Updated on 2022/04/01

写真a

 
TERADA, Tomoki
 
Organization
Graduate School of Engineering Applied Physics 3 Associate professor
Graduate School
Graduate School of Engineering
Undergraduate School
School of Engineering Physical Science and Engineering
Title
Associate professor
Contact information
メールアドレス
Other name(s)
Tomoki P. TERADA
External link

Degree 1

  1. Doctor of Science ( 1999.3   The University of Tokyo ) 

Research Interests 7

  1. Quantitative Biology

  2. Circadian Rhythm

  3. Molecular Motor

  4. Allosteric Transition

  5. Computational Biophysics

  6. Theoretical Biophysics

  7. Protein Science

Research Areas 3

  1. Others / Others  / Biophysics

  2. Others / Others  / Living Organism Physics/Chemical Physics

  3. Others / Others  / Living Organism Molecular Science

Current Research Project and SDGs 5

  1. A Study on the Molecular Mechanism of the Sliding Motion of Actin-Myosin System

  2. Study on molecular mechanisms of allosteric conformational changes of proteins

  3. Oscillation mechanism of protein-only circadian clock

  4. Mechanism of cell fate decision in stem cells

  5. Oscillation Mechanism of Segmentation Clock during Somitogenesis

Research History 9

  1. Nagoya University   Department of Applied Physics, Graduate School of Engineering   Associate professor

    2017.4

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    Country:Japan

  2. Nagoya University   Department of Computational Science and Engineering, Graduate School of Engineering   Associate professor

    2014.9 - 2017.3

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    Country:Japan

  3. Nagoya University   Department of Computational Science and Engineering, Graduate School of Engineering   Lecturer

    2011.4 - 2014.8

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    Country:Japan

  4. Nagoya University   Department of Applied Physics, Graduate School of Engineering   Lecturer

    2009.4 - 2011.3

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    Country:Japan

  5. Nagoya University   Department of Computational Science and Engineering, Graduate School of Engineering   Lecturer

    2005.8 - 2009.3

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    Country:Japan

  6. Nagoya University   Department of Complex Systems Science, Graduate School of Information Science   Research Fellow of the Japan Society for Promotion of Science

    2003.4 - 2005.8

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    Country:Japan

  7. Nagoya University   Division of Informatics for Natural Sciences, Graduate School of Human Informatics   Researcher of the Research and Development for Applying Advanced Computational Science and Technology, Japan Science and Technology Agency

    2002.2 - 2003.3

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    Country:Japan

  8. Nagoya University   Division of Informatics for Natural Sciences, Graduate School of Human Informatics   Researcher of the Research and Development for Applying Advanced Computational Science and Technology, Japan Science and Technology Agency

    2001.4 - 2001.9

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  9. Nagoya University   Division of Informatics for Natural Sciences, Graduate School of Human Informatics   Technician of the Research and Development for Applying Advanced Computational Science and Technology, Japan Science and Technology Agency

    1999.4 - 2001.3

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    Country:Japan

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Education 3

  1. The University of Tokyo   Graduate School, Division of Science   Department of Physics

    1996.4 - 1999.3

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    Country: Japan

  2. The University of Tokyo   Graduate School, Division of Science   Department of Physics

    1994.4 - 1996.3

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    Country: Japan

  3. The University of Tokyo   Faculty of Science   Department of Physics

    1990.4 - 1994.3

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    Country: Japan

Professional Memberships 3

  1. The Biophysical Society of Japan

  2. Protein Science Society of Japan

  3. 日本物理学会

Committee Memberships 1

  1. 日本物理学会   領域12 領域運営委員  

    2014.4 - 2015.3   

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    Committee type:Academic society

 

Papers 33

  1. Folding pathway of a multidomain protein depends on its topology of domain connectivity Reviewed

    Takashi Inanami, Tomoki P. Terada, Masaki Sasai

    Proceedings of the National Academy of Sciences of the United States of America   Vol. 111 ( 45 ) page: 15969 - 15974   2014.9

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    DOI: 10.1073/pnas.1406244111

  2. Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin Reviewed International coauthorship

    Qing-Miao Nie, Akio Togashi, Takeshi N. Sasaki, Mitsunori Takano, Masaki Sasai, Tomoki P. Terada

    PLoS Computational Biology   Vol. 10 ( 4 ) page: e1003552, 1-13   2014.4

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    Authorship:Last author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1371/journal.pcbi.1003552

  3. Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells Reviewed

    Masaki Sasai, Yudai Kawabata, Koh Makishi, Kazuhito Itoh, Tomoki P. Terada

    PLoS Computational Biology   Vol. 9 ( 12 ) page: e1003380,1-17   2013.12

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    A remarkable feature of the self-renewing population of embryonic stem cells (ESCs) is their phenotypic heterogeneity: Nanog and other marker proteins of ESCs show large cell-to-cell variation in their expression level, which should significantly influence the differentiation process of individual cells. The molecular mechanism and biological implication of this heterogeneity, however, still remain elusive. We address this problem by constructing a model of the core gene-network of mouse ESCs. The model takes account of processes of binding/unbinding of transcription factors, formation/dissolution of transcription apparatus, and modification of histone code at each locus of genes in the network. These processes are hierarchically interrelated to each other forming the dynamical feedback loops. By simulating stochastic dynamics of this model, we show that the phenotypic heterogeneity of ESCs can be explained when the chromatin at the Nanog locus undergoes the large scale reorganization in formation/dissolution of transcription apparatus, which should have the timescale similar to the cell cycle period. With this slow transcriptional switching of Nanog, the simulated ESCs fluctuate among multiple transient states, which can trigger the differentiation into the lineage-specific cell states. From the simulated transitions among cell states, the epigenetic landscape underlying transitions is calculated. The slow Nanog switching gives rise to the wide basin of ESC states in the landscape. The bimodal Nanog distribution arising from the kinetic flow running through this ESC basin prevents transdifferentiation and promotes the definite decision of the cell fate. These results show that the distribution of timescales of the regulatory processes is decisively important to characterize the fluctuation of cells and their differentiation process. The analyses through the epigenetic landscape and the kinetic flow on the landscape should provide a guideline to engineer cell differentiation.

