• Molecules and Cells
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• 제39권9호
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• pp.692-698
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• 2016

Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species. In addition, we identified Hanwoo-specific genes and proteins, and determined distinct changes in protein-protein interactions among five species (cattle, pig, horse, human, mouse) in the STRING network database by additionally considering indirect protein interactions. We found that the Hanwoo population was clearly different from the other four cattle populations. There were Hanwoo-specific genes related to its meat trait. Protein interaction rewiring analysis also confirmed that there were Hanwoo-specific protein-protein interactions that might have contributed to its unique meat quality.

• Genomics & Informatics
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• 제6권3호
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• pp.142-146
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• 2008

In order to understand the protein functions that are related to disease, it is important to detect the correlation between amino acid mutations and disease. Many mutation studies about disease-related proteins have been carried out through molecular biology techniques, such as vector design, protein engineering, and protein crystallization. However, experimental protein mutation studies are time-consuming, be it in vivo or in vitro. We therefore performed a bioinformatic analysis of known disease-related mutations and their protein structure changes in order to analyze the correlation between mutation and disease. For this study, we selected 111 diseases that were related to 175 proteins from the PDB database and 710 mutations that were found in the protein structures. The mutations were acquired from the Human Gene Mutation Database (HGMD). We selected point mutations, excluding only insertions or deletions, for detecting structural changes. To detect a structural change by mutation, we analyzed not only the structural properties (distance of pocket and mutation, pocket size, surface size, and stability), but also the physico-chemical properties (weight, instability, isoelectric point (IEP), and GRAVY score) for the 710 mutations. We detected that the distance between the pocket and disease-related mutation lay within $20\;{\AA}$ (98.5%, 700 proteins). We found that there was no significant correlation between structural stability and disease-causing mutations or between hydrophobicity changes and critical mutations. For large-scale mutational analysis of disease-causing mutations, our bioinformatics approach, using 710 structural mutations, called "Structural Mutatomics," can help researchers to detect disease-specific mutations and to understand the biological functions of disease-related proteins.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2003년도 가을 학술발표논문집 Vol.30 No.2 (2)
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• pp.826-828
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• 2003

이제까지 Protein이나 RNA와 같은 분자의 구조는, 대부분 X-ray crystallography나 Nuclear Magnetic Resonance (NMR) 방법을 통해 분석이 이루어 졌다. 이 방법들은 실제 분자를 직접 원자레벨에서 분석하는 방법으로, 분자를 구성하는 모든 원자의 3차원 좌표 정보를 얻어 낼 수 있다. 원자의 3차원 좌표 정보는 분자의 전체적인 모양과 구조를 이해하는데 유용한 정보이다. 하지만, 분자의 구조를 좀 더 완벽히 이해하기 위해서는 원자 레벨의 좌표 정보 보다는 좀 더 높은 차원에서의 구조 정보가 필요하다. 특히 분자의 구조를 예측하거나, 분자들 사이에 결합 관계를 예측하기 위해서는, 원자 레벨의 정보만으로는 필요한 모든 정보를 얻을 수 없다. 이러한 경우, 분자의 2차원 또는 3차원 구조 요소 (structural elements)가 더욱 좋은 정보를 제공해 줄 수 있다. Protein 분자의 경우. 이미 3차원 좌표 정보를 이용해서, 2차원 구조 요소를 알아내는 자동화된 방법이 알려져 있다. 그러나 RNA의 경우 protein에 비해 알려진 결정 구조가 적기 때문에. 아직까지 2차원 구조 요소나 3차원 구조 요소를 알아내는 자동화된 방법이 알려져 있지 않다. 따라서, 이제까지는 RNA의 구조 요소를 알아내기 위해, 사람이 직접 RNA분자의 3차원 좌표 정보를 분석함으로써 많은 시간과 노력이 필요했다. 이 때문에, 우리는 RNA의 원자들의 3차원 좌표 정보를 이용해서, 2차원 구조요소와 3차원 구조 요소 정보를 자동화된 방법으로 밝혀내는 알고리즘을 개발하였다. 우리는 분자를 구성하고 있는 원자들의 3차원 좌표 정보를 Protein data bank (PDB)에서 가져왔다. 우리의 알고리즘은 PDB file형태의 데이터라면 protein-RNA 복합체나 RNA 분자 모두에서 RNA의 2차원 구조 요소나 3차원 구조 요소를 얻어낼 수 있다. 우리의 연구는 RNA의 원자레벨의 3차원 좌표 정보를 이용해서 RNA의 구조 요소를 뽑아내는 첫 번째 시도로, 우리의 알고리즘을 통해 얻어진 구조 정보는 RNA의 구조 예측 연구나. protein-RNA complex의 결합 예측 연구에 많은 도움을 줄 수 있으리라 기대된다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.26-51
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• 2003

