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

研究成果: ジャーナルへの寄稿記事

2 引用 (Scopus)

抄録

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.

元の言語英語
ページ(範囲)711-718
ページ数8
ジャーナルKOBUNSHI RONBUNSHU
68
発行部数11
DOI
出版物ステータス出版済み - 1 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

これを引用

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.

:: KOBUNSHI RONBUNSHU, 巻 68, 番号 11, 01.01.2011, p. 711-718.

研究成果: ジャーナルへの寄稿記事

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. :: KOBUNSHI RONBUNSHU. 2011 ; 巻 68, 番号 11. pp. 711-718.
@article{5bf6ac2e9e0c4f14aaefbe7902025fa9,
title = "Structural study for helical biomacromolecular complexes of β,3-D-glucans and polynucleotide by molecular dynamics simulation",
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.",
author = "Tadashi Okobira and Kazuya Uezu and Kazuo Sakurai and Seiji Shinkai",
year = "2011",
month = "1",
day = "1",
doi = "10.1295/koron.68.711",
language = "English",
volume = "68",
pages = "711--718",
journal = "Kobunshi Ronbunshu",
issn = "0386-2186",
publisher = "The Society of Polymer Science, Japan",
number = "11",

}

TY - JOUR

T1 - Structural study for helical biomacromolecular complexes of β,3-D-glucans and polynucleotide by molecular dynamics simulation

AU - Okobira, Tadashi

AU - Uezu, Kazuya

AU - Sakurai, Kazuo

AU - Shinkai, Seiji

PY - 2011/1/1

Y1 - 2011/1/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84555177359&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84555177359&partnerID=8YFLogxK

U2 - 10.1295/koron.68.711

DO - 10.1295/koron.68.711

M3 - Article

AN - SCOPUS:84555177359

VL - 68

SP - 711

EP - 718

JO - Kobunshi Ronbunshu

JF - Kobunshi Ronbunshu

SN - 0386-2186

IS - 11

ER -