Faculty Profiles - TERADA, Tomoki

Papers - TERADA, Tomoki

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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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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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