    DOI: 10.1371/journal.pcbi.1003380

  4. Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor Reviewed

    Mitsunori Takano, Tomoki P. Terada, Masaki Sasai

    Proceedings of the National Academy of Sciences of the United States of America   Vol. 107 ( 17 ) page: 7769 - 7774   2010.4

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    The actomyosin molecular motor, the motor composed of myosin II and actin filament, is responsible for muscle contraction, converting chemical energy into mechanical work. Although recent single molecule and structural studies have shed new light on the energy-converting mechanism, the physical basis of the molecular-level mechanism remains unclear because of the experimental limitations. To provide a clue to resolve the controversy between the lever-arm mechanism and the Brownian ratchet-like mechanism, we here report an in silico single molecule experiment of an actomyosin motor. When we placed myosin on an actin filament and allowed myosin to move along the filament, we found that myosin exhibits a unidirectional Brownian motion along the filament. This unidirectionality was found to arise from the combination of a nonequilibrium condition realized by coupling to the ATP hydrolysis and a ratchet-like energy landscape inherent in the actin-myosin interaction along the filament, indicating that a Brownian ratchet-like mechanism contributes substantially to the energy conversion of this molecular motor.

    DOI: 10.1073/pnas.0911830107

  5. Correlation between evolutionary structural development and protein folding Reviewed

    Chioko Nagao, Tomoki P. Terada, Tetsuya Yomo, Masaki Sasai

    Proceedings of the National Academy of Sciences of the United States of America   Vol. 102 ( 52 ) page: 18950 - 18955   2005.12

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    Evolution should have played important roles in determining folding mechanisms and structures of proteins. In this article we discuss how the folding mechanisms had been affected by the early stage of evolution through which the uniqueness of structure had developed. Although the process of such early-time evolution has remained a mystery, a plausible scenario is that the evolution of proteins toward the ordered structures was guided by functional selection pressure as demonstrated in vitro and in silico. We examine the in silico functional selection of sequences and show that there is a significant correlation between two different processes toward the unique 3D structure, the evolutionary development of structure through sequence selection, and the folding process of the resultant sequence. This finding could be rephrased as protein folding recapitulates the emergence of topology in the molecular evolution. The correlation suggests a guideline for engineering foldable proteins.

    DOI: 10.1073/pnas.0509163102

  6. Conformational change of actomyosin complex drives the multiple stepping movement Reviewed

    Tomoki P. Terada, Masaki Sasai, Tetsuya Yomo

    Proceedings of the National Academy of Sciences of the United States of America   Vol. 99 ( 14 ) page: 9202-9206   2002.6

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    Actin-myosin (actomyosin) generates mechanical force by consuming ATP molecules. We apply the energy landscape perspective to address a controversial issue as to whether the myosin head moves with multiple steps after a single ATP hydrolysis or only a single mechanical event of the lever-arm swinging follows a single ATP hydrolysis. Here we propose a theoretical model in which the refolding of the partially unfolded actomyosin complex and the movement of the myosin head along the actin filament are coupled. A single ATP hydrolysis is followed by the formation of a high free-energy partially unfolded actomyosin complex, which then gradually refolds with a concomitant multiple stepping movement on the way to the lowest free-energy rigor state. The model quantitatively explains the single-molecular observation of the multiple stepping movement and is consistent with structural observations of the disorder in the actomyosin-binding process. The model also explains the observed variety in dwell time before each step, which is not accounted for by previous models, such as the lever-arm or ratchet models.

    DOI: 10.1073/pnas.132711799

  7. A Landscape-Based View on the Stepping Movement of Myosin VI International coauthorship

    Tomoki P. Terada, Qing-Miao Nie, Masaki Sasai

    Biophysical Journal   Vol. 118 ( 3 ) page: 436A - 437A   2020.2

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    Authorship:Lead author   Language:English   Publishing type:Research paper (other academic)  

    DOI: 10.1016/j.bpj.2019.11.2449

    Web of Science

  8. A landscape-based view on the stepping movement of myosin VI International coauthorship

    T. P. Terada, Q. M. Nie, M. Sasai

    European Biophysics Journal with Biophysics Letters   Vol. 48 ( Supplement 1 ) page: S234 - S234   2019.7

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    DOI: 10.1007/s00249-019-01373-4

    Web of Science

  9. Single-molecular and ensemble-level oscillations of cyanobacterial circadian clock Reviewed

    Sumita Das, Tomoki P. Terada, Masaki Sasai

    Biophysics and Physicobiology   Vol. 15   page: 136 - 150   2018.5

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    DOI: 10.2142/biophysico.15.0_136

    Web of Science

  10. Role of ATP Hydrolysis in Cyanobacterial Circadian Oscillator Reviewed

    Sumita Das, Tomoki P. Terada, Masaki Sasai

    Scientific Reports   Vol. 7   page: 17469   2017.12

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    DOI: 10.1038/s41598-017-17717-z

  11. Cooperativity and modularity in protein folding Invited Reviewed

    Masaki Sasai, George Chikenji, Tomoki P. Terada

    Biophysics and Physicobiology   Vol. 13   page: 281 - 293   2016.11

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    DOI: 10.2142/biophysico.13.0_281

  12. Importance of consensus region of multiple-ligand templates in a virtual screening method Reviewed

    Tatsuya Okuno, Koya Kato, Shintaro Minami, Tomoki P. Terada, Masaki Sasai, George Chikenji

    Biophysics and Physicobiology   Vol. 13   page: 149 - 156   2016.7

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    DOI: 10.2142/biophysico.13.0_149

  13. Loose Mechanism of Eukaryotic Gene Regulation and Chromatin Dynamics Invited Reviewed

    Masaki Sasai, Tomoki P. Terada

      Vol. 56 ( 2 ) page: 106 - 108   2016.3

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    DOI: 10.2142/biophys.56.106

  14. Physics of Cell Differentiation from Landscape Perspective Invited Reviewed

    Tomoki P. Terada

      Vol. 70 ( 10 ) page: 765 - 769   2015.10

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  15. VS-APPLE: A Virtual Screening Algorithm Using Promiscuous Protein–Ligand Complexes Reviewed

      Vol. 55 ( 6 ) page: 1108 - 1119   2015.6

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    DOI: 10.1021/acs.jcim.5b00134

  16. アクトミオシンの粗視化モデル解析:モーター機能におけるループの柔らかさの重要性 Invited Reviewed

    寺田智樹

    生物物理   Vol. 55 ( 3 ) page: 148 - 150   2015.5

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    DOI: 10.2142/biophys.55.148

  17. Conformational flexibility of loops of myosin enhances the global bias in the actin-myosin interaction landscape Invited Reviewed

