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Molecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods.

The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method combined with alanine-scanning mutagenesis is a very important tool for rational drug design. In this study, molecular dynamics (MD) and MM-PBSA were applied to calculate the binding free energy between the rat intestinal fatty... Full description

Journal Title: The journal of physical chemistry. B August 2, 2007, Vol.111(30), pp.9104-9113
Main Author: Zou, Hanjun
Other Authors: Luo, Cheng , Zheng, Suxin , Luo, Xiaomin , Zhu, Weiliang , Chen, Kaixian , Shen, Jianhua , Jiang, Hualiang
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: ISSN: 1520-6106
Link: http://search.proquest.com/docview/70710467/?pq-origsite=primo
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title: Molecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods.
format: Article
creator:
  • Zou, Hanjun
  • Luo, Cheng
  • Zheng, Suxin
  • Luo, Xiaomin
  • Zhu, Weiliang
  • Chen, Kaixian
  • Shen, Jianhua
  • Jiang, Hualiang
subjects:
  • Alanine–Chemistry
  • Animals–Genetics
  • Computational Biology–Methods
  • Computer Simulation–Chemistry
  • Fatty Acid-Binding Proteins–Genetics
  • Models, Molecular–Chemistry
  • Mutation–Chemistry
  • Palmitic Acid–Chemistry
  • Protein Binding–Chemistry
  • Rats–Chemistry
  • Thermodynamics–Chemistry
  • Fatty Acid-Binding Proteins
  • Palmitic Acid
  • Alanine
ispartof: The journal of physical chemistry. B, August 2, 2007, Vol.111(30), pp.9104-9113
description: The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method combined with alanine-scanning mutagenesis is a very important tool for rational drug design. In this study, molecular dynamics (MD) and MM-PBSA were applied to calculate the binding free energy between the rat intestinal fatty acid binding protein (IFABP) and palmitic acid (PA) to gain insight to the interaction details. Equally spaced snapshots along the trajectory were chosen to perform the binding free energy calculation, which yields a result highly consistent with experimental value with a deviation of 0.4 kcal/mol. Computational alanine scanning was performed on the same set of snapshots by mutating the residues in IFABP to alanine and recomputing the DeltaDeltaG(binding). By postprocessing a single trajectory of the wild-type complex, the average unsigned error of our calculated DeltaDeltaG(binding) is below 1.5 kcal/mol for most of the alanine mutations of the noncharged residues (67% in total). To further...
language: eng
source:
identifier: ISSN: 1520-6106
fulltext: fulltext
issn:
  • 15206106
  • 1520-6106
url: Link


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titleMolecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods.
creatorZou, Hanjun ; Luo, Cheng ; Zheng, Suxin ; Luo, Xiaomin ; Zhu, Weiliang ; Chen, Kaixian ; Shen, Jianhua ; Jiang, Hualiang
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identifierISSN: 1520-6106
subjectAlanine–Chemistry ; Animals–Genetics ; Computational Biology–Methods ; Computer Simulation–Chemistry ; Fatty Acid-Binding Proteins–Genetics ; Models, Molecular–Chemistry ; Mutation–Chemistry ; Palmitic Acid–Chemistry ; Protein Binding–Chemistry ; Rats–Chemistry ; Thermodynamics–Chemistry ; Fatty Acid-Binding Proteins ; Palmitic Acid ; Alanine
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descriptionThe molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method combined with alanine-scanning mutagenesis is a very important tool for rational drug design. In this study, molecular dynamics (MD) and MM-PBSA were applied to calculate the binding free energy between the rat intestinal fatty acid binding protein (IFABP) and palmitic acid (PA) to gain insight to the interaction details. Equally spaced snapshots along the trajectory were chosen to perform the binding free energy calculation, which yields a result highly consistent with experimental value with a deviation of 0.4 kcal/mol. Computational alanine scanning was performed on the same set of snapshots by mutating the residues in IFABP to alanine and recomputing the DeltaDeltaG(binding). By postprocessing a single trajectory of the wild-type complex, the average unsigned error of our calculated DeltaDeltaG(binding) is below 1.5 kcal/mol for most of the alanine mutations of the noncharged residues (67% in total). To further...
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titleMolecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods.
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