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
Literature Information
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.
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Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.










![trans-2-{[(Tert-butoxy)carbonyl]amino}cyclobutane-1-carboxylic acid structure trans-2-{[(Tert-butoxy)carbonyl]amino}cyclobutane-1-carboxylic acid structure](https://static.chemtradehub.com/structs/951/951173-25-4-27cd.webp)
![(3R,4aR,7aS,9aR,10S,11R,13aR,13bS,15aS,15bR)-3,11-Dihydroxy-10-(hydroxymethyl)-4,4,7a,10,13a,15b-hexamethyl-1,2,3,4,4a,7,7a,8,9,9a,10,11,12,13,13a,13b,14,15,15a,15b-icosahydro-5H-naphtho[2',1':4,5]cyc
lohepta[1,2-a]naphthalen-5-one structure (3R,4aR,7aS,9aR,10S,11R,13aR,13bS,15aS,15bR)-3,11-Dihydroxy-10-(hydroxymethyl)-4,4,7a,10,13a,15b-hexamethyl-1,2,3,4,4a,7,7a,8,9,9a,10,11,12,13,13a,13b,14,15,15a,15b-icosahydro-5H-naphtho[2',1':4,5]cyc
lohepta[1,2-a]naphthalen-5-one structure](https://static.chemtradehub.com/structs/538/53800-21-8-9f18.webp)