    Qing-Miao Nie, Masaki Sasai, Tomoki P. Terada

    Physical Chemistry Chemical Physics   Vol. 16 ( 14 ) page: 6441-6447   2014.1

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    A long-standing controversy on the mechanism of an actomyosin motor is the role of the Brownian motion of the myosin head in force generation. In order to shed light on this problem, we calculate free-energy landscapes of interaction between an actin filament and the head (S1) of myosin II by using a coarse-grained model of actomyosin. The results show that the free-energy landscape has a global gradient toward the strong-binding site on actin filament, which explains the biased Brownian motion of myosin S1 observed in a single-molecule experiment [Kitamura et al., Nature, 1999, 397, 129 and Biophysics, 2005, 1, 1]. The distinct global gradient in the landscape is brought about only when the conformation of loop 2 at the actin interface of myosin S1 is flexible. The conformational flexibility of loop 3 also contributes to the gradient in the landscape by compensating the role of loop 2. Though the structure of loop 2 is expanded in the weak-binding state, loop 2 shows the larger fluctuation of compaction and expansion due to the actin-myosin interactions as myosin S1 moves toward the strong-binding site on actin filament. Hence, the increase in the compaction-expansion fluctuation of loop 2, the stronger binding of myosin to actin, and the biased Brownian motion of myosin S1 are coupled with each other and should take place in a concurrent way. This predicted coupling should provide opportunities to further test the hypothesis of the biased Brownian motion in actomyosin.

    DOI: 10.1039/C3CP54464H

  18. Entropic Mechanism of Allosteric Communication in Conformational Transitions of Dihydrofolate Reductase. Invited Reviewed

    Tomoki P. Terada, Toru Kimura, Masaki Sasai

    The Journal of Physical Chemistry B   Vol. 117 ( 42 ) page: 12864 - 12877   2013.5

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    The mechanism of allosteric conformational transitions of Escherichia coli dihydrofolate reductase (DHFR) is investigated theoretically by applying a newly developed coarse-grained model. Functional forms of interaction potentials in the model depend on the local structural environments around those interactions to represent the many-residue effects due to atomic packing in each local region, and hence, this model is called "the chameleon model". The chameleon model consistently describes the free-energy landscape of two conformational transitions in the catalytic cycle of DHFR, which we call conformational transition 1 (CT1) and conformational transition 2 (CT2); CT1 is accompanied by the hydride transfer reaction, and CT2 is accompanied by the product ligand release. The transition state of CT1 is entropically stabilized by the disordering of loops at the peripheral regions of the protein, which enhances the positively correlated fluctuations at the center part of the protein, showing that the allosteric communication between distant regions through the central region is intrinsically associated with the entropic stabilization of the transition state. The transition state of CT2 is entropically stabilized through the mechanism that enhances the breathing motion of two domains, showing that the difference in the distribution of interactions brings about the difference in the transition mechanism between CT1 and CT2. The chameleon model opens a way to consistently describe the dynamical energy landscape of enzymatic reactions.

    DOI: 10.1021/jp402071m

  19. Dynamical Modeling of Three-Dimensional Genome Organization in Interphase Budding Yeast Reviewed

    Naoko Tokuda, Tomoki P. Terada, Masaki Sasai

    Biophysical Journal   Vol. 102 ( 2 ) page: 296 - 304   2012.1

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    Eukaryotic genome is organized in a set of chromosomes each of which consists of a chain of DNA and associated proteins. Processes involving DNA such as transcription, duplication, and repair, therefore, should be intrinsically related to the three-dimensional organization of the genome. In this article, we develop a computational model of the three-dimensional organization of the haploid genome of interphase budding yeast by regarding chromosomes as chains moving under the constraints of nuclear structure and chromatin-chromatin interactions. The simulated genome structure largely fluctuates with the diffusive movement of chromosomes. This fluctuation, however, is not completely random, as parts of chromosomes distribute in characteristic ways to form "territories" in the nucleus. By suitably taking account of constraints arising from the data of the chromosome-conformation-capture measurement, the model explains the observed fluorescence data of chromosome distributions and motions.

    DOI: 10.1016/j.bpj.2011.12.005

  20. Synchronization of Circadian Oscillation of Phosphorylation Level of KaiC in vitro Reviewed

    Tetsuro Nagai, Tomoki P. Terada, Masaki Sasai

    Biophysical Journal   Vol. 98 ( 11 ) page: 2469 - 2477   2010.6

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    In recent experimental reports, robust circadian oscillation of the phosphorylation level of KaiC has been reconstituted by incubating three cyanobacterial proteins, KaiA, KaiB, and KaiC, with ATP in vitro. This reconstitution indicates that protein-protein interactions and the associated ATP hydrolysis suffice to generate the oscillation, and suggests that the rhythm arising from this protein-based system is the circadian clock pacemaker in cyanobacteria. The mechanism of this reconstituted oscillation, however, remains elusive. In this study, we extend our previous model of oscillation by explicitly taking two phosphorylation sites of KaiC into account and we apply the extended model to the problem of synchrony of two oscillatory samples mixed at different phases. The agreement between the simulated and observed data suggests that the combined mechanism of the allosteric transition of KaiC hexamers and the monomer shuffling between them plays a key role in synchronization among KaiC hexamers and hence underlies the population-level oscillation of the ensemble of Kai proteins. The predicted synchronization patterns in mixtures of unequal amounts of two samples provide further opportunities to experimentally check the validity of the proposed mechanism. This mechanism of synchronization should be important in vivo for the persistent oscillation when Kai proteins are synthesized at random timing in cyanobacterial cells.

    DOI: 10.1016/j.bpj.2010.02.036

  21. Mechanism of Robust Circadian Oscillation of KaiC Phosphorylation In Vitro Reviewed

    Kohei Eguchi, Mitsumasa Yoda, Tomoki P. Terada and Masaki Sasai

    Biophysical Journal   Vol. 95 ( 4 ) page: 1773 - 1784   2008.5

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    By incubating the mixture of three cyanobacterial proteins, KaiA, KaiB, and KaiC, with ATP in vitro, T. Kondo and his colleagues in recent work reconstituted the robust circadian rhythm of the phosphorylation level of KaiC. This finding indicates that protein-protein interactions and the associated hydrolysis of ATP suffice to generate the circadian rhythm. Several theoretical models have been proposed to explain the rhythm generated in this "protein-only" system, but the clear criterion to discern different possible mechanisms was not known. In this article, we discuss a model based on two basic assumptions: the assumption of the allosteric transition of a KaiC hexamer and the assumption of the monomer exchange between KaiC hexamers. The model shows a stable rhythmic oscillation of the phosphorylation level of KaiC, which is robust against changes in concentration of Kai proteins. We show that this robustness gives a clue to distinguish different possible mechanisms. We also discuss the robustness of oscillation against the change in the system size. Behaviors of the system with the cellular or subcellular size should shed light on the role of the protein-protein interactions in in vivo circadian oscillation.

