CALCULATION OF RELATIVE BINDING OF FREE-ENERGY OF VANCOMYCIN WITH DIACETYL-L-LYSYL-D-ALANYL-D-ALANINE AND DIACETYL-L-LYSYL-L-ALANYL-L-ALANINE

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Please use this identifier to cite or link to this item: http://ir.lib.ncu.edu.tw/handle/987654321/26630

Title:	CALCULATION OF RELATIVE BINDING OF FREE-ENERGY OF VANCOMYCIN WITH DIACETYL-L-LYSYL-D-ALANYL-D-ALANINE AND DIACETYL-L-LYSYL-L-ALANYL-L-ALANINE
Authors:	CHEN,WY;WANG,LK;WU,CF;TSENG,CY
Contributors:	化學工程與材料工程學系
Keywords:	ANTIBIOTIC VANCOMYCIN;RISTOCETIN-A;COMPLEX;PROTEIN;PEPTIDES;NOE
Date:	1995
Issue Date:	2010-06-29 17:32:47 (UTC+8)
Publisher:	中央大學
Abstract:	By means of a free energy perturbation method implemented with molecular dynamics, the relative binding of free energies of vancomycin with Ac-2-L-Lys-D-Ala-D-Ala and with Ac-2-L-Lys-L-Ala-L-Ala peptide ligands were calculated. A transition state between the vancomycin complex with the D-form peptide and the complex with the L-form peptide was employed as the perturbation final stage in order to overcome the difficulties of calculating the perturbation between isomers. The calculated relative binding of free energy was 5.15 kcal/mol in water, which compared well with an experimental value of 8.4 kcal/mol. Structure analysis were performed on the number of possible hydrogen bondings, the hydrophobic interactions between peptide ligands and vancomycin, and the bonding angle between designated nuclei. The calculated structure results were all well supported by the NMR data. An investigation of the relative free energy calculation suggests that relative binding affinity in a host-guest system can be achieved by molecular dynamic simulation and the finite difference thermodynamic integration method.
Relation:	JOURNAL OF FERMENTATION AND BIOENGINEERING
Appears in Collections:	[National Central University Department of Chemical & Materials Engineering] journal & Dissertation

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