Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations

BMC Bioinformatics

Research Article

Andrés Fernando González Barrios¹  Camilo Andrés Mora Osorio¹ 

[1] Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Carrera 1E No. 19A-40, Edificio Mario Laserna, Bogotá, DC, Colombia;

关键词: Molecular dynamics;    Free energy calculations;    Group contribution method;    Residues chain;   

DOI  :  10.1186/s12859-016-1399-5

 received in 2016-04-15, accepted in 2016-12-01,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundCalculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium.Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces. Multiple MD of the twenty classic amino acids located at the interface of rectangular simulation boxes with a dodecane-water medium were performed.ResultsA GCM to calculate the free energy of entire peptides is then proposed. The method uses the summation of the Gibbs free energy of each amino acid adjusted in function of its presence or absence in the chain as well as its hydrophobic characteristics.ConclusionValidation of the equation was performed with twenty-one peptides all simulated using MD in dodecane-water rectangular boxes in previous work, obtaining an average relative error of 16%.

【 授权许可】

CC BY   
© The Author(s). 2016

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