The simulation study of protein-protein interfaces based on the 4-helix bundle structure

Masaki Fukuda, Yu Komatsu, Ryota Morikawa, Takeshi Miyakawa, Masako Takasu, Satoshi Akanuma, Akihiko Yamagishi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

Docking of two protein molecules is induced by intermolecular interactions. Our purposes in this study are: designing binding interfaces on the two proteins, which specifically interact to each other; and inducing intermolecular interactions between the two proteins by mixing them. A 4-helix bundle structure was chosen as a scaffold on which binding interfaces were created. Based on this scaffold, we designed binding interfaces involving charged and nonpolar amino acid residues. We performed molecular dynamics (MD) simulation to identify suitable amino acid residues for the interfaces. We chose YciF protein as the scaffold for the protein-protein docking simulation. We observed the structure of two YciF protein molecules (I and II), and we calculated the distance between centroids (center of gravity) of the interfaces' surface planes of the molecules I and II. We found that the docking of the two protein molecules can be controlled by the number of hydrophobic and charged amino acid residues involved in the interfaces. Existence of six hydrophobic and five charged amino acid residues within an interface were most suitable for the protein-protein docking.

Original languageEnglish
Title of host publicationAIP Conference Proceedings
Pages606-609
Number of pages4
Volume1518
DOIs
Publication statusPublished - 2013
Externally publishedYes
Event4th International Symposium on Slow Dynamics in Complex Systems: Keep Going Tohoku - Sendai, Japan
Duration: 2012 Dec 22012 Dec 7

Other

Other4th International Symposium on Slow Dynamics in Complex Systems: Keep Going Tohoku
CountryJapan
CitySendai
Period12/12/212/12/7

Fingerprint

helices
bundles
proteins
simulation
amino acids
molecules
center of gravity
centroids
interactions
molecular dynamics

Keywords

  • 4-helix bundle
  • intermolecular interaction
  • MD simulation
  • protein-protein docking

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Cite this

Fukuda, M., Komatsu, Y., Morikawa, R., Miyakawa, T., Takasu, M., Akanuma, S., & Yamagishi, A. (2013). The simulation study of protein-protein interfaces based on the 4-helix bundle structure. In AIP Conference Proceedings (Vol. 1518, pp. 606-609) https://doi.org/10.1063/1.4794642

The simulation study of protein-protein interfaces based on the 4-helix bundle structure. / Fukuda, Masaki; Komatsu, Yu; Morikawa, Ryota; Miyakawa, Takeshi; Takasu, Masako; Akanuma, Satoshi; Yamagishi, Akihiko.

AIP Conference Proceedings. Vol. 1518 2013. p. 606-609.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Fukuda, M, Komatsu, Y, Morikawa, R, Miyakawa, T, Takasu, M, Akanuma, S & Yamagishi, A 2013, The simulation study of protein-protein interfaces based on the 4-helix bundle structure. in AIP Conference Proceedings. vol. 1518, pp. 606-609, 4th International Symposium on Slow Dynamics in Complex Systems: Keep Going Tohoku, Sendai, Japan, 12/12/2. https://doi.org/10.1063/1.4794642
Fukuda M, Komatsu Y, Morikawa R, Miyakawa T, Takasu M, Akanuma S et al. The simulation study of protein-protein interfaces based on the 4-helix bundle structure. In AIP Conference Proceedings. Vol. 1518. 2013. p. 606-609 https://doi.org/10.1063/1.4794642
Fukuda, Masaki ; Komatsu, Yu ; Morikawa, Ryota ; Miyakawa, Takeshi ; Takasu, Masako ; Akanuma, Satoshi ; Yamagishi, Akihiko. / The simulation study of protein-protein interfaces based on the 4-helix bundle structure. AIP Conference Proceedings. Vol. 1518 2013. pp. 606-609
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