Micro-second time-resolved X-ray single-molecule internal motions of SARS-CoV-2 spike variants

Daisuke Sasaki; Tatsuya Arai; Yue Yang; Masahiro Kuramochi; Wakako Furuyama; Asuka Nanbo; Hiroshi Sekiguchi; Nobuhiro Morone; Kazuhiro Mio; Yuji C. Sasaki

Biochemistry and Biophysics Reports (Jul 2024)

Micro-second time-resolved X-ray single-molecule internal motions of SARS-CoV-2 spike variants

Daisuke Sasaki,
Tatsuya Arai,
Yue Yang,
Masahiro Kuramochi,
Wakako Furuyama,
Asuka Nanbo,
Hiroshi Sekiguchi,
Nobuhiro Morone,
Kazuhiro Mio,
Yuji C. Sasaki

Affiliations

Daisuke Sasaki: Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan; AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Chiba, 277-0882, Japan
Tatsuya Arai: Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan; AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Chiba, 277-0882, Japan
Yue Yang: Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan; AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Chiba, 277-0882, Japan
Masahiro Kuramochi: Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Naka-narusawa, Hitachi, Ibaraki, 316-8511, Japan
Wakako Furuyama: National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
Asuka Nanbo: National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
Hiroshi Sekiguchi: Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan
Nobuhiro Morone: MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
Kazuhiro Mio: AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Chiba, 277-0882, Japan
Yuji C. Sasaki: Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan; AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Chiba, 277-0882, Japan; Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan; Corresponding author. Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 7H8 #609 Kiban Bldg., 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.

Journal volume & issue: Vol. 38
p. 101712

Abstract

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Single-molecule intramolecular dynamics were successfully measured for three variants of SARS-CoV-2 spike protein, alpha: B.1.1.7, delta: B.1.617, and omicron: B.1.1.529, with a time resolution of 100 μs using X-rays. The results were then compared with respect to the magnitude and directions of motions for the three variants. The largest 3-D intramolecular movement was observed for the omicron variant irrespective of ACE2 receptor binding. A more detailed analysis of the intramolecular motions revealed that the distribution state of intramolecular motion for the three variants was completely different with and without ACE2 receptor binding. The molecular dynamics for the trimeric spike protein of the omicron variant increased when ACE2 binding occurred. At that time, the diffusion constant increased from 71.0 [mrad2/ms] to 91.1 [mrad2/ms].

Published in Biochemistry and Biophysics Reports

ISSN: 2405-5808 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Science: Biology (General); Science: Chemistry: Organic chemistry: Biochemistry
Website: http://www.journals.elsevier.com/biochemistry-and-biophysics-reports/

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