Yasumasa Joti

Yasumasa Joti

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Yasumasa Joti

Yasumasa Joti

Publications by authors named "Yasumasa Joti"

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Design of a liquid cell toward three-dimensional imaging of unidirectionally-aligned particles in solution using X-ray free-electron lasers.

Phys Chem Chem Phys 2020 Feb 23;22(5):2622-2628. Epub 2019 Aug 23.

Research Institute for Electronic Science, Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo 001-0021, Japan.

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http://dx.doi.org/10.1039/c9cp03658jDOI Listing
February 2020

An Efficient Timer and Sizer of Biomacromolecular Motions.

Structure 2020 Feb 25;28(2):259-269.e8. Epub 2019 Nov 25.

Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan; Physics Division, National Center for Theoretical Sciences, Hsinchu, Taiwan. Electronic address:

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http://dx.doi.org/10.1016/j.str.2019.10.020DOI Listing
February 2020

Viscosity-adjustable grease matrices for serial nanocrystallography.

Sci Rep 2020 Jan 28;10(1):1371. Epub 2020 Jan 28.

RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.

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http://dx.doi.org/10.1038/s41598-020-57675-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6987181PMC
January 2020

Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra.

Biophys Physicobiol 2019 29;16:240-247. Epub 2019 Nov 29.

School of Life Sciences and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.

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http://dx.doi.org/10.2142/biophysico.16.0_240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6975922PMC
November 2019

Universality and Structural Implications of the Boson Peak in Proteins.

Biophys J 2019 Jul 14;117(2):229-238. Epub 2019 Jun 14.

Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan; Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, Tokai, Naka, Ibaraki, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2019.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700671PMC
July 2019

Strategy for Stabilization of CutA1 Proteins Due to Ion-Ion Interactions at Temperatures of over 100 °C.

Biochemistry 2018 05 18;57(18):2649-2656. Epub 2018 Apr 18.

RIKEN SPring-8 Center , 1-1-1 Kouto , Sayo, Hyogo 679-5148 , Japan.

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http://dx.doi.org/10.1021/acs.biochem.8b00103DOI Listing
May 2018

Ion-ion interactions in the denatured state contribute to the stabilization of CutA1 proteins.

Sci Rep 2018 05 16;8(1):7613. Epub 2018 May 16.

Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo, Hyogo, 679-5198, Japan.

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http://dx.doi.org/10.1038/s41598-018-25825-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5955972PMC
May 2018

Software for the data analysis of the arrival-timing monitor at SACLA.

J Synchrotron Radiat 2018 Mar 7;25(Pt 2):592-603. Epub 2018 Feb 7.

Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.

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http://dx.doi.org/10.1107/S1600577517016654DOI Listing
March 2018

Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA.

Structure 2018 01 7;26(1):7-19.e5. Epub 2017 Dec 7.

Department of Medical Chemistry and Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan; Japan Science and Technology Agency (JST) and Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09692126173035
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http://dx.doi.org/10.1016/j.str.2017.11.005DOI Listing
January 2018

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL.

J Synchrotron Radiat 2017 07 14;24(Pt 4):727-737. Epub 2017 Jun 14.

Advanced Institute of Computational Science, RIKEN, 6-7-1 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.

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http://dx.doi.org/10.1107/S1600577517007767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493022PMC
July 2017

Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging.

Mol Cell 2017 Jul 14;67(2):282-293.e7. Epub 2017 Jul 14.

Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.06.018DOI Listing
July 2017

X-ray free electron laser single-particle analysis for biological systems.

Curr Opin Struct Biol 2017 04 10;43:163-169. Epub 2017 May 10.

XFEL Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.

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http://dx.doi.org/10.1016/j.sbi.2017.03.014DOI Listing
April 2017

Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure.

IUCrJ 2016 Nov 26;3(Pt 6):420-429. Epub 2016 Sep 26.

Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA.