    DOI: 10.1529/biophysj.107.127555

  22. Monomer-Shuffling and Allosteric Transition in KaiC Circadian Oscillation Reviewed

    Mitsumasa Yoda, Kohei Eguchi, Tomoki P. Terada, Masaki Sasai

    PLoS ONE   Vol. 2 ( 5 ) page: e408,1-8   2007.5

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    Circadian rhythms in living organisms have long been attributed solely to a transcription-translation loop comprising a negative or positive feedback. The rhythms in cyanobacteria are known to be modulated by kaiC, kaiA and kaiB genes. It was recently shown, however, that their product proteins KaiC, KaiA and KaiB are sufficient to reconstitute the circadian rhythm in the phosphorylation level of KaiC in vitro. It has since been unclear why such an oscillatory behavior can occur in the absence of the apparent transcription-translation feedback. In the meantime, it has been reported that the monomer exchange between KaiC hexamers occurs in a phosphorylation-dependent manner, which suggests that the monomer shuffling is also involved in the circadian rhythm (H. Kageyama et al., Mol. Cell, 23, 161 (2006)). To further clarify the role of the monomer shuffling, we have performed a computational modeling of interactions among Kai proteins assuming the allosteric transition of KaiC hexamer as well as the monomer shuffling. The results show that the existence of both monomer shuffling and allosteric transition can synchronize the phosphorylation level of the KaiC hexamers, and stabilizes its oscillation.

    DOI: 10.1371/journal.pone.0000408

  23. タンパク質のダイナミクスとインフォマティクス Invited Reviewed

    笹井理生, 寺田智樹

    高分子   Vol. 51 ( 6 ) page: 448   2002.6

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    DOI: 10.1295/kobunshi.51.448

  24. 分子進化とフォールディング機構 Invited

    笹井理生, 寺田智樹

    蛋白質 核酸 酵素   Vol. 47 ( 6 ) page: 677 - 683   2002.5

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  25. Nucleotide binding to the chaperonin GroEL: noncooperative binding of ATP analogs and ADP, and cooperative effect of ATP Reviewed

    Tomonao Inobe, Tadashi Makio, Etsuko Takasu-Ishikawa, Tomoki P. Terada, Kunihiro Kuwajima

    Biochimica et Biophysica Acta   Vol. 1545 ( 1-2 ) page: 160 - 173   2001.2

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    Chaperonin-assisted protein folding proceeds through cycles of ATP binding and hydrolysis by GroEL, which undergoes a large structural change by the ATP binding or hydrolysis. One of the main concerns of GroEL is the mechanism of the productive and cooperative structural change of GroEL induced by the nucleotide. We studied the cooperative nature of GroEL by nucleotide titration using isothermal titration calorimetry and fluorescence spectroscopy. Our results indicated that the binding of ADP and ATP analogs to a single ring mutant (SR1), as well as that to GroEL, was non-cooperative. Only ATP induces an apparently cooperative conformational change in both proteins. Furthermore, the fluorescence changes of pyrene-labeled GroEL indicated that GroEL has two kinds of nucleotide binding sites. The fluorescence titration result fits well with a model in which two kinds of binding sites are both non-cooperative and independent of each other. These results suggest that the binding and hydrolysis of ATP may be necessary for the cooperative transition of GroEL.

    DOI: 10.1016/S0167-4838(00)00274-0

  26. Equilibrium and Kinetic Studies on Folding of the Authentic and Recombinant Forms of Human α-Lactalbumin by Circular Dichroism Spectroscopy Reviewed International coauthorship

    Tapan K. Chaudhuri, Munehito Arai, Tomoki P. Terada, Teikichi Ikura, Kunihiro Kuwajima

    Biochemistry   Vol. 39 ( 50 ) page: 15643 - 15651   2000.11

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    The equilibrium and kinetics of the unfolding and refolding of authentic and recombinant human α-lactalbumin, the latter of which had an extra methionine residue at the N-terminus, were studied by circular dichroism spectroscopy, and the results were compared with the results for bovine and goat α-lactalbumins obtained in our previous studies. As observed in the bovine and goat proteins, the presence of the extra methionine residue in the recombinant protein remarkably destabilized the native state, and the destabilization was entirely ascribed to an increase in the rate of unfolding. The thermodynamic stability of the native state against the unfolded state was lower, and the thermodynamic stability of the molten globule state against the unfolded state was higher for the human protein than for the other α-lactalbumins previously studied. Thus, the population of the molten globule intermediate was higher during the equilibrium unfolding of human α-lactalbumin by guanidine hydrochloride. Unlike the molten globule states of the bovine and goat proteins, the human α-lactalbumin molten globule showed remarkably more intense circular dichroism ellipticity than the native state in the far-ultraviolet region below 225 nm. During refolding from the unfolded state, human α-lactalbumin thus exhibited overshoot kinetics, in which the alpha-helical peptide ellipticity exceeded the native value when the molten globule folding intermediate was formed in the burst phase. The subsequent folding involved reorganization of nonnative secondary structures. It should be noted that the rate constant of the major refolding phase was approximately the same among the three types of α-lactalbumin and that the rate constant of unfolding was accelerated 18-600 times in the human protein, and these results interpreted the lower thermodynamic stability of this protein.

    DOI: 10.1021/bi001735j

  27. Thermodynamics of nucleotide binding to the chaperonin GroEL studied by isothermal titration calorimetry: evidence for noncooperative nucleotide binding Reviewed

    Tomoki P. Terada, Kunihiro Kuwajima

    Biochimica et Biophysica Acta   Vol. 1431 ( 2 ) page: 269 - 281   1999.5

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    We characterized the thermodynamics of binding reactions of nucleotides ADP and ATPγS (a nonhydrolyzable analog of ATP) to GroEL in a temperature range of 5°C to 35°C by isothermal titration calorimetry. Analysis with a noncooperative binding model has shown that the bindings of nucleotides are driven enthalpically with binding constants of 7×103 M-1 and 4×104 M-1 for ADP and ATPγS, respectively, at 26°C and that the heat capacity change ΔCp is about 100 cal/molcharacterK for both the nucleotides. The stoichiometries of binding were about 8 and 9 molecules for ADP and ATPγS, respectively, per GroEL tetradecamer at 5°C, and both increased with temperature to reach about 14 (ADP) and 12 (ATPγS) for both nucleotides at 35°C. The absence of initial increase of binding heat as well as Hill coefficient less than 1.2, which were obtained from the fitting to the model curve by assuming positive cooperativity, showed that there was virtually no positive cooperativity in the nucleotide bindings. Incorporating a difference in affinity for the nucleotide (ADP and ATPγS) between the two rings of GroEL into the noncooperative binding model improved the goodness of fitting and the difference in the affinity increased with decreasing temperature.

