Evaluation of the protein interfaces that form an intermolecular four-helix bundle as studied by computer simulation

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

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Rational design of protein surface is important for creating higher order protein structures, but it is still challenging. In this study, we designed in silico the several binding interfaces on protein surfaces that allow a de novo protein-protein interaction to be formed. We used a computer simulation technique to find appropriate amino acid arrangements for the binding interface. The protein-protein interaction can be made by forming an intermolecular four-helix bundle structure, which is often found in naturally occurring protein subunit interfaces. As a model protein, we used a helical protein, YciF. Molecular dynamics simulation showed that a new protein-protein interaction is formed depending on the number of hydrophobic and charged amino acid residues present in the binding surfaces. However, too many hydrophobic amino acid residues present in the interface negatively affected on the binding. Finally, we found an appropriate arrangement of hydrophobic and charged amino acid residues that induces a protein-protein interaction through an intermolecular four-helix bundle formation.

Original languageEnglish
Pages (from-to)498-503
Number of pages6
JournalMolecular Simulation
Volume40
Issue number6
DOIs
Publication statusPublished - 2014 May 3
Externally publishedYes

Fingerprint

Helix
helices
bundles
Protein-protein Interaction
Bundle
Computer Simulation
computerized simulation
Amino Acids
proteins
Proteins
Protein
evaluation
Computer simulation
Evaluation
Arrangement
amino acids
Amino acids
Protein Structure
Molecular Dynamics Simulation
Membrane Proteins

Keywords

  • Four-helix bundle
  • MD simulation
  • Protein-protein interface

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Modelling and Simulation
  • Chemistry(all)
  • Chemical Engineering(all)
  • Materials Science(all)
  • Information Systems

Cite this

Fukuda, M., Komatsu, Y., Yamada, H., Morikawa, R., Miyakawa, T., Takasu, M., ... Yamagishi, A. (2014). Evaluation of the protein interfaces that form an intermolecular four-helix bundle as studied by computer simulation. Molecular Simulation, 40(6), 498-503. https://doi.org/10.1080/08927022.2013.824571

Evaluation of the protein interfaces that form an intermolecular four-helix bundle as studied by computer simulation. / Fukuda, Masaki; Komatsu, Yu; Yamada, Hironao; Morikawa, Ryota; Miyakawa, Takeshi; Takasu, Masako; Akanuma, Satoshi; Yamagishi, Akihiko.

In: Molecular Simulation, Vol. 40, No. 6, 03.05.2014, p. 498-503.

Research output: Contribution to journalArticle

Fukuda, Masaki ; Komatsu, Yu ; Yamada, Hironao ; Morikawa, Ryota ; Miyakawa, Takeshi ; Takasu, Masako ; Akanuma, Satoshi ; Yamagishi, Akihiko. / Evaluation of the protein interfaces that form an intermolecular four-helix bundle as studied by computer simulation. In: Molecular Simulation. 2014 ; Vol. 40, No. 6. pp. 498-503.
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