Constructing protein nano-fiber and estimation of the electronic state around metal ions

Yu Komatsu*, Masaki Fukuda, Hironao Yamada, Shuhei Kawamoto, Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Satoshi Yokojima, Satoshi Akanuma, Akihiko Yamagishi

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


We aim to construct a nano-fiber using proteins by mixing two kinds of proteins. The binding sites are expected to be formed between two α-helices of one protein and two α-helices of another protein. As model proteins, we use Lac repressor four helix protein (LARFH), sulerythrin, and 3-isopropylmalate dehydrogenase. With these proteins, we performed molecular dynamics (MD) simulations with a coarse-grained (CG) model. In MD simulations with the CG model for LARFH, we found that the molecules approached faster in the system where the mutant protein with positively charged amino acids was placed with the mutant protein with negatively charged amino acids than in the system containing two wild-type protein molecules. In the system with the variants, the number of contact interfaces with the positive variant-negative variant combination after 150 ns simulation is larger than that with the positive-positive variants combination or the negative-negative variants combination. Sulerythrin has two pairs of Fe2+ and Zn2+. Electronic structure calculation was performed around metal ions in sulerythrin. By electronic structure calculation for sulerythrin around metal ions, the electric charge and spin density were estimated.

Original languageEnglish
Pages (from-to)3750-3755
Number of pages6
JournalInternational Journal of Quantum Chemistry
Issue number24
Publication statusPublished - 2012 Dec 15
Externally publishedYes


  • coarse-grained model
  • density functional theory
  • four-helix bundle
  • nano-fiber
  • self-assembly

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry


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