    DOI: 10.1016/S0167-4838(99)00049-7

  28. Effect of the Extra N-terminal Methionine Residue on the Stability and Folding of Recombinant α-Lactalbumin Expressed in Escherichia coli Reviewed International coauthorship

    Tapan K. Chaudhuri, Katsunori Horii, Takao Yoda, Munehito Arai, Shinji Nagata, Tomoki P. Terada, Hidefumi Uchiyama, Teikichi Ikura, Kouhei Tsumoto, Hiroshi Kataoka, Masaaki Matsushima, Kunihiro Kuwajima, Izumi Kumagai

    Journal of Molecular Biology   Vol. 285 ( 3 ) page: 1179 - 1194   1999.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    The structure, stability, and unfolding-refolding kinetics of Escherichia coli-expressed recombinant goat α-lactalbumin were studied by circular dichroism spectroscopy, X-ray crystallography, and stopped-flow measurements, and the results were compared with those of the authentic protein prepared from goat milk. The electric properties of the two proteins were also studied by gel electrophoresis and ion-exchange chromatography. Although the overall structures of the authentic and recombinant proteins are the same, the extra methionine residue at the N terminus of the recombinant protein remarkably affects the native-state stability and the electric properties. The native state of the recombinant protein was 3.5 kcal/mol less stable than the authentic protein, and the recombinant protein was more negatively charged than the authentic one. The recombinant protein unfolded 5.7 times faster than the authentic one, although there were no significant differences in the refolding rates of the two proteins. The destabilization of the recombinant protein can be fully interpreted in terms of the increased unfolding rate of the protein, indicating that the N-terminal region remains unorganized in the transition state of refolding, and hence is not involved in the folding initiation site of the protein. A comparison of the X-ray structures of recombinant α-lactalbumin determined here with that of the authentic protein shows that the structural differences between the proteins are confined to the N-terminal region. Theoretical considerations for the differences in the conformational and solvation free energies between the proteins show that the destabilization of the recombinant protein is primarily due to excess conformational entropy of the N-terminal methionine residue in the unfolded state, and also due to less exposure of hydrophobic surface on unfolding. The results suggest that when the N-terminal region of a protein has a rigid structure, expression of the protein by E. coli, which adds the extra methionine residue, destabilizes the native state through a conformational entropy effect. It also shows that differences in the electrostatic interactions of the N-terminal amino group with the side-chain atoms of Thr38, Asp37, and Asp83 bring about a difference in the pKa value of the N-terminal amino group between the proteins, resulting in a greater negative net charge of the recombinant protein at neutral pH.

    DOI: 10.1006/jmbi.1998.2362

  29. Observation of kaonic hydrogen atom x rays Reviewed International coauthorship

    T.M. Ito, R.S. Hayano, S.N. Nakamura, T.P. Terada, M. Iwasaki, D.R. Gill, L. Lee, A. Olin, M. Salomon, S. Yen, K. Bartlett, G.A. Beer, G. Mason, G. Trayling, H. Outa, T. Taniguchi, Y. Yamashita, R. Seki

    Physical Review C   Vol. 58 ( 4 ) page: 2366 - 2382   1998.10

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1103/PhysRevC.58.2366

  30. A new approach to measure kaonic hydrogen X-rays Reviewed International coauthorship

    S.N. Nakamura, M. Iwasaki, K. Bartlett, G.A. Beer, D.R. Gill, R.S. Hayano, T.M. Ito, M. Kuwata, L. Lee, G. Mason, H. Ohkubo, A. Olin, H. Outa, M. Salomon, R. Seki, K. Shibuya, T. Taniguchi, T.P. Terada, G. Trayling, T. Watanabe, Y. Yamashita, S. Yen

    Nuclear Instruments and Methods in Physics Research A   Vol. 408 ( 2-3 ) page: 438 - 452   1998.5

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    Language:English   Publishing type:Research paper (scientific journal)  

    Previous kaonic hydrogen X-ray experiments suffered from a poor signal-to-background level. This has been overcome in the present measurement through the use of a gaseous hydrogen target and the imposition of a two-charged-pion tagging requirement. In this paper a full technical description is given of the experimental methods employed.

    DOI: 10.1016/S0168-9002(98)00201-0

  31. Observation of Kaonic Hydrogen Kα X Rays Reviewed International coauthorship

    M. Iwasaki, R.S. Hayano, T.M. Ito, S.N. Nakamura, T.P. Terada, D.R. Gill, L. Lee, A. Olin, M. Salomon, S. Yen, K. Bartlett, G.A. Beer, G. Mason, G. Trayling, H. Outa, T. Taniguchi, Y. Yamashita, R. Seki

    Physical Review Letters   Vol. 78 ( 16 ) page: 3067 - 3069   1997.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1103/PhysRevLett.78.3067

  32. Cascade calculation of hadronic hydrogen atoms Reviewed

    T.P. Terada and R.S. Hayano

    Physical Review C   Vol. 55 ( 1 ) page: 73 - 87   1997.1

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    Cascade calculations of hadronic hydrogen atoms are performed to obtain the x-ray yields as a function of the target density. An extension of Leon-Bethe's Stark mixing rates to m(not equal)0 states is made without the introduction of the parameter kSTK, which is necessary in the Borie-Leon model to enhance the Stark mixing rates. Although the energies of their L x rays are too low to observe, we can roughly estimate the 2p absorption width of pionic and kaonic hydrogen atoms from the measured K x-ray yields.

    DOI: 10.1103/PhysRevC.55.73

  33. A Pulse-Processor Based on Rise Time Measurement of Trapezoidal Waveforms by Using a Count-Up ADC Reviewed

    M. Kuwata, H. Maeda, K. Husimi, S. Ohkawa, M. Iwasaki, S.N. Nakamura, T.M. Ito, T. Terada

    IEEE Transactions on Nuclear Science   Vol. 43 ( 3 ) page: 1626 - 1628   1996.6

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    Language:English   Publishing type:Research paper (scientific journal)  

    In order to raise the throughput of low-energy X-ray signals appearing in a background of high-energy pulses, a new pulse-processor that measures the rise time of a trapezoidal waveform instead of the peak height has been developed. A rectangular pre-filter and a gated integrator are used to make the wave-shape at the shaper output linear. A rectangular pulse is formed by adding a differentiated step signal and its integration. The rise time of the trapezoidal waveform is inversely proportional to the height of the input step pulse. Therefore, processing time for a high-energy pulse is shorter than that for low-energy one. Consequently, the pile-up loss of the low-energy X-rays is reduced.

