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Katsuhiko MURAKAMI
2018 Farumashia  
doi:10.14894/faruawpsj.54.9_862 fatcat:lngz5fghyrc7hhqo47sxejip4u

Structural Biology of Bacterial RNA Polymerase

Katsuhiko Murakami
2015 Biomolecules  
Since its discovery and characterization in the early 1960s (Hurwitz, J. The discovery of RNA polymerase. J. Biol. Chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial RNA polymerase (RNAP). In the late 1990s, structural information pertaining to bacterial RNAP has emerged that provided unprecedented insights into the function and mechanism of RNA transcription. In this review, I list all structures related to bacterial
more » ... AP (as determined by X-ray crystallography and NMR methods available from the Protein Data Bank), describe their contributions to bacterial transcription research and discuss the role that small molecules play in inhibiting bacterial RNA transcription.
doi:10.3390/biom5020848 pmid:25970587 pmcid:PMC4496699 fatcat:hlrewsddhrfibddief6pp2glgq

Archaeal RNA polymerase

Akira Hirata, Katsuhiko S Murakami
2009 Current Opinion in Structural Biology  
. solfataricus E/F binds tightly to its core (their interaction is maintained in the presence of 3.5 M urea at 70 °C) suggesting stoichiometric association regardless of growth conditions (Hirata and Murakami  ...  Fe-S cluster in the S. solfataricus D subunit (1 Fe-S cluster, group 1) is oxygen stable whereas the Fe-S cluster in the A. fulgidus D subunit (2 Fe-S clusters, group 2) is oxygen-labile (Hirata and Murakami  ... 
doi:10.1016/ pmid:19880312 pmcid:PMC2806685 fatcat:734j2a7tjfewvngzi45g7jnh5y

Structural basis of ribosomal RNA transcription regulation [article]

Katsuhiko Murakami, Yeonoh Shin, M. Zuhaib Qayyum, Danil Pupov, Daria Esyunina, Andrey Kulbachinskiy
2020 bioRxiv   pre-print
Proc Natl Acad Sci U S A 113, E1787-1795, (2016). 336 24 Pupov, D., Petushkov, I., Esyunina, D., Murakami, K. S. & Kulbachinskiy, A.  ...  Nucleic acids research 46, 11477-11487, (2018). 339 25 Murakami, K. S., Masuda, S. & Darst, S. A. Structural basis of transcription initiation: of ribosomal RNA transcription.  ... 
doi:10.1101/2020.06.05.136721 fatcat:iq7jhe42jve3bo4ssvye7spfei

Valve replacement in children and peri-and postoperative complications
臨床 小児人工弁置換術の問題点

Katsuhiko Tatsuno, Toshio Kikuchi, Eiichi Mannoji, Shigekazu Mimori, Katsuhiko Mori, Yasuo Murakami, Seimei Nakae
1983 Shinzo  
doi:10.11281/shinzo1969.15.8_871 fatcat:mqaxablherfrfceqwhojp6a7wq

Gene Recognition Using Multiple Gene-Finding Programs

Katsuhiko Murakami, Toshihisa Takagi
1997 Genome Informatics Series  
This paper demonstrates how effective re-analysis of the results of multiple gene finding programs is. Four simple algorithms to integrate the results of some programs are proposed and tested. Our experiments show that it is effective to use multiple gene finding programs simultaneously. We also developed a client program by which one can easily use the algorithm through the Internet.
doi:10.11234/gi1990.8.308 fatcat:nuun4dzfjrhevnnvj6lzgizd24

Classification and associated lesions of infundibular ventricular septal defect
臨床 漏斗部心室中隔欠損症における欠損孔の形態と合併症

Katsuhiko Tatsuno, Naoyuki Ishigami, Toshio Kikuchi, Yukihiro Takahashi, Yasuo Murakami, Katsuhiko Mori, Sigekazu Mimori
1989 Shinzo  
doi:10.11281/shinzo1969.21.7_837 fatcat:ieh4t646gfhadmz5tx6ptvohp4


Osamu SANGEN, Kouzi YAMAMOTO, Tadayuki MURAKAMI, Katsuyuki OGURA, Kohei SANUI, Katsuhiko NAKAMAE
1996 Kobunshi  
村 上 忠幸 Tadayuki MURAKAMI 兵 庫 県 立姫 路 東 高 等 学 校 ・教 諭 高分 子45巻10月 号(1996年) 739 特集-高分子教育の現状と将来 予 備 校 にお け る化 学教 育 の一 例 An Example of Chemical Education in a Preparatory School 高等 学 校 の化 学 教 育 に用 い られ る教科 書  ... 
doi:10.1295/kobunshi.45.736 fatcat:srextzcdazbvtm5gumoihrupaq

