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Nakagawa, Hiroshi; Saio, Tomohide*; Nagao, Michihiro*; Inoue, Rintaro*; Sugiyama, Masaaki*; Ajito, Satoshi; Tominaga, Taiki*; Kawakita, Yukinobu
Biophysical Journal, 120(16), p.3341 - 3354, 2021/08
Times Cited Count：4 Percentile：38.66(Biophysics)A multi-domain protein can have various conformations in solution. Interactions with other molecules result in the stabilization of one of the conformations and change in the domain dynamics. SAXS, a well-established experimental technique, can be employed to elucidate the conformation of a multi-domain protein in solution. NSE spectroscopy is a promising technique for recording the domain dynamics in nanosecond and nanometer scale. Despite the great efforts, there are still under development. Thus, we quantitatively removed the contribution of diffusion dynamics and hydrodynamic interactions from the NSE data via incoherent scattering, revealing the differences in the domain dynamics of the three functional states of a multi-domain protein, MurD. The differences among the three states can be explained by two domain modes.
Nagao, Michihiro*; Kelley, E. G.*; Faraone, A.*; Saito, Makina*; Yoda, Yoshitaka*; Kurokuzu, Masayuki*; Takata, Shinichi; Seto, Makoto*; Butler, P. D.*
Physical Review Letters, 127(7), p.078102_1 - 078102_7, 2021/08
Times Cited Count：19 Percentile：88.38(Physics, Multidisciplinary)Zhai, Y.*; Luo, P.*; Nagao, Michihiro*; Nakajima, Kenji; Kikuchi, Tatsuya*; Kawakita, Yukinobu; Kienzle, P. A.*; Z, Y.*; Faraone, A.*
Physical Chemistry Chemical Physics, 23(12), p.7220 - 7232, 2021/03
Times Cited Count：3 Percentile：27(Chemistry, Physical)Motokawa, Ryuhei; Kobayashi, Toru; Endo, Hitoshi; Mu, J.*; Williams, C. D.*; Masters, A. J.*; Antonio, M. R.*; Heller, W. T.*; Nagao, Michihiro*
ACS Central Science, 5(1), p.85 - 96, 2019/01
Times Cited Count：46 Percentile：86.05(Chemistry, Multidisciplinary)Kofu, Maiko; Faraone, A.*; Tyagi, M.*; Nagao, Michihiro*; Yamamuro, Osamu*
Physical Review E, 98(4), p.042601_1 - 042601_6, 2018/10
Times Cited Count：4 Percentile：36.54(Physics, Fluids & Plasmas)Nemoto, Fumiya*; Kofu, Maiko; Nagao, Michihiro*; Oishi, Kazuki*; Takata, Shinichi; Suzuki, Junichi*; Yamada, Takeshi*; Shibata, Kaoru; Ueki, Takeshi*; Kitazawa, Yuzo*; et al.
Journal of Chemical Physics, 149(5), p.054502_1 - 054502_11, 2018/08
Times Cited Count：19 Percentile：70.02(Chemistry, Physical)Motokawa, Ryuhei; Endo, Hitoshi*; Nagao, Michihiro*; Heller, W. T.*
Solvent Extraction and Ion Exchange, 34(5), p.399 - 406, 2016/07
Times Cited Count：5 Percentile：19.64(Chemistry, Multidisciplinary)Takahashi, Nobuaki; Nishida, Koji*; Inoue, Rintaro*; Ogawa, Hiroki*; Kanaya, Toshiji*; Nagao, Michihiro*
NSL News Letter, 2007-4, p.155 - 157, 2007/04
We have studied dynamics of poly(vinyl alcohol) (PVA) gel in a mixture of deuterated dimethyl sulfoxide (DMSO-d
) and D
O (60/40 by volume) during heating process from 25
C to 80C using neutron spin-echo (NSE) techniques.
Kanaya, Toshiji*; Takahashi, Nobuaki; Nishida, Koji*; Seto, Hideki*; Nagao, Michihiro*; Takeda, Takayoshi*
Physica B; Condensed Matter, 385-386(1), p.676 - 681, 2006/11
Times Cited Count：13 Percentile：52.05(Physics, Condensed Matter)We report neutron spin-echo measurements on three types of poly(vinyl alcohol) (PVA) gels. The first is PVA gel in a mixture of dimethyl sulfoxide (DMSO) and water with volume ratio 60/40, the second is PVA gel in an aqueous borax solution and the third is chemically cross-linked PVA gel. The observed normalized intermediate scattering functions I(Q,t)/I(Q,0) were very different among them. The I(Q,t)/I(Q,0) of the first and third gels showed a non-decaying component in addition to a decaying component, but the second one did not have the non-decaying one. This clearly indicates that the fluctuations in the first and third PVA gels consist of static and dynamic fluctuations whereas the second PVA gel does include only the dynamic fluctuations. The dynamic and static fluctuations of the PVA gels were analyzed in terms of a restricted motion in the gel network and the Zimm motion, respectively.