    DOI: 10.1109/23.507160

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Books 2

  1. Genome Computing - toward genome reality beyond bioinformatics

    ( Role: Joint author)

    2013.1  ( ISBN:978-4-320-12272-7

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    Responsible for pages:173-219   Language:Japanese Book type:Scholarly book

  2. 細胞の物理生物学

    笹井理生, 伊藤一仁, 千見寺浄慈, 寺田智樹 ( Role: Joint author)

    共立出版  2011.12  ( ISBN:978-4320057166

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    Language:Japanese Book type:Scholarly book

Presentations 42

  1. Free energy landscape analysis of conformational transition of NtrC by chameleon model

    Taisei Nagata, Masaki Sasai, Tomoki P. Terada

    The 59th Annual Meeting of the Biophysical Society of Japan  2021.11.26  The Biophysical Society of Japan

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    Event date: 2021.11

    Language:English   Presentation type:Oral presentation (general)  

    Venue:Online   Country:Japan  

    We study the conformational transition by coarse-grained molecular dynamics simulation. We use chameleon model, an extended model of Go-like model with which we can calculate the free energy landscape of confrontational transitions (Terada et al., J. Phys. Chem. B 117, 12864 (2013)). We focus on the NtrC receiver domain which exhibits allosteric transition with the register shift of anα-helix. The chameleon model was applied to NtrC and the simulation results showed a free energy landscape with two states corresponding to active and inactive states. Therefore, we performed a free energy landscape analysis of conformational transition of NtrC. Free energy landscape analysis shows that the α-helix rotates in the intermediate state between active and inactive states.

  2. A study on the conformational transition of adenylate kinase by the chameleon model

    Itsuki Yoshida, Masaki Sasai, Tomoki P. Terada

    The 59th Annual Meeting of the Biophysical Society of Japan  2021.11.26  The Biophysical Society of Japan

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    Event date: 2021.11

    Language:English   Presentation type:Oral presentation (general)  

    Venue:Online   Country:Japan  

    Chameleon model is the model for description of two-state conformational transition of proteins. In the model, the interaction between residues changes depending on how similar the environment around the residues is to one state and the other state. We applied the model to the conformational transition of adenylate kinase. We calculated the rates of conformational transition from the free energy difference between fully closed state and transition state which is the rate-limiting step of the enzymatic activity. We found that the temperature dependence of calculated conformational transition rates is similar to that of experimental enzymatic activity, showing that chameleon model gives a good approximation of free energy landscape of conformational transition.

  3. A landscape-based view on the stepping movement of myosin VI International coauthorship

    Tomoki P. Terada, Qing-Miao Nie, Masaki Sasai

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    Event date: 2020.9

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  4. Three-state model of muscle contraction with switched free energy landscapes and power stroke

    Kaima Matsuda, Masaki Sasai, Tomoki P. Terada

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    Event date: 2020.9

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  5. Conformational transition of NtrC elucidated by the improvement of dihedral angle potential in chameleon model

    Taisei Nagata, Masaki Sasai, Tomoki P. Terada

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    Event date: 2020.9

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  6. ミオシンVIの歩行メカニズムの自由エネルギーランドスケープ解析

    寺田智樹, Qing-Miao Nie, 笹井理生

    日本物理学会第75回年次大会 

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    Event date: 2020.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:名古屋大学   Country:Japan  

  7. A landscape-based view on the stepping movement of myosin VI International conference

    Tomoki P. Terada, Qing-Miao Nie, Masaki Sasai

    64th Annual Meeting of the Biophysical Society 

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    Event date: 2020.2

    Language:English   Presentation type:Poster presentation  

    Country:United States  

  8. Effects of interhead connection on the stepping motion of myosin VI

    Tomoki P. Terada, Qing-Miao Nie, Masaki Sasai

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    Event date: 2019.9

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  9. A landscape-based view on the stepping movement of myosin VI International conference

    Tomoki P. Terada, Qing-Miao Nie, Masaki Sasai

    Joint 12th EBSA, 10th ICBP-IUPAP Biophysics Congress 

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    Event date: 2019.7

    Language:English   Presentation type:Poster presentation  

    Country:Spain  

  10. Free energy landscape for the Brownian motion of the leading head of myosin VI during the stepping motion Invited International conference

    Tomoki P. Terada

    The 2nd workshop on Advances in Theory and Computation of Complex Systems - Biological Systems 

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    Event date: 2018.12

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Nanjing University   Country:Japan  

  11. Free energy landscape for the Brownian motion of the leading head of myosin VI during the stepping motion

    Tomoki P. Terada, Qing-Miao Nie, Masaki Sasai

    The 56th Annual Meeting of The Biophysical Society of Japan 

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    Event date: 2018.9

    Language:English   Presentation type:Oral presentation (general)  

    Venue:Okayama University   Country:Japan  

  12. ミオシンの構造変化とバイアスブラウン運動の協調的関係 Invited

    寺田智樹

    第三回CUTEシンポジウム:コンピュータ化学 -計算科学と実験化学との接点- 

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    Event date: 2016.3

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:三重大学   Country:Japan  

  13. ミオシンのバイアスブラウン運動を自由エネルギーランドスケープから考える Invited

    寺田 智樹

    自然科学研究機構計算科学研究センター スーパーコンピュータワークショップ“複雑な研究対象へと挑戦する計算分子科学“ 

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    Event date: 2015.9

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:岡崎コンファレンスセンター   Country:Japan  

  14. ミオシンのバイアスブラウン運動を自由エネルギーランドスケープから考える Invited

    寺田 智樹

    第5回分子モーター討論会 

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    Event date: 2015.6

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:東京大学駒場キャンパス   Country:Japan  

  15. Coupling between phosphorylation rhythm and ATP hydrolysis rate in KaiC protein studied by stochastic simulation Invited International conference

    Tomoki P. Terada

    2015 International Workshop on Computational Science and Engineering 

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    Event date: 2015.5

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  16. Stochastic simulation of coupling between phosphorylation rhythm and ATP hydrolysis in KaiC protein

    Tomoki P. Terada, Kenju Narita, Masaki Sasai

    The Physical Society of Japan 2015 Spring Meeting 

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    Event date: 2015.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  17. Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin

    Tomoki P. Terada,Qing-Miao Nie,Akio Togashi,Takeshi N. Sasaki,Mitsunori Takano,Masaki Sasai

    The Physical Society of Japan 2014 Autumn Meeting 

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    Event date: 2014.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  18. Stochastic modeling of the interplay between ATPase activity and structural transition in KaiC proteins Invited International conference

