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Journal Articles

X-ray scattering $$cdot$$ neutron scattering

Nakagawa, Hiroshi; Matsuo, Tatsuhito*

Jikken Igaku, 39(10), p.1667 - 1673, 2021/06

X-ray and neutron scattering are methods to reveal the structural state, assembly state, and intermolecular interactions of biomolecules in solution. Synchrotron X-rays provide highly accurate solution scattering data in a short time. Deuterated labeling can be used to make specific molecules invisible in neutron beams, allowing us to selectively observe only the molecules of interest in a molecular population. Neutron beams with energies comparable to thermal fluctuations are also suitable for measuring molecular motion. Although its application to the analysis of phase separation phenomena is currently limited, it is an effective method for analyzing phase separation states on the nano- to meso-scale and for studying the liquid-liquid phase separation.

Journal Articles

Segmental motions of proteins under non-native states evaluated using quasielastic neutron scattering

Fujiwara, Satoru*; Matsuo, Tatsuhito*; Sugimoto, Yasunobu*; Shibata, Kaoru

Journal of Physical Chemistry Letters (Internet), 10(23), p.7505 - 7509, 2019/12

 Times Cited Count:0 Percentile:0.01(Chemistry, Physical)

Characterization of the dynamics of disordered polypeptide chains is required to elucidate the behavior of intrinsically disordered proteins and proteins under non-native states related to the folding process. Here we develop a method using quasielastic neutron scattering, combined with small-angle X-ray scattering and dynamic light scattering, to evaluate segmental motions of proteins as well as diffusion of the entire molecules and local side-chain motions. We apply this method to RNase A under the unfolded and molten-globule (MG) states. The diffusion coefficients arising from the segmental motions are evaluated and found to be different between the unfolded and MG states. The values obtained here are consistent with those obtained using the fluorescence-based techniques. These results demonstrate not only feasibility of this method but also usefulness to characterize the behavior of proteins under various disordered states.

Journal Articles

Dynamic properties of human $$alpha$$-synuclein related to propensity to amyloid fibril formation

Fujiwara, Satoru*; Kono, Fumiaki*; Matsuo, Tatsuhito*; Sugimoto, Yasunobu*; Matsumoto, Tomoharu*; Narita, Tetsuhiro*; Shibata, Kaoru

Journal of Molecular Biology, 431(17), p.3229 - 3245, 2019/08

 Times Cited Count:3 Percentile:27.91(Biochemistry & Molecular Biology)

$$alpha$$-synuclein ($$alpha$$Syn) is an intrinsically disordered protein (IDP) with unknown function. $$alpha$$Syn is known to form amyloid fibrils, which are implicated with the pathogenesis of Parkinson's disease and other synucleinopathies. Elucidating the mechanism of fibril formation of $$alpha$$Syn is therefore important for understanding the mechanism of the pathogenesis of these diseases. Here, using the quasielastic neutron scattering (QENS) and small-angle X-ray scattering (SAXS) techniques, we investigated the dynamic and structural properties of $$alpha$$Syn. These results imply that fibril formation of $$alpha$$Syn requires not only the enhanced local motions but also the segmental motions such that the proper inter-molecular interactions are possible.

Journal Articles

Difference in the hydration water mobility around F-actin and myosin subfragment-1 studied by quasielastic neutron scattering

Matsuo, Tatsuhito; Arata, Toshiaki*; Oda, Toshiro*; Nakajima, Kenji; Kawamura, Seiko; Kikuchi, Tatsuya; Fujiwara, Satoru

Biochemistry and Biophysics Reports (Internet), 6, p.220 - 225, 2016/07

Journal Articles

Dynamical behavior of human $$alpha$$-synuclein studied by quasielastic neutron scattering

Fujiwara, Satoru; Araki, Katsuya*; Matsuo, Tatsuhito; Yagi, Hisashi*; Yamada, Takeshi*; Shibata, Kaoru; Mochizuki, Hideki*

PLOS ONE (Internet), 11(4), p.e0151447_1 - e0151447_17, 2016/04

 Times Cited Count:18 Percentile:67.4(Multidisciplinary Sciences)

Journal Articles

Structures of the troponin core domain containing the cardiomyopathy-causing mutants studied by small-angle X-ray scattering

Matsuo, Tatsuhito; Takeda, Soichi*; Oda, Toshiro*; Fujiwara, Satoru

Biophysics and Physicobiology (Internet), 12, p.145 - 158, 2015/12

Journal Articles

Internal dynamics of F-actin and myosin subfragment-1 studied by quasielastic neutron scattering

Matsuo, Tatsuhito; Arata, Toshiaki*; Oda, Toshiro*; Nakajima, Kenji; Kawamura, Seiko; Kikuchi, Tatsuya; Fujiwara, Satoru

Biochemical and Biophysical Research Communications, 459(3), p.493 - 497, 2015/04

 Times Cited Count:4 Percentile:16.86(Biochemistry & Molecular Biology)

Journal Articles

Difference in hydration structures between F-actin and myosin subfragment-1 detected by small-angle X-ray and neutron scattering

