
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• 1993

단백질이 어떻게 비수용성이 되는지를 알기위해, 클로람페니콜 아세틸전이효소와 베타-락타메이즈를 과잉생산하여 그들의 수용성과 활성을 측정하였다. 클로람페니콜 아세틸전이효소는 총단백질의 9에서 45%를 차지하였으며, inclusion body 형성없이 완전히 수용성이었으며, 효소활성은 만들어진 양과 비례하였다. 또한 30℃에서 T7 발현체계에 의해 생성된 베타-락타메이즈는 수용성의 숙성체였으나, 37℃에서는 비수용성이 되었다. 세포질에 있는 대부분의 베타-락타메이즈는 비수용성이었고. 페리플라즘 공간에서는 대부분이 수용성이었다. 단백질의 올바른 폴딩을 도와주는 chaperone의 일종인 GroEL 단백질은 본 실험조선에서는 베타-락타베이즈의 수용성을 별로 높이지는 못했다. 세포 내에서 inclusion body의 형성은 단백질의 높은 종도보다는 각각 단밸질 자체의 특성과 관련된 듯하다.

• Molecules and Cells
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• 제20권1호
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• pp.1-16
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• 2005

The peptidyl transferase center (PTC) is located in a protein free environment, thus confirming that the ribosome is a ribozyme. This arched void has dimensions suitable for accommodating the 3'ends of the A-and the P-site tRNAs, and is situated within a universal sizable symmetry-related region that connects all ribosomal functional centers involved in amino-acid polymerization. The linkage between the elaborate PTC architecture and the A-site tRNA position revealed that the A-to P-site passage of the tRNA 3'end is performed by a rotatory motion, which leads to stereochemistry suitable for peptide bond formation and for substrate mediated catalysis, thus suggesting that the PTC evolved by genefusion. Adjacent to the PTC is the entrance of the protein exit tunnel, shown to play active roles in sequence-specific gating of nascent chains and in responding to cellular signals. This tunnel also provides a site that may be exploited for local co-translational folding and seems to assist in nascent chain trafficking into the hydrophobic space formed by the first bacterial chaperone, the trigger factor. Many antibiotics target ribosomes. Although the ribosome is highly conserved, subtle sequence and/or conformational variations enable drug selectivity, thus facilitating clinical usage. Comparisons of high-resolution structures of complexes of antibiotics bound to ribosomes from eubacteria resembling pathogens, to an archaeon that shares properties with eukaryotes and to its mutant that allows antibiotics binding, demonstrated the unambiguous difference between mere binding and therapeutical effectiveness. The observed variability in antibiotics inhibitory modes, accompanied by the elucidation of the structural basis to antibiotics mechanism justifies expectations for structural based improved properties of existing compounds as well as for the development of novel drugs.