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http://dx.doi.org/10.1107/S2052252516013956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5094444PMC
November 2016

Data processing pipeline for serial femtosecond crystallography at SACLA.

J Appl Crystallogr 2016 Jun 18;49(Pt 3):1035-1041. Epub 2016 Apr 18.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo , 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1107/S1600576716005720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886989PMC
June 2016

Microcrystal delivery by pulsed liquid droplet for serial femtosecond crystallography.

Acta Crystallogr D Struct Biol 2016 Apr 24;72(Pt 4):520-3. Epub 2016 Mar 24.

Japan Synchrotron Radiation Research Institute, Koto, Sayo, Hyogo 679-5198, Japan.

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http://dx.doi.org/10.1107/S2059798316001480DOI Listing
April 2016

Yolk/Shell Assembly of Gold Nanoparticles by Size Segregation in Solution.

J Am Chem Soc 2016 Mar 3;138(10):3274-7. Epub 2016 Mar 3.

Research Institute for Electronic Science, Hokkaido University , Sapporo 001-0021, Japan.

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http://dx.doi.org/10.1021/jacs.5b12456DOI Listing
March 2016

Synthesis of Janus-like gold nanoparticles with hydrophilic/hydrophobic faces by surface ligand exchange and their self-assemblies in water.

Langmuir 2015 Apr 1;31(14):4054-62. Epub 2015 Apr 1.

†Research Institute for Electronic Science, Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo 001-0021, Japan.

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http://pubs.acs.org/doi/10.1021/la504647z
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http://dx.doi.org/10.1021/la504647zDOI Listing
April 2015

Chromatin structure revealed by X-ray scattering analysis and computational modeling.

Methods 2014 Dec 26;70(2-3):154-61. Epub 2014 Aug 26.

RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; XFEL Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.

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http://dx.doi.org/10.1016/j.ymeth.2014.08.008DOI Listing
December 2014

Chromosomes without a 30-nm chromatin fiber.

Nucleus 2012 Sep-Oct;3(5):404-10. Epub 2012 Jul 31.

XFEL Division; Japan Synchrotron Radiation Research Institute, Sayo-cho, Japan.

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http://dx.doi.org/10.4161/nucl.21222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3474659PMC
February 2013

Detecting coupled collective motions in protein by independent subspace analysis.

J Chem Phys 2010 Nov;133(18):185102

Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1063/1.3498745DOI Listing
November 2010

Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra.

Biophys J 2008 Jun 29;94(11):4435-43. Epub 2008 Feb 29.

Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1529/biophysj.107.118042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2480692PMC
June 2008

Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline staphylococcal nuclease.

J Phys Chem B 2008 Mar 23;112(11):3522-8. Epub 2008 Feb 23.

Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1021/jp710039pDOI Listing
March 2008

Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation.

Phys Rev E Stat Nonlin Soft Matter Phys 2007 Apr 24;75(4 Pt 1):041912. Epub 2007 Apr 24.

Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

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http://dx.doi.org/10.1103/PhysRevE.75.041912DOI Listing
April 2007

[Protein energy landscape and dynamics studied by molecular simulations and neutron scattering].

Tanpakushitsu Kakusan Koso 2006 Jul;51(8):972-8

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July 2006

Protein boson peak originated from hydration-related multiple minima energy landscape.

J Am Chem Soc 2005 Jun;127(24):8705-9

Neutron Science Research Center, Japan Atomic Energy Research Institute, 8-1 Umemidai, Kizu-cho, Souraku-gun, Kyoto 619-0215, Japan.

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http://dx.doi.org/10.1021/ja0425886DOI Listing
June 2005

Nonlinear temperature dependence of the crystal structure of lysozyme: correlation between coordinate shifts and thermal factors.

Acta Crystallogr D Biol Crystallogr 2002 Sep 23;58(Pt 9):1421-32. Epub 2002 Aug 23.

Department of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Japan.

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http://dx.doi.org/10.1107/S0907444902011277DOI Listing
September 2002