Matsuo, Tatsuhito; Arata, Toshiaki*; Oda, Toshiro*; Fujiwara, Satoru

Biophysics, 9, p.99 - 106, 2013/07

Journal Articles

Dynamics of cardiomyopathy-causing mutant of troponin measured by neutron scattering

Matsuo, Tatsuhito; Natali, F.*; Plazanet, M.*; Zaccai, G.*; Fujiwara, Satoru

Journal of the Physical Society of Japan, 82(Suppl.A), p.SA020_1 - SA020_5, 2013/01

 Times Cited Count:1 Percentile:12.72(Physics, Multidisciplinary)

Troponin is a protein that regulates the muscle contraction depending on the intracellular Ca$$^{2+}$$ concentration. K247R mutation of TnT is known to cause the hypertrophic cardiomyopathy. In this work, neutron scattering was used to detect possible changes in dynamics of troponin caused by mutation. Elastic incoherent neutron scattering experiments were carried out on solution samples of the wild type, and K247R mutant at the IN13 spectrometer at the Institut Laue-Langevin, at temperatures between 280 K and 292 K with an interval of 3 K. From the measured scattering data, force constants ($$<$$k$$>$$), which reflect the resilience of the protein, were calculated. The $$<$$k$$>$$ values for the wild type and K247R mutant were 0.077 (0.035) N/m and 0.046 (0.026) N/m (mean(s.d.)), respectively. This suggests that the disease-causing mutant is more flexible than the wild type. The large flexibility might modulate Ca$$^{2+}$$ signal transmission mechanism, leading to the functional aberration.

Journal Articles

An X-ray diffraction study on a single rod outer segment from frog retina

Yagi, Naoto*; Matsuo, Tatsuhito; Ota, Noboru*

Journal of Synchrotron Radiation, 19(4), p.574 - 578, 2012/07

 Times Cited Count:1 Percentile:7.9(Instruments & Instrumentation)

X-ray diffraction patterns were recorded from isolated single rod outer segments of frog. The outer segments in Ringer's solution were exposed to a 6 $$mu$$m microbeam (15 keV) at the BL40XU beamline, SPring-8. The diffraction pattern demonstrated a remarkable regularity in the stacking and flatness of the disk membranes. The electron density profile calculated from the intensity of up to tenth-order reflections showed a pair of bilayers that comprise a disk membrane. The structure of the disk membrane and the changes in the profile on swelling generally agreed with previous reports. Radiation damage was significant with an irradiation of 5 $$times$$ 10$$^{5}$$ Gy which is much lower than the known damaging dose on proteins at the liquid-nitrogen temperature.

Journal Articles

X-ray diffraction recording from single axonemes of eukaryotic flagella

Nishiura, Masaya*; Toba, Shiori*; Takao, Daisuke*; Miyashiro, Daisuke*; Sakakibara, Hitoshi*; Matsuo, Tatsuhito; Kamimura, Shinji*; Oiwa, Kazuhiro*; Yagi, Naoto*; Iwamoto, Hiroyuki*

Journal of Structural Biology, 178(3), p.329 - 337, 2012/06

 Times Cited Count:3 Percentile:10.38(Biochemistry & Molecular Biology)

We report the first X-ray diffraction patterns recorded from single axonemes of eukaryotic flagella with a diameter of only $$<$$0.2 $$mu$$m, by using the technique of cryomicrodiffraction. A spermatozoon isolated from Drosophila melanogaster, was mounted straight in a glass capillary, quickly frozen and its 800-$$mu$$m segment was irradiated end-on with intense synchrotron radiation X-ray microbeams (diameter, 2 $$mu$$m) at 74 K. Well-defined diffraction patterns were recorded, consisting of a large number of isolated reflection spots. The patterns had features of an 18-fold rotational symmetry as expected from the axonemal structure. The diffraction patterns were compared with the results of model calculations based on a published electron micrograph of the Drosophila axoneme. The comparison provided information on the native state of axoneme, including estimates of axonemal diameter and interdoublet spacing.

Journal Articles

A Compact intermediate state of calmodulin in the process of target binding

Yamada, Yoshiteru*; Matsuo, Tatsuhito; Iwamoto, Hiroyuki*; Yagi, Naoto*

Biochemistry, 51(19), p.3963 - 3970, 2012/05

 Times Cited Count:16 Percentile:44.74(Biochemistry & Molecular Biology)

Calmodulin undergoes characteristic conformational changes by binding Ca$$^{2+}$$. We measured the conformational changes of calmodulin upon Ca$$^{2+}$$ and mastoparan binding using the time-resolved small-angle X-ray scattering technique combined with flash photolysis of caged calcium. This measurement system covers the time range of 0.5-180 ms. Within 10 ms of the stepwise increase in Ca$$^{2+}$$ concentration, we identified a distinct compact conformational state with a drastically different molecular dimension. This process is too fast to study with a conventional stopped-flow apparatus. The compact conformational state was also observed without mastoparan, indicating that the calmodulin forms a compact globular conformation by itself upon Ca$$^{2+}$$ binding. This new conformational state of calmodulin seems to regulate Ca$$^{2+}$$ binding and conformational changes in the N-terminal domain.

