Prof. Nobuo Shimamoto

National Institute of Genetics, Japan

Emeritus Professor

Email: [email protected]

Qualifications

1966-1971 Faculty of Science, Kyoto University, Japan

1971-1977 Physics, Graduate School of Kyoto University, Japan

Publications (Selected)

1. Kabata, H., Aramaki, H., & Shimamoto, N. (2022). Single-molecule evidence for a chemical ratchet in binding between the cam repressor and its operator. Nanoscale, 14(36), 13315-13323.
2. Shimamoto, N. Illusion of Transcriptional Regulations by Rapid DNA Binding of a Regulator and Essential Requirement of Abortive Initiation for Regulations. Available at SSRN 4170492.
3. Shimamoto, N. (2021). The Limitation of the Combination of Transition State Theory and Thermodynamics for the Reactions of Proteins and Nucleic Acids. Biomolecules, 12(1), 28.
4. Kinebuchi, T., & Shimamoto, N. (2021). One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by Chemical Ratchet Mechanism. Scientific Reports, 11(1), 4255.
5. Shimamoto, N., & Imashimizu, M. (2020). RNA polymerase and transcription mechanisms: The forefront of physicochemical studies of chemical reactions. Biomolecules, 11(1), 32.
6. Shimamoto, N., Toda, M., Nara, S., Komatsuzaki, T., Kamagata, K., Kinebuchi, T., & Tomizawa, J. I. (2020). Dependence of DNA length on binding affinity between TrpR and trpO of DNA. Scientific Reports, 10(1), 15624.
7. Imashimizu, M., Tokunaga, Y., Afek, A., Takahashi, H., Shimamoto, N., & Lukatsky, D. B. (2020). Control of transcription initiation by biased thermal fluctuations on repetitive genomic sequences. Biomolecules, 10(9), 1299.
8. Imashimizu, M., Kireeva, M. L., Lubkowska, L., Kashlev, M., & Shimamoto, N. (2019). The role of pyrophosphorolysis in the initiation-to-elongation transition by E. coli RNA polymerase. Journal of molecular biology, 431(14), 2528-2542.
9. Shcherbakova, K., Nakayama, H., & Shimamoto, N. (2015). Role of 100S ribosomes in bacterial decay period. Genes to Cells, 20(10), 789-801.
10. Nakayama, H., & Shimamoto, N. (2014). Modern and simple construction of plasmid: saving time and cost. Journal of Microbiology, 52, 891-897.
11. Imashimizu, M., Shimamoto, N., Oshima, T., & Kashlev, M. (2014). Transcription elongation: Heterogeneous tracking of RNA polymerase and its biological implications. Transcription, 5(1), e28285.
12. Shimamoto, N. (2013). Nanobiology of RNA polymerase: biological consequence of inhomogeneity in reactant. Chemical Reviews, 113(11), 8400-8422.
13. Imashimizu, M., Kireeva, M. L., Shimamoto, N., & Kashlev, M. (2013). Roles of Pyrophosphorolysis in Transcription Initiation. Biophysical Journal, 104(2), 584a.
14. Aramaki, H., Kabata, H., Takeda, S., Itou, H., Nakayama, H., & Shimamoto, N. (2011). Formation of repressor‐inducer‐operator ternary complex: negative cooperativity of d‐camphor binding to CamR. Genes to Cells, 16(12), 1200-1207.
15. Imashimizu, M., Tanaka, K., & Shimamoto, N. (2011). Comparative study of cyanobacterial and E. coli RNA polymerases: misincorporation, abortive transcription, and dependence on divalent cations. Genetics research international, 2011(1), 572689.
16. Geertz, M., Travers, A., Mehandziska, S., Sobetzko, P., Chandra Janga, S., Shimamoto, N., & Muskhelishvili, G. (2011). Structural coupling between RNA polymerase composition and DNA supercoiling in coordinating transcription: a global role for the omega subunit?. MBio, 2(4), 10-1128.

Profile Details

WoS ResearcherID: AAJ-4999-2020

https://orcid.org/0000-0001-7579-0084

https://www.nig.ac.jp/nig/research/organization-top/organization/emeritus

https://www.researchgate.net/profile/Nobuo-Shimamoto