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

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

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
Volume112
Issue number24
DOIs
Publication statusPublished - 2012 Dec 15
Externally publishedYes

Fingerprint

Electronic states
Metal ions
metal ions
proteins
fibers
Fibers
electronics
Proteins
helices
Lac Repressors
Mutant Proteins
Electronic structure
Molecular dynamics
3-Isopropylmalate Dehydrogenase
amino acids
Amino Acids
Electric charge
Molecules
molecular dynamics
electronic structure

Keywords

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

ASJC Scopus subject areas

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

Cite this

Komatsu, Y., Fukuda, M., Yamada, H., Kawamoto, S., Miyakawa, T., Morikawa, R., ... Yamagishi, A. (2012). Constructing protein nano-fiber and estimation of the electronic state around metal ions. International Journal of Quantum Chemistry, 112(24), 3750-3755. https://doi.org/10.1002/qua.24206

Constructing protein nano-fiber and estimation of the electronic state around metal ions. / Komatsu, Yu; Fukuda, Masaki; Yamada, Hironao; Kawamoto, Shuhei; Miyakawa, Takeshi; Morikawa, Ryota; Takasu, Masako; Yokojima, Satoshi; Akanuma, Satoshi; Yamagishi, Akihiko.

In: International Journal of Quantum Chemistry, Vol. 112, No. 24, 15.12.2012, p. 3750-3755.

Research output: Contribution to journalArticle

Komatsu, Y, Fukuda, M, Yamada, H, Kawamoto, S, Miyakawa, T, Morikawa, R, Takasu, M, Yokojima, S, Akanuma, S & Yamagishi, A 2012, 'Constructing protein nano-fiber and estimation of the electronic state around metal ions', International Journal of Quantum Chemistry, vol. 112, no. 24, pp. 3750-3755. https://doi.org/10.1002/qua.24206
Komatsu, Yu ; Fukuda, Masaki ; Yamada, Hironao ; Kawamoto, Shuhei ; Miyakawa, Takeshi ; Morikawa, Ryota ; Takasu, Masako ; Yokojima, Satoshi ; Akanuma, Satoshi ; Yamagishi, Akihiko. / Constructing protein nano-fiber and estimation of the electronic state around metal ions. In: International Journal of Quantum Chemistry. 2012 ; Vol. 112, No. 24. pp. 3750-3755.
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