SANS simulation of aggregated protein in aqueous solution

Masaaki Sugiyama; Kei Hamada; Koichi Kato; Eiji Kurimoto; Kenta Okamoto; Yukio Morimoto; Susumu Ikeda; Sachio Naito; Michihiko Furusaka; Keiji Itoh; Kazuhiro Mori; Toshiharu Fukunaga

doi:10.1016/j.nima.2008.11.121

SANS simulation of aggregated protein in aqueous solution

Masaaki Sugiyama, Kei Hamada, Koichi Kato, Eiji Kurimoto, Kenta Okamoto, Yukio Morimoto, Susumu Ikeda, Sachio Naito, Michihiko Furusaka, Keiji Itoh, Kazuhiro Mori, Toshiharu Fukunaga

Research output: Contribution to journal › Article › peer-review

8 Citations (Scopus)

Abstract

Small-angle neutron scattering (SANS) of aggregated protein in an aqueous solution is simulated based on the crystallographic data of the protein. After obtaining the crystallographic data of the target protein, hydrogen atoms are added to the data and then some hydrogen atoms are replaced with deuterium atoms. The structure models are made with this data and then their gyration radii and SANS intensities are calculated. Compared the calculated SANS data with the experimental one, the most probable structure is determined. With this analysis method, the aggregate structure of proteasome α7-subunit (PRSα) in an aqueous solution was investigated. Three structural models, a simple monomer and two types of dimers, were supposed as the aggregated structure of PRSα. The analysis showed that the best compromised structure was the dimer, which was consistent with electron microscopy observation.

Original language	English
Pages (from-to)	272-274
Number of pages	3
Journal	Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment
Volume	600
Issue number	1
DOIs	https://doi.org/10.1016/j.nima.2008.11.121
Publication status	Published - Feb 21 2009
Externally published	Yes

Keywords

Complex protein
Large structure analysis
Proteasome
SANS
Solution scattering

ASJC Scopus subject areas

Nuclear and High Energy Physics
Instrumentation

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Sugiyama, M., Hamada, K., Kato, K., Kurimoto, E., Okamoto, K., Morimoto, Y., Ikeda, S., Naito, S., Furusaka, M., Itoh, K., Mori, K., & Fukunaga, T. (2009). SANS simulation of aggregated protein in aqueous solution. Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 600(1), 272-274. https://doi.org/10.1016/j.nima.2008.11.121

SANS simulation of aggregated protein in aqueous solution. / Sugiyama, Masaaki; Hamada, Kei; Kato, Koichi; Kurimoto, Eiji; Okamoto, Kenta; Morimoto, Yukio; Ikeda, Susumu; Naito, Sachio; Furusaka, Michihiko; Itoh, Keiji; Mori, Kazuhiro; Fukunaga, Toshiharu.

In: Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 600, No. 1, 21.02.2009, p. 272-274.

Research output: Contribution to journal › Article › peer-review

Sugiyama, M, Hamada, K, Kato, K, Kurimoto, E, Okamoto, K, Morimoto, Y, Ikeda, S, Naito, S, Furusaka, M, Itoh, K, Mori, K & Fukunaga, T 2009, 'SANS simulation of aggregated protein in aqueous solution', Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, vol. 600, no. 1, pp. 272-274. https://doi.org/10.1016/j.nima.2008.11.121

Sugiyama, Masaaki ; Hamada, Kei ; Kato, Koichi ; Kurimoto, Eiji ; Okamoto, Kenta ; Morimoto, Yukio ; Ikeda, Susumu ; Naito, Sachio ; Furusaka, Michihiko ; Itoh, Keiji ; Mori, Kazuhiro ; Fukunaga, Toshiharu. / SANS simulation of aggregated protein in aqueous solution. In: Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 2009 ; Vol. 600, No. 1. pp. 272-274.

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abstract = "Small-angle neutron scattering (SANS) of aggregated protein in an aqueous solution is simulated based on the crystallographic data of the protein. After obtaining the crystallographic data of the target protein, hydrogen atoms are added to the data and then some hydrogen atoms are replaced with deuterium atoms. The structure models are made with this data and then their gyration radii and SANS intensities are calculated. Compared the calculated SANS data with the experimental one, the most probable structure is determined. With this analysis method, the aggregate structure of proteasome α7-subunit (PRSα) in an aqueous solution was investigated. Three structural models, a simple monomer and two types of dimers, were supposed as the aggregated structure of PRSα. The analysis showed that the best compromised structure was the dimer, which was consistent with electron microscopy observation.",

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AU - Kato, Koichi

AU - Kurimoto, Eiji

AU - Okamoto, Kenta

AU - Morimoto, Yukio

AU - Ikeda, Susumu

AU - Naito, Sachio

AU - Furusaka, Michihiko

AU - Itoh, Keiji

AU - Mori, Kazuhiro

AU - Fukunaga, Toshiharu

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AB - Small-angle neutron scattering (SANS) of aggregated protein in an aqueous solution is simulated based on the crystallographic data of the protein. After obtaining the crystallographic data of the target protein, hydrogen atoms are added to the data and then some hydrogen atoms are replaced with deuterium atoms. The structure models are made with this data and then their gyration radii and SANS intensities are calculated. Compared the calculated SANS data with the experimental one, the most probable structure is determined. With this analysis method, the aggregate structure of proteasome α7-subunit (PRSα) in an aqueous solution was investigated. Three structural models, a simple monomer and two types of dimers, were supposed as the aggregated structure of PRSα. The analysis showed that the best compromised structure was the dimer, which was consistent with electron microscopy observation.

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