Structural study for helical biomacromolecular complexes of β,3-D-glucans and polynucleotide by molecular dynamics simulation

Tadashi Okobira, Kazuya Uezu, Kazuo Sakurai, Seiji Shinkai

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

It is well known that natural β-1,3-D-glucans take a right-handed 61 triple helix in aqueous solution. Recently, the most stable static models of β-1,3-D-glucans and β-1,3-D-glucan/polynucleotides were calculated by using the molecular orbital method to compare their hydrogen bonds, helical pitch and other structural properties. In this paper, we report the molecular dynamics simulation to understand the behavior of β-1,3-D-glucans and β-1,3-D-glucan/polynucleotides in aqueous solution under ambient pressure and at ambient temperature. The helical pitches of β-1,3-D-glucans and β-1,3-D-glucan/polynucleotides were extended by thermal fluctuation, and the degree of extensibility was strongly affected by the number of side chains attached to the β-1,3-D-glucans. The hydrogen bonds via water molecules between the side chain and the main chain and/or the side chain dominated the extension behavior. The extension of the helical pitch of a β-1,3-D-glucan/polynucleotide complex was constrained by the hydrogen bond between the phosphate groups of the polynucleotide and the hydroxyl groups of the β-1,3-D-glucan.

Original languageEnglish
Pages (from-to)711-718
Number of pages8
JournalKobunshi Ronbunshu
Volume68
Issue number11
DOIs
Publication statusPublished - Jan 1 2011

Fingerprint

Polynucleotides
Molecular dynamics
hydrogen
Computer simulation
aqueous solution
Hydrogen bonds
phosphate group
simulation
Molecular orbitals
Structural properties
Phosphates
polyglucosan
temperature
Molecules
water
Hydroxyl Radical
Water

All Science Journal Classification (ASJC) codes

  • Chemical Engineering (miscellaneous)
  • Materials Science (miscellaneous)
  • Environmental Science(all)
  • Polymers and Plastics

Cite this

Structural study for helical biomacromolecular complexes of β,3-D-glucans and polynucleotide by molecular dynamics simulation. / Okobira, Tadashi; Uezu, Kazuya; Sakurai, Kazuo; Shinkai, Seiji.

In: Kobunshi Ronbunshu, Vol. 68, No. 11, 01.01.2011, p. 711-718.

Research output: Contribution to journalArticle

Okobira, Tadashi ; Uezu, Kazuya ; Sakurai, Kazuo ; Shinkai, Seiji. / Structural study for helical biomacromolecular complexes of β,3-D-glucans and polynucleotide by molecular dynamics simulation. In: Kobunshi Ronbunshu. 2011 ; Vol. 68, No. 11. pp. 711-718.
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