Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers

Takashi Ozawa; Hironao Yamada; Takeshi Miyakawa; Ryota Morikawa; Sota Yagi; Satoshi Akanuma; Akihiko Yamagishi; Masako Takasu

doi:10.1145/3180382.3180390

Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers

Takashi Ozawa, Hironao Yamada, Takeshi Miyakawa, Ryota Morikawa, Sota Yagi, Satoshi Akanuma, Akihiko Yamagishi, Masako Takasu

School of Human Sciences

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

Artificial creation of fibers utilizing proteins has been a target of bionanotechnology. Yagi et al. succeeded in designing artificial protein fibers using two types of proteins: LARFH and sulerythrin. Binding interfaces were designed for sulerythrin and LARFH by introducing mutations, and the fibrous structures were confirmed by atomic force microscopy. However, branching was observed in the fibrous structure, possibly because of non-specific interactions between the proteins. In this study, we analyzed the behavior and binding sites of sulerythrin mutants and LARFH mutants using coarse-grained molecular dynamics (MD) simulation. Binding simulations were performed for a system of one sulerythrin and one LARFH, and also of two sulerythrin molecules and four LARFH molecules. These results suggested that glutamic acids originally possessed by sulerythrin contribute to non-specific binding at sites other than the designed interfaces.

Original language	English
Title of host publication	Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018
Publisher	Association for Computing Machinery
Pages	43-47
Number of pages	5
ISBN (Electronic)	9781450353410
DOIs	https://doi.org/10.1145/3180382.3180390
Publication status	Published - 2018 Jan 18
Event	8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018 - Tokyo, Japan Duration: 2018 Jan 18 → 2018 Jan 20

Publication series

Name	ACM International Conference Proceeding Series

Other

Other	8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018
Country/Territory	Japan
City	Tokyo
Period	18/1/18 → 18/1/20

Keywords

Fibrosis
LARFH
MD simulation
Nanotechnology
Sulerythrin

ASJC Scopus subject areas

Software
Human-Computer Interaction
Computer Vision and Pattern Recognition
Computer Networks and Communications

Access to Document

10.1145/3180382.3180390

Cite this

Ozawa, T., Yamada, H., Miyakawa, T., Morikawa, R., Yagi, S., Akanuma, S., Yamagishi, A., & Takasu, M. (2018). Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers. In Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018 (pp. 43-47). (ACM International Conference Proceeding Series). Association for Computing Machinery. https://doi.org/10.1145/3180382.3180390

Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers. / Ozawa, Takashi; Yamada, Hironao; Miyakawa, Takeshi et al.
Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. Association for Computing Machinery, 2018. p. 43-47 (ACM International Conference Proceeding Series).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Ozawa, T, Yamada, H, Miyakawa, T, Morikawa, R, Yagi, S , Akanuma, S, Yamagishi, A & Takasu, M 2018, Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers. in Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. ACM International Conference Proceeding Series, Association for Computing Machinery, pp. 43-47, 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018, Tokyo, Japan, 18/1/18. https://doi.org/10.1145/3180382.3180390

Ozawa T, Yamada H, Miyakawa T, Morikawa R, Yagi S , Akanuma S et al. Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers. In Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. Association for Computing Machinery. 2018. p. 43-47. (ACM International Conference Proceeding Series). doi: 10.1145/3180382.3180390

Ozawa, Takashi ; Yamada, Hironao ; Miyakawa, Takeshi et al. / Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers. Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. Association for Computing Machinery, 2018. pp. 43-47 (ACM International Conference Proceeding Series).

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abstract = "Artificial creation of fibers utilizing proteins has been a target of bionanotechnology. Yagi et al. succeeded in designing artificial protein fibers using two types of proteins: LARFH and sulerythrin. Binding interfaces were designed for sulerythrin and LARFH by introducing mutations, and the fibrous structures were confirmed by atomic force microscopy. However, branching was observed in the fibrous structure, possibly because of non-specific interactions between the proteins. In this study, we analyzed the behavior and binding sites of sulerythrin mutants and LARFH mutants using coarse-grained molecular dynamics (MD) simulation. Binding simulations were performed for a system of one sulerythrin and one LARFH, and also of two sulerythrin molecules and four LARFH molecules. These results suggested that glutamic acids originally possessed by sulerythrin contribute to non-specific binding at sites other than the designed interfaces.",

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AU - Ozawa, Takashi

AU - Yamada, Hironao

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AU - Morikawa, Ryota

AU - Yagi, Sota

AU - Akanuma, Satoshi

AU - Yamagishi, Akihiko

AU - Takasu, Masako

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N2 - Artificial creation of fibers utilizing proteins has been a target of bionanotechnology. Yagi et al. succeeded in designing artificial protein fibers using two types of proteins: LARFH and sulerythrin. Binding interfaces were designed for sulerythrin and LARFH by introducing mutations, and the fibrous structures were confirmed by atomic force microscopy. However, branching was observed in the fibrous structure, possibly because of non-specific interactions between the proteins. In this study, we analyzed the behavior and binding sites of sulerythrin mutants and LARFH mutants using coarse-grained molecular dynamics (MD) simulation. Binding simulations were performed for a system of one sulerythrin and one LARFH, and also of two sulerythrin molecules and four LARFH molecules. These results suggested that glutamic acids originally possessed by sulerythrin contribute to non-specific binding at sites other than the designed interfaces.

AB - Artificial creation of fibers utilizing proteins has been a target of bionanotechnology. Yagi et al. succeeded in designing artificial protein fibers using two types of proteins: LARFH and sulerythrin. Binding interfaces were designed for sulerythrin and LARFH by introducing mutations, and the fibrous structures were confirmed by atomic force microscopy. However, branching was observed in the fibrous structure, possibly because of non-specific interactions between the proteins. In this study, we analyzed the behavior and binding sites of sulerythrin mutants and LARFH mutants using coarse-grained molecular dynamics (MD) simulation. Binding simulations were performed for a system of one sulerythrin and one LARFH, and also of two sulerythrin molecules and four LARFH molecules. These results suggested that glutamic acids originally possessed by sulerythrin contribute to non-specific binding at sites other than the designed interfaces.

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KW - MD simulation

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Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers

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Keywords

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