TY - GEN
T1 - Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers
AU - Ozawa, Takashi
AU - Yamada, Hironao
AU - Miyakawa, Takeshi
AU - Morikawa, Ryota
AU - Yagi, Sota
AU - Akanuma, Satoshi
AU - Yamagishi, Akihiko
AU - Takasu, Masako
N1 - Funding Information:
This work was supported by JSPS KAKENHI Grant Number JP17K00418 and also by MEXT*-Supported Program for the Strategic Research Foundation at Private Universities, 2015-2018) (* Ministry of Education, Culture, Sports, Science and Technology).
Publisher Copyright:
© 2018 Association for Computing Machinery.
PY - 2018/1/18
Y1 - 2018/1/18
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.
KW - Fibrosis
KW - LARFH
KW - MD simulation
KW - Nanotechnology
KW - Sulerythrin
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U2 - 10.1145/3180382.3180390
DO - 10.1145/3180382.3180390
M3 - Conference contribution
AN - SCOPUS:85046808732
T3 - ACM International Conference Proceeding Series
SP - 43
EP - 47
BT - Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018
PB - Association for Computing Machinery
T2 - 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018
Y2 - 18 January 2018 through 20 January 2018
ER -