Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with molecules.
We present a computational study of a recently developed molecular fractionation with conjugated caps (MFCC) method for application to peptide/protein that has disulfide bonds. Specifically, we employ the MFCC approach to generate peptide fragments in which a disulfide bond is cut and a pair of conjugated caps are inserted. The method is tested on two peptides interacting with a water molecule. The first is a dipeptide consisting of two cysteines (Cys-Cys) connected by a disulfide bond and the second is a seven amino acid peptide consisting of Gly-Cys-Gly-Gly-Gly-Cys-Gly with a disulfide cross link. One-dimensional peptide-water potential curves are computed using the MFCC method at various ab initio levels for a number of interaction geometries. The calculated interaction energies are found to be in excellent agreement with the results obtained from the corresponding full system ab initio calculations for both peptide/water systems. The current study provides further numerical support for the accuracy of the MFCC method in full quantum mechanical calculation of protein/peptide that contains disulfide bonds.
Department of Chemistry, New York University, New York, New York 10003, USA.
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Chen
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Zhang
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Zhang
D001665:Binding Sites; D005591:Chemical Fractionation; D003198:Computer Simulation; D004220:Disulfides / Q000737:chemistry*; D004735:Energy Transfer; D019563:Mechanics; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D011789:Quantum Theory; D014867:Water / Q000737:chemistry*
D004220:Disulfides; D010455:Peptides; D014867:Water