Takahashi, Nobuaki; Nishida, Koji*; Tsubouchi, Tsuyoshi*; Ogawa, Hiroki*; Inoue, Rintaro*; Kanaya, Toshiji*; Nagao, Michihiro*
ISSP Activity Report on Neutron scattering Research; Experimental Reports (CD-ROM), 13, 2 Pages, 2006/00
no abstracts in English
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
Takahashi, Nobuaki; Kanaya, Toshiji*; Nishida, Koji*; Seto, Hideki*; Nagao, Michihiro*; Takeda, Takayoshi*
no journal, ,
We have extensively studied nano-scale structure and dynamics of three types of poly(vinyl alcohol) (PVA) gels by using small-angle neutron scattering (SANS) and neutron spin-echo (NSE) techniques; two physical gels and one chemical gel. The first one was a PVA gel in a mixture of deuterated dimethyl sulfoxide (DMSO-d6) and D2O with volume fraction of DMSO-d6 being 0.6, in which cross-links were made of crystallites. On the basis of NSE results, SANS intensity was divided into static and dynamic fluctuations to find that the former contribution was dominant in the present wave vector (Q) range. The latter, dynamic fluctuations were analyzed in terms of fluctuations of cross-links in the quasi-equilibrium position. The second gel was PVA in aqueous borax solution. The intermediate scattering functions of the gel as well as the sol were well described by Zimm mode and gel mode in Q regions of above and below a critical wave vector (Qc). The last one was the chemically cross-linked PVA gel. The intermediate scattering function was also described by Zimm mode in a short-time region, suggesting that it behaves like polymer solution. However, in a long-time region, the data points deviated from Zimm-scaled master curve, suggesting that it was restricted by the cross-links made of covalent bonds.
Kofu, Maiko; Faraone, A.*; Tyagi, M.*; Nagao, Michihiro*; Yamamuro, Osamu*
no journal, ,
The self-diffusion of molecules in a liquid is basically governed by Fick's law. It is known that the self-part of the van Hove correlation function is written as the Gaussian function with respect to 
and decays exponentially with time (Debye relaxation). In the case, the relaxation time obeys the relation 
. In glass-forming materials, however, the relaxation process is often described by the non-Debye KWW function, ![$$exp [-(t/tau)^{beta}]$$](/search/images/EROGK4DQEBNS0KDUF3OHIYLVFFPHWXDCMV0GC5K3EQ.gif)
. A natural question arises as to whether the relation is valid for the non- Debye diffusion process. To address this issue, we have investigated in detail the 
-dependence of the relaxation times for two different types of liquid, a molecular liquid (3-methylpentane) and an ionic liquid (C4mimTFSI). The measurements were done using neutron spin echo, backscattering and chopper spectrometers at NIST. Two crossover points were clearly found. The first crossover can be due to coupling with structural relaxation and the second one is Gaussian to non-Gaussian transition. This is the first clear experimental evidence for the two crossover.
Nakagawa, Hiroshi; Saio, Tomohide*; Sugiyama, Masaaki*; Inoue, Rintaro*; Nagao, Michihiro*
no journal, ,
It is necessary for the understanding of structure polymorphism of various molecules and interacting protein and the plastic molecules base to clarify the fluctuation of the domain as the mer. In this study, I targeted protein MurD consisting of three domains and a ligand was in a free state and analyzed domain exercise by the quantum beam dispersion method using X-rays and the neutron and the correlation structure analytical method that fused of the molecules simulation about an ATP-binding state, three states of the Compound1-binding state. By the solution small angle scattering experiment, I showed that the solution structure of the 3 state was different. In addition, I showed good agreement with the dispersion profile obtained from the molecular simulation and confirmed that I could discuss solution structure in atom resolving power from experimental data of the low resolving power. I extracted a domain campaign in conjunction with the function from the chief ingredient analysis of the molecular simulation result. Furthermore, a result to suggest what a fluctuation and a couple of the amino acid residue that this domain campaign participated in the combination with interaction molecules of MurD did was provided. By the method that fused by an experiment method of dynamic solution structure analysis including a neutron spin echo and technique of the calculation science in addition to small angle scattering, I visualize domain exercise of protein in atom resolving power and, in the announcement, argue by a function of the protein from the dynamic structure that a couple did between the hierarchies of different space scale.
Kofu, Maiko; Faraone, A.*; Tyagi, M.*; Nagao, Michihiro*; Yamamuro, Osamu*
no journal, ,
no abstracts in English
Kofu, Maiko; Kajiwara, Takashi*; Kawamura, Seiko; Kikuchi, Tatsuya*; Nakajima, Kenji; Matsuura, Masato*; Shibata, Kaoru; Nagao, Michihiro*; Yamamuro, Osamu*
no journal, ,
no abstracts in English
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.
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.