Large scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in thePDB. PSIMAP incorporates both functional and evolutionary information into a single network. It makes it possible to age protein domains in terms of taxonomic diversity, interaction and function. One consequence of it is to predict the most important protein domain structure in evolution. We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: ${\bullet}$ Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. ${\bullet}$ Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. ${\bullet}$ Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. This led to the prediction of the oldest and most important protein domain in evolution of lift. ${\bullet}$ Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level.

• 한국자기공명학회논문지
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• 제4권2호
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• pp.74-81
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• 2000

Saccharomyces cerevisiae Dna2 protein has biochemical activities: DNA-dependent ATPase, DNA helicase and DNA nuclease and is essential for cell viability. Especially, Pro$\^$504/ is determined as an important residue in ATPase, helicase, and nuclease activity. We synthesized and determined the three-dimensional solution structure of N-terminal domain comprising residues of Val$\^$501/ -_Phe$\^$508/ (Dna2$\^$pep/) using two-dimensional $^1$H-NMR and dynamical simulated annealing calculations. On the basis of a total of 44 experimental restraints including NOEs, $^3$J$\_$$\alpha$$\beta$/ and $^3$J$\_$$\alpha$$\beta$/ coupling constants, the solution structures of Dna2$\^$epe/ were calculated with the program CNS. The 23 lowest energy structures were selected out of 50 final simulated-annealing structures. The atomic RMSDs of the final 23 structures fur the individual residues were calculated with respect to the average structure. The mean RMSDs for the 23 structures were 0.042 nm for backbone atoms and 0.316 nm for all heavy atoms, respectively. The Ramachandran plot indicates that the $\Phi$, Ψ angles of the 23 final structures are properly distributed in energetically acceptable regions. Solution structure of Dna2$\^$pep/ showed a single unique turn spanning residues of Asn$\^$503/ Val$\^$506/.

• Journal of Plant Biotechnology
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• 제33권1호
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• pp.1-9
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• 2006

도처에 분포하는 peroxiredoxins (Prxs)은 세포 내 방어신호전달 과정에서 다양한 기능을 하는 것으로 나타났다. Prxs는 크게 typical 2-Cys Prx, atypical 2-Cys Prx와 1-Cys Prx의 세 부류로 분류되는데, 이것들은 cysteine 잔기의 수와 촉매기전에 따라 구분된다. 세 종류의 단백질 중, N-말단에 peroxidatic cysteine 잔기를 포함하는 typical 2-Cys Prx는 $H_2O_2$ 분해과정 동안 과산화물-의존적인 sulfenic acid로의 산화와 thiol-의존적 환원과정이 순환되어 일어난다. Sulfenic acid는 고농도의 $H_2O_2$와 Trx, Trx reductase와 NADPH를 포함하는 촉매 요소의 존재하에 cysteine sulfenic acid로 과산화 될 수 있다 과산화된 2-Cys Prx는 ATP 의존성 효소인 sulfiredoxin의 작용에 의해 천천히 환원된다. 세포가 강력한 산화나 열 충격 스트레스에 노출되면, 2-Cys Prx는 LMW 단백질에서 HMW complex로 구조를 변화시켜 peroxidase에서 chaperone으로 기능의 전환을 일으킨다. 2-Cys Prx의 C-말단 부분 역시 이러한 구조적 전환에 중요한 역할을 한다. 따라서, C-말단이 잘려진 단백질은 과산화가 되지 않고 단백질의 구조와 기능이 조절될 수 없다. 이러한 반응들은 활성 자리인 peroxidatic cysteine 잔기에 의해 일차적으로 유도되며, 그것은 세포에서 '$H_2O_2$ sensor' 로서 작용하다. 2-Cys Prx의 가역적인 구조와 기능 변화는 세포가 외부자극에 적응하는 수단으로 작용하며, 아마도 세포내 방어신호체계를 활성화 시키는 것으로 생각된다. 특히, chloroplast에 존재하는 식물 2-Cys Prx는 촉매반응 동안 주된 구조적인 변화를 나타내는 역동적인 단백질 구조를 가지고 있어서, 산화-환원 의존적으로 super-complex를 형성하고 가역적으로 thylakoid membrane에 부착한다.

