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Issue 10, 2013
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A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method

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Abstract

To examine the stabilities and binding characteristics, fragment molecular orbital (FMO) calculations were performed for the two binding modes of hen egg-white lysozyme with tri-N-acetyl-D-glucosamine (tri-NAG). Solvent effects were considered using an explicit solvent model. For comparison with the computational results, we experimentally determined the enthalpic contribution of the binding free-energy. Our calculations showed that the binding mode observed by X-ray analysis was more stable than the other binding mode by −6.2 kcal mol−1, where it was found that the interaction of protein with solvent molecules was crucial for this stability. The amplitude of this energy difference was of the same order as the experimental enthalpic contribution. Our detailed analysis using the energies divided into each residue was also consistent with a previous mutant study. In addition, the electron density analysis showed that the formal charge of the lysozyme (+8.0 e) was reduced to +5.16 e by charge transfer with solvent molecules.

Graphical abstract: A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method

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Publication details

The article was received on 08 Aug 2012, accepted on 17 Jan 2013 and first published on 21 Jan 2013


Article type: Paper
DOI: 10.1039/C3CP42761G
Citation: Phys. Chem. Chem. Phys., 2013,15, 3646-3654
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    A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method

    T. Ishikawa, R. R. Burri, Y. O. Kamatari, S. Sakuraba, N. Matubayasi, A. Kitao and K. Kuwata, Phys. Chem. Chem. Phys., 2013, 15, 3646
    DOI: 10.1039/C3CP42761G

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