Oral presentation

Structural changes of troponin by cardiomyopathy-causing mutations

Fujiwara, Satoru; Matsuo, Tatsuhito; Matsumoto, Fumiko; Oda, Toshiro*; Takeda, Soichi*

no journal, , 

Oral presentation

Time-resolved measurements of structural changes of troponin and intracellular Ca$$^{2+}$$ concentrations during twitch of frog skeletal muscle

Matsuo, Tatsuhito; Iwamoto, Hiroyuki*; Yagi, Naoto*

no journal, , 

To elucidate the behavior of troponin during twitch of frog skeletal muscle, structural changes of troponin and changes of the intracellular Ca$$^{2+}$$ concentration ([Ca]i) were monitored by X-ray diffraction and fluo3-AM at the sarcomere length (SL) of 2.8 $$mu$$m and 4.0 $$mu$$m. [Ca]i was converted to the concentration of Ca$$^{2+}$$ bound to troponin ([CaTn]). At 4.0 $$mu$$m SL, the troponin reflection intensity at 38.5 nm$$^{-1}$$ began to increase at 3 ms after the stimulus when [CaTn] has already reached a half of its peak, and returned to the resting level more quickly than [CaTn]. At 2.8 $$mu$$m SL, the X-ray intensity showed a drastic decrease and the decay of [CaTn] was slower. These results indicate that (1) structures of troponin molecules begin to change only after many of them have bound Ca$$^{2+}$$, and return to its resting conformation even when some still bind Ca$$^{2+}$$ in no filament overlap state, (2) the dissociation of Ca$$^{2+}$$ appears to be slowed down and conformations are largely affected by crossbridges.

Oral presentation

Dynamics of cardiomyopathy-causing mutant of troponin observed by neutron scattering

Matsuo, Tatsuhito; Natali, F.*; Zaccai, G.*; Fujiwara, Satoru

no journal, , 

Troponin is a protein that regulates the muscle contraction depending on the intracellular Ca2+ concentration. K247R mutation of TnT is known to cause the hypertrophic cardiomyopathy. In this work, neutron scattering was used to detect possible changes in dynamics of troponin caused by mutation. Elastic incoherent neutron scattering experiments were carried out on solution samples of the wild type, and K247R mutant at the IN13 spectrometer at the Institut Laue-Langevin, at temperatures between 280 K and 292 K with an interval of 3 K. From the measured scattering data, force constants ($$<$$k$$>$$), which reflect the resilience of the protein, were calculated. The $$<$$k$$>$$ values for the wild type and K247R mutant were 0.077 (0.035) N/m and 0.046 (0.026) N/m (mean(s.d.)), respectively. This suggests that the disease-causing mutant is more flexible than the wild type. The large flexibility might modulate Ca2+ signal transmission mechanism, leading to the functional aberration.

Oral presentation

Internal dynamics of protein during amyloid fibril formation observed by neutron scattering

Fujiwara, Satoru; Yamada, Takeshi*; Matsuo, Tatsuhito; Takahashi, Nobuaki; Kamazawa, Kazuya*; Kawakita, Yukinobu; Shibata, Kaoru*

no journal, , 

Oral presentation

Dynamics of the amyloid-formaing protein observed by neutron scattering

Fujiwara, Satoru; Yamada, Takeshi*; Matsuo, Tatsuhito; Takahashi, Nobuaki; Kamazawa, Kazuya*; Kawakita, Yukinobu; Shibata, Kaoru*

no journal, , 

no abstracts in English

Oral presentation

Analysis of the internal dynamics of the amyloid fibril-forming protein by neutron scattering

Fujiwara, Satoru; Yamada, Takeshi*; Matsuo, Tatsuhito; Takahashi, Nobuaki; Kamazawa, Kazuya*; Kawakita, Yukinobu; Shibata, Kaoru*

no journal, , 

no abstracts in English

Oral presentation

Characterization of the structural and dynamic properties of hydration water around F-actin detected by neutron and X-ray scattering

Matsuo, Tatsuhito; Arata, Toshiaki*; Oda, Toshiro*; Fujiwara, Satoru

no journal, , 

The structural and dynamic properties of hydration water around F-actin and myosin S1 were investigated using small-angle neutron/X-ray scattering and quasi-elastic neutron scattering. S1 was shown to have typical hydration water, which has 10-15% higher average density with lower mobility than bulk water. On the other hand, F-actin was shown to have hydration water with unusual properties: the average density of the hydration water is at least 19% higher than that of bulk water and mobility is close to that of bulk water. These results indicate the diversity of hydration shell around proteins in terms of both structural and dynamic properties. The unusual hydration water around F-actin may be related to the suggested existence of "hyper-mobile water" around F-actin.

Oral presentation

Changes in the dynamics of the muscle thin filaments observed by neutron scattering

Fujiwara, Satoru; Matsuo, Tatsuhito; Yamada, Takeshi*; Takahashi, Nobuaki*; Kamazawa, Kazuya*; Kawakita, Yukinobu; Shibata, Kaoru

no journal, , 

35 (Records 1-20 displayed on this page)