Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)

Yuji Mochizuki, Katsumi Yamashita, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Naoki Taguchi, Yoshio Okiyama, Misako Tsuboi, Tatsuya Nakano, Shigenori Tanaka

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30 Citations (Scopus)

Abstract

Two proteins on the influenza virus surface have been well known. One is hemagglutinin (HA) associated with the infection to cells. The fragment molecular orbital (FMO) calculations were performed on a complex consisting of HA trimer and two Fab-fragments at the third-order Møller-Plesset perturbation (MP3) level. The numbers of residues and 6-31G basis functions were 2351 and 201276, and thus a massively parallel-vector computer was utilized to accelerate the processing. This FMO-MP3 job was completed in 5.8 h with 1024 processors. Another protein is neuraminidase (NA) involved in the escape from infected cells. The FMO-MP3 calculation was also applied to analyze the interactions between oseltamivir and surrounding residues in pharmacophore.

Original languageEnglish
Pages (from-to)346-352
Number of pages7
JournalChemical Physics Letters
Volume493
Issue number4-6
DOIs
Publication statusPublished - 2010 Jun 25
Externally publishedYes

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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    Mochizuki, Y., Yamashita, K., Fukuzawa, K., Takematsu, K., Watanabe, H., Taguchi, N., Okiyama, Y., Tsuboi, M., Nakano, T., & Tanaka, S. (2010). Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA). Chemical Physics Letters, 493(4-6), 346-352. https://doi.org/10.1016/j.cplett.2010.05.034