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

Research output: Chapter in Book/Report/Conference proceedingConference 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 languageEnglish
Title of host publicationProceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018
PublisherAssociation for Computing Machinery
Pages43-47
Number of pages5
ISBN (Electronic)9781450353410
DOIs
Publication statusPublished - 2018 Jan 18
Event8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018 - Tokyo, Japan
Duration: 2018 Jan 182018 Jan 20

Publication series

NameACM International Conference Proceeding Series

Other

Other8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018
CountryJapan
CityTokyo
Period18/1/1818/1/20

Keywords

  • Fibrosis
  • LARFH
  • MD simulation
  • Nanotechnology
  • Sulerythrin

ASJC Scopus subject areas

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

Fingerprint Dive into the research topics of 'Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers'. Together they form a unique fingerprint.

Cite this