    Tomoki P. Terada

    Joint Annual Meeting of the Japanese Society for Mathematical Biology and the Society for Mathematical Biology 2014 (JSMB/SMB 2014) 

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    Event date: 2014.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  19. ES細胞の細胞運命決定における非平衡性の役割 Invited

    寺田智樹

    明星大学セミナー 

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    Event date: 2012.12

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:明星大学理工学部   Country:Japan  

  20. The role of non-adiabaticity in cell-fate decision of ES cells Invited International conference

    Tomoki P. Terada

    The 3rd International Workshop on "Multiscale Characterizations of Biological Systems: From Molecules to Networks" 

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    Event date: 2012.6

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:China  

  21. 二重最適化問題としての蛋白質フォールディングとその進化 Invited

    寺田智樹

    第1回協定講座シンポジウム「計算アルゴリズムと化学・生物学の融合」 

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    Event date: 2012.2

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:神戸大学統合研究拠点   Country:Japan  

  22. ゆらぎが決める蛋白質の多様な機能 Invited

    寺田智樹

    生物に学ぶ柔軟なシステムの探索: ゆらぎと多様性をキーワードとして 

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    Event date: 2011.9

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  23. The chameleon model: a novel approach to conformational transitions of proteins International conference

    Tomoki P. Terada, Takahiro Yamashita, Shogo Yokota, Toru Kimura, Masaki Sasai

    The 1st KIAS Conference on Subcellular Dynamics 

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    Event date: 2011.7

    Language:English   Presentation type:Poster presentation  

    Country:Korea, Republic of  

  24. Chameleon model: A Novel Approach to Conformational Transitions of Proteins Invited International conference

    Tomoki P. Terada

    The 2nd International Workshop on Multiscale Characterizations of Biological Systems: From Molecules to Networks 

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    Event date: 2011.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  25. Chameleon model: A Novel Approach to Conformational Transitions of Proteins Invited International conference

    Tomoki P. Terada

    Third Korea-Japan Seminars on Biomolecular Sciences: - Experiments and Simulations 

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    Event date: 2011.2

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Korea, Republic of  

  26. タンパク質の構造転移メカニズムのカメレオンモデルによる理解 Invited

    寺田智樹

    生物物理の未来研究会 

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    Event date: 2010.9

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:名古屋大学 ベンチャービジネスラボラトリー ベンチャーホール   Country:Japan  

    タンパク質が熱揺らぎで構造転移をすることが、最近の一分子測定やNMRなどの実験からわかってきた。われわれは、構造転移を記述しうる粗視化モデル相互作用として、局所的相互作用がその周囲の変化に合わせて変化すると仮定するカメレオンモデルを提唱している。このモデルをアデニル酸キナーゼに対して適用した結果、実験で観測された二状態的な構造転移が再現されるとともに、モデルで計算された構造転移速度の温度変化が実測された酵素反応速度の温度変化とよく対応することがわかった。これらの結果は、カメレオンモデルが構造転移の

  27. カメレオンモデルによるタンパク質の二状態的構造転移の自由エネルギーランドスケープ解析 Invited

    寺田智樹

    第10回日本蛋白質科学会年会 

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    Event date: 2010.6

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    タンパク質がリガンド結合に伴い構造を変えることは長い間知られてきたが、近年は一定条件のもとで熱揺らぎで起こる構造転移に対しても、一分子実験やNMRなどによる実験的な特徴づけが進んできた。理論的立場からは、フォールディング研究における郷モデルの延長として、二つの結晶構造をともにエネルギー的に安定化する実効的相互作用が提唱されてきたが、二状態的な自由エネルギーランドスケープが得られるということ以上には実験事実との対応付けは行われていない。われわれはそれらの研究とは異なり、局所的相互作用がその周囲の変化

  28. Takano-Terada-Sasai model Invited

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    Event date: 2009.10

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  29. Contribution of hydrophobic and electrostatic interactions in the biased motion of myosin head along actin filament

    45th Annual Meeting of the Biophysical Society of Japan 

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    Event date: 2007.12

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

    We have simulated the motion of myosin head along the actin filament with coarse-grained molecular dynamics with introduceing the sequence-dependent water-mediated potential. This potential have three variants depending on the degree of unfolding of each protein prior to binding. The simulation with this potential elucidates the contribution of hydrophobic and electrostatic interactions in the biased motion as well as the importance of coupled folding and binding.

  30. ミオシン滑り運動とカメレオンGoモデル Invited

    寺田智樹

    次世代生命体統合・分子スケール 秋のミニ集会 

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    Event date: 2007.11

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    ミオシン頭部の一方向的な滑り運動についての粗視化モデルを用いた分子動力学計算、および、カメレオンGoモデルによるアロステリック転移の分子動力学計算について

  31. Molecular dynamics simulation of biased motion of myosin head along actin filament International conference

    Discussions on Theory and simulation of biomolecular systems 

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    Event date: 2006.12

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  32. Molecular dynamics simulation of biased motion of myosin head along actin filament International conference

    Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan 

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    Event date: 2006.11

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  33. アクトミオシンの粗視化モデルによる分子動力学計算 -レバーアーム模型ではない何かを求めて-

    寺田智樹

    CRESTチームミーティング 

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    Event date: 2005.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京大学山上会館   Country:Japan  

  34. アクトミオシンの粗視化モデルによる分子動力学計算III

    寺田智樹、笹井理生

    日本生物物理学会第43回年会 

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    Event date: 2005.11

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  35. 蛋白質のやわらかさとミオシンの一方向的な滑り運動 Invited

    笹井理生、寺田智樹

    生体分子とゆらぎ研究会2005 

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    Event date: 2005.6

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  36. アクトミオシンの粗視化モデルによる分子動力学計算II

    寺田智樹、笹井理生

    日本生物物理学会第42回年会 

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    Event date: 2004.12

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  37. アクトミオシンの粗視化モデルによる分子動力学計算

    寺田智樹、笹井理生

    日本生物物理学会第41回年会 

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    Event date: 2003.9

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  38. アクトミオシンの滑り運動の一分子観測に対する新しい視点 Invited

    寺田智樹

    日本生物物理学会第41回年会 

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    Event date: 2003.9

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  39. アクトミオシンの一方向的な滑り運動とエネルギーランドスケープ理論 Invited

    寺田智樹

    第3回日本蛋白質科学会 

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    Event date: 2003.6

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  40. Conformational change of actomyosin complex drives the multiple stepping movement Invited