Clinical Application of Genetic Analysis in Obesity

2010 Oleoscience  
Recently, obese subjects have increased because of the change of lifestyles such as westernization of the eating habits or the lack of exercise in Japan. Prevention of obesity is important to prevent metabolic syndrome such as dyslipidemia, hyperglycemia, hypertention and arteriosclerotic disease. Obesity, which is induced by multiple causes, is mainly determined by the interaction between genetic and environmental factors. To search the gene associated with obesity, candidate gene analysis and
more » ... whole genome analysis are carried out using the single nucleotide polymorphisms (SNPs). As the result, several candidate genes have been reported to associate with obesity. It is necessary to diagnose multiple SNPs associated with obesity in many subjects to prevent obesity as the personalized medicine for the future. The SmartAmp (Smart Amplification Process) method is expected to be applied clinically for personalized medicine because of the simple, rapid and accurate diagnosis of SNPs.
doi:10.5650/oleoscience.10.351 fatcat:tyabxq6c45bmjbe7egdtmuawhi

Inclusion Particle Growth during Solidification of Stainless Steel

Mikio Suzuki, Ryuji Yamaguchi, Katsuhiko Murakami, Masayuki Nakada
2001 ISIJ International  
Inclusion particles in stainless steel were investigated in continuously cast slabs in a full scale caster and ingots cast in several kinds of molds under laboratory conditions. Under such conditions particle size near slab surfaces was seen to be smaller. However, it was increasing with increasing depth going into the slab interior. In order to understand the mechanism of inclusion particle growth we applied four different mathematical models to predict the size distribution of particles. Of
more » ... e four, the Ostwald ripening model, usually only applied to aqueous colloid phenomena, provided the best correlation with experimental results. This suggests that particles formed during solidification grow by "diffusion coalescence" due to the difference in solubility of neighboring particles which in turn is dependent on particle size.
doi:10.2355/isijinternational.41.247 fatcat:cp55ywx75ncidfpjeiqu7lg5xy

Bacterial RNA polymerases: the wholo story

Katsuhiko S Murakami, Seth A Darst
2003 Current Opinion in Structural Biology  
Recent structural and biophysical results have provided unprecedented insights into the structure and function of the bacterial RNA polymerase holoenzyme as it goes through the steps of transcription initiation. Comparisons with structural analyses of evolutionarily unrelated RNA polymerases reveal unexpected general features of the initiation process.
doi:10.1016/s0959-440x(02)00005-2 pmid:12581657 fatcat:tq56z2jfqvc4jiyazgieryy3ey

A Transcription Regulatory Region Analysis System

Katsuhiko Murakami, Yohinori Ohta, Koji Tanikawa, Hiroki Nakae, Shigeo Ihara, Toshihisa Takagi
2000 Genome Informatics Series  
doi:10.11234/gi1990.11.297 fatcat:ywgtfbnlkvbqtjcbl55iqcevm4

X-ray Crystal Structure ofEscherichia coliRNA Polymerase σ70Holoenzyme

Katsuhiko S. Murakami
2013 Journal of Biological Chemistry  
I thank Nobuyuki Fujita and Shoko Murakami for technical advice for constructing an RNAP-overexpressing vector (pGEMABC).  ... 
doi:10.1074/jbc.m112.430900 pmid:23389035 pmcid:PMC3610985 fatcat:axeli2vfnzg2fiues5xczlxq4y

Inactivation of SMC2 shows a synergistic lethal response inMYCN-amplified neuroblastoma cells

Yuko Murakami-Tonami, Satoshi Kishida, Ichiro Takeuchi, Yuki Katou, John M Maris, Hitoshi Ichikawa, Yutaka Kondo, Yoshitaka Sekido, Katsuhiko Shirahige, Hiroshi Murakami, Kenji Kadomatsu
2014 Cell Cycle  
doi:10.4161/cc.27983 pmid:24553121 pmcid:PMC4013162 fatcat:wrapxjehhzdw7npbgzsrfl2qdq

Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase [article]

Yeonoh Shin, Mark Hedglin, Katsuhiko Murakami
2019 bioRxiv   pre-print
Turnbough, Jr, Catherine Sutherland and Shoko Murakami for critically reading the manuscript. This work was supported by NIH grants R01 GM087350 and R35 GM131860 (K.S.M.).  ... 
doi:10.1101/732214 fatcat:76afmwk2mbgyvaq3gszhq7anbi
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