• Journal of Microbiology and Biotechnology
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• 제17권8호
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• pp.1385-1389
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• 2007

5-Enolpyruvylshikimate-3-phosphate (EPSP) synthase catalyzes the formation of EPSP and inorganic phosphate from shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) in the biosynthesis of aromatic amino acids. To delineate the domain-specific function, we successfully isolated the discontinuous C-terminal domain (residues 1-21, linkers, 240-427) of EPSP synthase (427 residues) by site-directed mutagenesis. The engineered C-terminal domains containing no linker (CTD), or with gly-gly ($CTD^{GG}$) and gly-ser-ser-gly ($CTD^{GSSG}$) linkers were purified and characterized as having distinct native-like secondary and tertiary structures. However, isothermal titration calorimetry (ITC), $^{15}N-HSQC$,\;and\;^{31}P-NMR$ revealed that neither its substrate nor inhibitor binds the isolated domain. The isolated domain maintained structural integrity, but did not function as the half of the full-length protein.

• Molecules and Cells
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• 제25권1호
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• pp.70-77
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• 2008

Proteome analysis was performed to identify proteins differentially expressed in an Arabidopsis mutant, ntm1-D. In this mutant the NAC transcription factor NTM1 is constitutively expressed and the resultant phenotypic changes include dwarfism, serrated leaves, and altered floral structures, probably due to reduced cell division. Marked elevation of proteins mediating environmental stress responses, including annexin, vegetative storage proteins, beta-glucosidase homolog 1, and glutathione transferases was observed. Overexpression of annexin was confirmed by RT-PCR and Western blotting. These observations suggest that the reduced growth observed in the ntm1-D mutant is caused by enhancement of its stress responses, possibly resulting in a cost in fitness.

• 한국응용약물학회:학술대회논문집
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• 한국응용약물학회 1994년도 춘계학술대회 and 제3회 신약개발 연구발표회
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• pp.304-304
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• 1994

The possible mechanisms of ginseng saponins on the inhibition of development of morphine tolerance and physical dependence were investigated in the aspects of morphine metabolism by morphine 6-dehydrogenase. Administration of morphine causes a reduction of non-protein sulfhydryl contents in liver, because morphinone is metabolized from morphine by morphine 6-dehydrogenase conjugates with sulfhydryl compounds. However, ginseng saponins inhibited the activity of morphine 6-dehydrogenase which catalized the production of morphinone from morphine. In addition, ginseng' saponins inhibited the reduction of non-protein sulfhydryl levels by Increasing the level of hepatic glutathione. These results suggest that the dual action of the above plays an important role in the inhibition of development of morphine tolerance and physical dependence. On the other hand, it was observed that less polar components of ginseng saponins with parent structures were more active components in vitro.

• BMB Reports
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• 제48권2호
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• pp.81-90
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• 2015

p73 is a structural and functional homologue of the p53 tumor suppressor protein. Like p53, p73 induces apoptosis and cell cycle arrest and transactivates p53-responsive genes, conferring its tumor suppressive activity. In addition, p73 has unique roles in neuronal development and differentiation. The importance of p73-induced apoptosis lies in its capability to substitute the pro-apoptotic activity of p53 in various human cancer cells in which p53 is mutated or inactive. Despite the great importance of p73-induced apoptosis in cancer therapy, little is known about the molecular basis of p73-induced apoptosis. In this review, we discuss the p73 structures reported to date, detailed structural comparisons between p73 and p53, and current understanding of the transcription-dependent and -independent mechanisms of p73-induced apoptosis.