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Authors
Fujiwara, Shin-ichi Department of Biological Regulation, Faculty of Medicine, Tottori University Researchers DB KAKEN
Amisaki, Takashi Department of Biological Regulation, Faculty of Medicine, Tottori University Researchers DB KAKEN
Abstract
Human serum albumin (HSA) has seven common fatty acid (FA) binding sites. In this study, we used the molecular mechanics Poisson-Boltzmann surface area method to identify high affinity FA binding sites on HSA in terms of binding free energy. Using multiple HSA-FA (myristate, palmitate) complex models constructed by molecular dynamics simulations, two methods were performed in molecular mechanics Poisson-Boltzmann surface area, the “three-trajectory method” and the “single-trajectory method”. The former, which is less precise than the latter but may be more accurate as it includes the effects of conformational change upon binding, was used to classify high and low affinity sites. As a result, Sites 2, 4, and 5 were identified as high affinity sites for both FAs. The latter method, which is precise because energies are calculated from snapshots of the same trajectory for HSA-FAcomplex, was performed to compare the magnitude of binding free energy for these sites. The order of magnitude was 5 > 4 > 2, identical to that of a previous publication by others. In this way, a combination of the two methods was effectively used to identify high affinity sites. This study therefore provides an insight into the quantitative identification of high affinity FA binding sites on HSA.
Publisher
Elsevier Inc.
Content Type
Journal Article
Link
ISSN・ISBN
00063495
NCID
AA00566095
Journal Title
Biophysical journal
Volume
94
Issue
1
Start Page
95
End Page
103
Published Date
2008-01
Publisher-DOI
Text Version
Author
Rights
Copyright © 2008 The Biophysical Society. Published by Elsevier Inc. All rights reserved. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/
Citation
Shin-ichi Fujiwara, Takashi Amisaki.. Identification of High Affinity Fatty Acid Binding Sites on Human Serum Albumin by MM-PBSA Method. Biophysical journal. 2008, 94(1), 95-103
Department
Faculty of Medicine/Graduate School of Medical Sciences/University Hospital
Language
English