Revealing an origin of temperature-dependent structural change in intrinsically disordered proteins

Inoue, Rintaro*; Oda, Takashi; Nakagawa, Hiroshi; Tominaga, Taiki*; Ikegami, Takahisa*; Konuma, Tsuyoshi*; Iwase, Hiroki*; Kawakita, Yukinobu; Sato, Mamoru*; Sugiyama, Masaaki*

Biophysical Journal, 124(3), p.540 - 548, 2025/02

https://doi.org/10.1016/j.bpj.2024.12.022

Data collection for dilute protein solutions via a neutron backscattering spectrometer

Tominaga, Taiki*; Nakagawa, Hiroshi; Sahara, Masae*; Oda, Takashi*; Inoue, Rintaro*; Sugiyama, Masaaki*

Life (Internet), 12(5), p.675_1 - 675_9, 2022/05

https://doi.org/10.3390/life12050675

The background scattering of sample cells suitable for aqueous protein solution samples, conducted with a neutron backscattering spectrometer, was evaluated. It was found that the scattering intensity of an aluminum sample cell coated with boehmite using DO was lower than that of a sample cell coated with regular water (HO). In addition, meticulous attention to cells with small individual weight differences and the positional reproducibility of the sample cell relative to the spectrometer neutron beam position enabled the accurate subtraction of the scattering profiles of the DO buffer and the sample container. Consequently, high quality information on protein dynamics could be extracted from dilute protein solutions.

Dynamics of proteins with different molecular structures under solution condition

Inoue, Rintaro*; Oda, Takashi*; Nakagawa, Hiroshi; Tominaga, Taiki*; Saio, Tomohide*; Kawakita, Yukinobu; Shimizu, Masahiro*; Okuda, Aya*; Morishima, Ken*; Sato, Nobuhiro*; et al.

Scientific Reports (Internet), 10, p.21678_1 - 21678_10, 2020/12

https://doi.org/10.1038/s41598-020-78311-4

Incoherent quasielastic neutron scattering (iQENS) is a fascinating technique for investigating the internal dynamics of protein. However, both low flux of neutron beam and absence of analytical procedure for extracting the internal dynamics from iQENS profile have been obstacles for studying it under physiological condition (in solution). Thanks to the recent development of neutron source, spectrometer and computational technique, they enable us to decouple internal dynamics, translational and rotational diffusions from the iQENS profile. The internal dynamics of two proteins: globular domain protein (GDP) and intrinsically disordered protein (IDP) in solution were studied. It was found that the average relaxation rate of IDP was larger than that of GDP. Through the detailed analyses on their internal dynamics, it was revealed that the fraction of mobile H atoms in IDP was much higher than that in GDP. Interestingly, the fraction of mobile H atoms was closely related to the fraction of H atoms on highly solvent exposed surfaces. The iQENS study presented that the internal dynamics were governed by the highly solvent exposed amino acid residues depending upon protein molecular architectures.

Solution neutron scattering

Sugiyama, Masaaki*; Inoue, Rintaro*; Nakagawa, Hiroshi; Saio, Tomohide*

Hamon, 30(1), p.16 - 25, 2020/02

https://doi.org/10.5611/hamon.30.1_16

Neutron has distinct features as a scattering probe to analyze structure and dynamics of biological macromolecules. The theme of this review is to try to describe how we did/do utilize them. And "How we should utilize them more effectively in the trend of integrative structural biology?" with solution scattering.

Neutron biology for next generation; Report from J-PARC workshop "Neutron Biology for Next Generation"; March 22nd-23rd, 2017, Ibaraki Quantum Beam Research Center

Sugiyama, Masaaki*; Nakagawa, Hiroshi; Inoue, Rintaro*; Kawakita, Yukinobu

JAEA-Review 2017-024, 40 Pages, 2017/12

JAEA-Review-2017-024.pdf:8.69MB

Now-a-days, promotion of life science by utilizing neutron (neutrons biology) is highly demanded in our country, following installation and improvement of high quality and intensity neutron sources at J-PARC and JRR-3. Aiming at accelerating development of neutrons biology in our country, an international workshop "Neutron biology for next generation" was held as a J-PARC Workshop at Ibaraki Quantum Beam Research Center from 22 March to 23 March in 2017. In the workshop, latest instruments, new-fashioned methodologies, recent scientific results and future perspectives were extensively discussed by domestic neutron instrumental scientists and domestic/foreign neutron biologists. This is a report of the workshop summarized by organizers.

