title: 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.
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.
authors: CREST Project, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
authors: Takeshi
authors: T
authors: Ishikawa
authors: Raghunadha Reddy
authors: RR
authors: Burri
authors: Yuji O
authors: YO
authors: Kamatari
authors: Shun
authors: S
authors: Sakuraba
authors: Nobuyuki
authors: N
authors: Matubayasi
authors: Akio
authors: A
authors: Kitao
authors: Kazuo
authors: K
authors: Kuwata
mesh_terms: D001665:Binding Sites; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry*; D011485:Protein Binding; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014312:Trisaccharides / Q000737:chemistry*
chemical_list: D012997:Solvents; D014312:Trisaccharides; C019117:N,N',N''-triacetylchitotriose; C421864:hen egg lysozyme; D009113:Muramidase