Adsorption of xenon on a protein arising from the translational motion of solvent molecules

Ryo Akiyama, Yasuhito Karino, Hokuto Obama, Ayako Yoshifuku

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

A simple method was used to predict binding sites and to calculate the binding free energy for a xenon atom on a protein to determine the importance of the translational motion of water molecules in molecular recognition. We examined xenon bound on myoglobin and on a fragment of ammonium transporter. Despite the simplicity of our method, the predicted binding sites and the experimental results agree very well, and the estimated values of the free energy gain are also reasonable. We discuss the van der Waals picture of molecular recognition between a protein and a small hydrophobic molecule, such as an anesthetic molecule, which gives us a simple physical justification for the idea of a "lock and key" relationship used in conventional structure-based drug design programs.

Original languageEnglish
Pages (from-to)3096-3101
Number of pages6
JournalPhysical Chemistry Chemical Physics
Volume12
Issue number13
DOIs
Publication statusPublished - 2010

Fingerprint

Xenon
translational motion
xenon
Molecular recognition
proteins
Adsorption
Free energy
Molecules
adsorption
free energy
Binding Sites
anesthetics
molecules
transporter
myoglobin
Proteins
Myoglobin
Ammonium Compounds
Anesthetics
drugs

All Science Journal Classification (ASJC) codes

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

Cite this

Adsorption of xenon on a protein arising from the translational motion of solvent molecules. / Akiyama, Ryo; Karino, Yasuhito; Obama, Hokuto; Yoshifuku, Ayako.

In: Physical Chemistry Chemical Physics, Vol. 12, No. 13, 2010, p. 3096-3101.

Research output: Contribution to journalArticle

Akiyama, Ryo ; Karino, Yasuhito ; Obama, Hokuto ; Yoshifuku, Ayako. / Adsorption of xenon on a protein arising from the translational motion of solvent molecules. In: Physical Chemistry Chemical Physics. 2010 ; Vol. 12, No. 13. pp. 3096-3101.
@article{5d6d52388c7c419593a937405e6d1387,
title = "Adsorption of xenon on a protein arising from the translational motion of solvent molecules",
abstract = "A simple method was used to predict binding sites and to calculate the binding free energy for a xenon atom on a protein to determine the importance of the translational motion of water molecules in molecular recognition. We examined xenon bound on myoglobin and on a fragment of ammonium transporter. Despite the simplicity of our method, the predicted binding sites and the experimental results agree very well, and the estimated values of the free energy gain are also reasonable. We discuss the van der Waals picture of molecular recognition between a protein and a small hydrophobic molecule, such as an anesthetic molecule, which gives us a simple physical justification for the idea of a {"}lock and key{"} relationship used in conventional structure-based drug design programs.",
author = "Ryo Akiyama and Yasuhito Karino and Hokuto Obama and Ayako Yoshifuku",
year = "2010",
doi = "10.1039/b921314g",
language = "English",
volume = "12",
pages = "3096--3101",
journal = "Physical Chemistry Chemical Physics",
issn = "1463-9076",
publisher = "Royal Society of Chemistry",
number = "13",

}

TY - JOUR

T1 - Adsorption of xenon on a protein arising from the translational motion of solvent molecules

AU - Akiyama, Ryo

AU - Karino, Yasuhito

AU - Obama, Hokuto

AU - Yoshifuku, Ayako

PY - 2010

Y1 - 2010

N2 - A simple method was used to predict binding sites and to calculate the binding free energy for a xenon atom on a protein to determine the importance of the translational motion of water molecules in molecular recognition. We examined xenon bound on myoglobin and on a fragment of ammonium transporter. Despite the simplicity of our method, the predicted binding sites and the experimental results agree very well, and the estimated values of the free energy gain are also reasonable. We discuss the van der Waals picture of molecular recognition between a protein and a small hydrophobic molecule, such as an anesthetic molecule, which gives us a simple physical justification for the idea of a "lock and key" relationship used in conventional structure-based drug design programs.

AB - A simple method was used to predict binding sites and to calculate the binding free energy for a xenon atom on a protein to determine the importance of the translational motion of water molecules in molecular recognition. We examined xenon bound on myoglobin and on a fragment of ammonium transporter. Despite the simplicity of our method, the predicted binding sites and the experimental results agree very well, and the estimated values of the free energy gain are also reasonable. We discuss the van der Waals picture of molecular recognition between a protein and a small hydrophobic molecule, such as an anesthetic molecule, which gives us a simple physical justification for the idea of a "lock and key" relationship used in conventional structure-based drug design programs.

UR - http://www.scopus.com/inward/record.url?scp=77949493289&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77949493289&partnerID=8YFLogxK

U2 - 10.1039/b921314g

DO - 10.1039/b921314g

M3 - Article

C2 - 20237695

AN - SCOPUS:77949493289

VL - 12

SP - 3096

EP - 3101

JO - Physical Chemistry Chemical Physics

JF - Physical Chemistry Chemical Physics

SN - 1463-9076

IS - 13

ER -