    Dynamics and Function of Nano-Biomechines 

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    Event date: 2002.11

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  41. Conformational change of actomyosin complex drives the multiple stepping movement International conference

    The 16th Symposium of the Protein Society 

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    Event date: 2002.8

    Language:English   Presentation type:Poster presentation  

  42. アクトミオシンの滑り運動の一方向性は構造変化の一方向性とカップルしている

    寺田智樹、笹井理生、四方哲也

    第2回日本蛋白質科学会 

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    Event date: 2002.6

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

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Research Project for Joint Research, Competitive Funding, etc. 1

  1. アクチン・ミオシン系の滑り運動の分子機構の研究

    2007.4 - 2009.3

    財団法人豊田理化学研究所 

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    Grant type:Competitive

KAKENHI (Grants-in-Aid for Scientific Research) 2

  1. A stochastic description of protein conformational transition by global landscape calculation

    Grant number:19K06597  2019.4 - 2022.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\4290000 ( Direct Cost: \3300000 、 Indirect Cost:\990000 )

  2. タンパク質の分子内・分子間コミュニケーションによる構造転移の基礎理論

    2006.4 - 2008.3

    科学研究費補助金  若手研究(B),課題番号:18770128

    寺田 智樹

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    Authorship:Principal investigator 

 

Teaching Experience (On-campus) 58

  1. First Year Seminar A

    2020

  2. Applied Physics Tutorial IVa

    2020

  3. Bioscience

    2020

  4. Advanced Lectures on Computational Physics

    2020

  5. First Year Seminar A

    2019

  6. Applied Physics Tutorial IVb

    2019

  7. Bioscience

    2019

  8. 計算物性工学特論

    2018

  9. Applied Physics Tutorial IVb

    2018

  10. 基礎セミナー

    2018

  11. 生物科学

    2018

  12. 生物科学

    2017

  13. 基礎セミナー

    2017

  14. Applied Physics Tutorial IVb

    2017

  15. 計算物理工学特論

    2016

  16. 生物科学

    2016

  17. 基礎セミナー

    2016

  18. Applied Physics Tutorial IV

    2016

  19. 基礎セミナー

    2015

  20. 生物科学

    2015

  21. Applied Physics Tutorial IV

    2015

  22. 生物科学

    2014

  23. 計算機物理学および演習

    2014

  24. 計算物理工学特論

    2014

  25. Applied Physics Tutorial IV

    2014

  26. 応用物理学演習第5

    2013

  27. 統計力学B

    2013

  28. 生物科学

    2013

  29. 計算機物理学および演習

    2013

  30. 計算物理工学特論

    2012

  31. 計算機物理学および演習

    2012

  32. 応用物理学演習第5

    2012

  33. 統計力学B

    2012

  34. 計算機物理学および演習

    2011

  35. 応用物理学演習第5

    2011

  36. 統計力学B

    2011

  37. 応用物理学演習第5

    2010

  38. 統計力学B

    2010

  39. 計算機物理学および演習

    2010

  40. 生体物理学特論

    2010

  41. 統計力学B

    2009

     詳細を見る

    物質の微視的な性質と巨視的な性質を結びつける学問体系である統計力学の基礎的概念を、統計力学Aに続いて量子統計力学の導入およびそのいくつかの典型的な応用例を取り扱うことにより学ぶ。

  42. 計算機物理学および演習

    2009

     詳細を見る

    物理学における様々な問題を計算機を用いて調べる基本的な手法を学び,演習を通じて,応用する能力を身に着ける。

  43. 応用物理学演習第5

    2009

     詳細を見る

    量子力学B、統計力学Bの演習を行う。

  44. 応用物理学セミナー

    2008

     詳細を見る

    物性科学や計算科学における基礎および最新の問題をとりあげて、発表、討論を通じて物理学と現代の科学技術との関わりについて理解を深める。創造力、表現力及び討論する力を学ぶ。

  45. 計算機物理学および演習

    2008

     詳細を見る

    物理学における様々な問題を計算機を用いて調べる基本的な手法を学び,演習を通じて,応用する能力を身に着ける。

  46. 応用物理学演習第5

    2008

     詳細を見る

    量子力学B、統計力学Bの演習を行う。

  47. 統計力学B

    2008

     詳細を見る

    物質の微視的な性質と巨視的な性質を結びつける学問体系である統計力学の基礎的概念を、統計力学Aに続いて量子統計力学の導入およびそのいくつかの典型的な応用例を取り扱うことにより学ぶ。

  48. 計算物理工学特論

    2008

     詳細を見る

    タンパク質科学において計算科学がいかに用いられているかの実例を通して、 理論・計算生物物理学の基礎について講義する。

  49. 応用物理学セミナー

    2007

     詳細を見る

    物性科学や計算科学における基礎および最新の問題をとりあげて、発表、討論を通じて物理学と現代の科学技術との関わりについて理解を深める。創造力、表現力及び討論する力を学ぶ。

  50. 計算機物理学および演習

    2007

     詳細を見る

    物理学における様々な問題を計算機を用いて調べる基本的な手法を学び,演習を通じて,応用する能力を身に着ける。

  51. 応用物理学演習第5

    2007

     詳細を見る

    量子力学B、統計力学Bの演習を行う。

  52. 統計力学B

    2007

     詳細を見る

    物質の微視的な性質と巨視的な性質を結びつける学問体系である統計力学の基礎的概念を、統計力学Aに続いて量子統計力学の導入およびそのいくつかの典型的な応用例を取り扱うことにより学ぶ。

  53. 応用物理学演習第5

    2006

     詳細を見る

    量子力学B、統計力学Bの演習を行う。

  54. 応用物理学セミナー

    2006

     詳細を見る

    物性科学や計算科学における基礎および最新の問題をとりあげて、発表、討論を通じて物理学と現代の科学技術との関わりについて理解を深める。創造力、表現力及び討論する力を学ぶ。

  55. 計算物理工学特論

    2006

     詳細を見る

    タンパク質科学において計算科学がいかに用いられているかの実例を通して、
    理論・計算生物物理学の基礎について講義する。

  56. 統計力学B

    2006

     詳細を見る

    物質の微視的な性質と巨視的な性質を結びつける学問体系である統計力学の基礎的概念を、統計力学Aに続いて量子統計力学の導入およびそのいくつかの典型的な応用例を取り扱うことにより学ぶ。

  57. 微分積分学II

    2005

  58. 応用物理学セミナー

    2005

     詳細を見る

    物性科学や計算科学における基礎および最新の問題をとりあげて、発表、討論を通じて物理学と現代の科学技術との関わりについて理解を深める。創造力、表現力及び討論する力を学ぶ。

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