Novel neutron scattering techniques using neutron transmission spectra

Oba, Yojiro*; Morooka, Satoshi; Sato, Hirotaka*; Sato, Nobuhiro*; Inoue, Rintaro*; Sugiyama, Masaaki*

Hamon, 26(4), p.170 - 173, 2016/11

https://doi.org/10.5611/hamon.26.4_170

Small-angle neutron scattering for biology; Application of SANS to biological study

Endo, Hitoshi; Sugiyama, Masaaki*; Inoue, Rintaro*

Hamon, 22(3), p.258 - 267, 2012/08

https://doi.org/10.5611/hamon.22.3_258

In this text, the authors introduce two powerful techniques and one developing one for Small-Angle Neutron Scattering (SANS). The most fascinating feature of neutron as a scattering probe is its isotope effect in hydrogen. The first topic is concerning about recent progress on Contrast Variation Method: the author shows how to apply the contrast variation method to protein-mineral complex system and analyze the data. The second is concerning about deuteration-labeling: the author shows kinetics analysis in quaternary structure of homo-oligomeric protein with this technique. The final topic is concerning about the next generation analysis: an analysis method coupling SANS with neutron spin echo for dynamics of tertiary structure of protein.

Neutron spin-echo studies on crossover from single chain motion to collective dynamics

Kanaya, Toshiji; Takahashi, Nobuaki; Inoue, Rintaro*; Matsuba, Go*; Nishida, Koji*; Nagao, Michihiro*

ISSP Activity Report on Neutron scattering Research; Experimental Reports (CD-ROM), 13, 1 Pages, 2006/00

Thermal neutron spin-echo studies on dynamics of a glass-forming polymer in a high range

Kanaya, Toshiji*; Kakurai, Kazuhisa; Tsukushi, Itaru*; Inoue, Rintaro*; Watanabe, Hiroshi*; Nishi, Masakazu*; Nakajima, Kenji; Takemura, Kazuhiro*; Furuya, Hidemine*

Journal of the Physical Society of Japan, 74(12), p.3236 - 3240, 2005/12

https://doi.org/10.1143/JPSJ.74.3236

We performed thermal neutron spin echo measurements on a glass-forming polymer, deuterated polybutadiene (-[CD-CD=CD-CD]-; PB-d), in a high range up to 3.5 covering the first and second peaks of the structure factor S(), and evaluated the decay rate () of the coherent intermediate scattering function as a function of . In contrast to the previous experimental findings on the first peak of S() at = 1.5, no "de Gennes" type narrowing was observed on the second peak at = 2.9. This novel finding indicates that the narrowing is hidden by the distinct motions of the soft -CD-CD- and =CD-CD- units and the self-motions of the rigid and soft units in the range around the second peak.

Analysis of hierarchy of structure and dynamics of multidomain proteins

Nakagawa, Hiroshi; Saio, Tomohide*; Nagao, Michihiro*; Inoue, Rintaro*; Sugiyama, Masaaki*; Tominaga, Taiki*; Kawakita, Yukinobu

no journal, , 

The flexible conformation of a multidomain protein is responsible for its biological function. 3-domain protein: MurD (47kDa) changes its domain conformation sequentially from open to semi-closed to closed conformation during enzymatic reactions. However, the dynamics of the domains in each conformation is unknown. In this study, we combined small-angle X-ray and neutron scattering (SAXS and SANS), dynamic light scattering (DLS), neutron back scattering (NBS), neutron spin echo (NSE), and molecular dynamics (MD) simulations to investigate the conformational dynamics of MurD in the three corresponding states (apo and ATP, inhibitor-bound state). The analysis showed that the conformational dynamics of MurD during the enzymatic reaction was not affected. The analysis suggests that the changes in domain dynamics during enzymatic reactions are related to the affinity and reaction efficiency with ligands that bind specifically to each reaction state.