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

Publication Date 2013-01-21
DOI 10.1039/C3CP42761G
Impact Factor 3.676
Authors


View Original

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.

Related Literature

Modeling the sensing characteristics of chemi-resistive thin film semi-conducting gas sensors

Abhishek Ghosh, S. B. Majumder

2017-08-14 Paper

DOI: 10.1039/C7CP04241H

Role of carboxylic acid groups in the reduction of nitric oxide by carbon at low temperature, as exemplified by graphene oxide

Q. Gao, X. M. Li, J. Z. Zhou, X. X. Ruan, Q. Liu, G. R. Qian

2017-08-02 Paper

DOI: 10.1039/C7CP01541K

X-ray spectroscopy on the active ion in laser crystals

P. S. Miedema, R. Mitzner, S. Ganschow, M. Beye

2017-07-26 Paper

DOI: 10.1039/C7CP03026F

Spectroscopic characterization of the on-surface induced (cyclo)dehydrogenation of a N-heteroaromatic compound on noble metal surfaces

I. Palacio, A. L. Pinardi, J. I. Martínez, A. Preobrajenski, A. Cossaro, A. Jancarik, I. Stará, I. Starý, J. Méndez, J. A. Martín-Gago, M. F. López

2017-07-31 Paper

DOI: 10.1039/C7CP03955G

Ab initio study of Li, Mg and Al insertion into rutile VO2: fast diffusion and enhanced voltages for multivalent batteries

Vadym V. Kulish, Daniel Koch, Sergei Manzhos

2017-07-31 Paper

DOI: 10.1039/C7CP04360K

Efficient 3He/4He separation in a nanoporous graphenylene membrane

Yuanyuan Qu, Mingwen Zhao

2017-07-18 Paper

DOI: 10.1039/C7CP03422A

Front cover

Cover

DOI: 10.1039/C7CP90185B

Sum frequency generation vibrational spectroscopy of methacrylate-based functional monomers at the hydrophilic solid–liquid interface

Narendra M. Adhikari, Uvinduni I. Premadasa, Katherine L. A. Cimatu

2017-07-26 Paper

DOI: 10.1039/C7CP03113K

You might also like

Compound Q&A

Is 6-(3-Fluorophenyl)picolinic acid (CAS: 887982-40-3) safe?

6-(3-Fluorophenyl)picolinic acid is generally considered safe for laboratory use...

887982-40-36-(3-Fluorophenyl)pi...
Compound Q&A

What industries use (3R)-3-Pyrrolidinol (CAS: 2799-21-5)?

(3R)-3-Pyrrolidinol is used in the pharmaceutical industry as a precursor for dr...

2799-21-5(3R)-3-Pyrrolidinol
Compound Q&A

What precautions should be taken when handling (4R,5R)-4,5-Diethoxycarbonyl-2,2-dimethyldioxolane (CAS: 59779-75-8)?

When handling (4R,5R)-4,5-Diethoxycarbonyl-2,2-dimethyldioxolane (CAS: 59779-75-...

59779-75-8(4R,5R)-4,5-Diethoxy...
Compound Q&A

How is 1-(6-Chloroimidazo[1,2-b]pyridazin-3-yl)ethanone (CAS: 90734-71-7) typically synthesized?

1-(6-Chloroimidazo[1,2-b]pyridazin-3-yl)ethanone is often synthesized via a mult...

90734-71-71-(6-Chloroimidazo[1...
Compound Q&A

What is the market or research trend for N-Ethyl-3,4-dimethylbenzylamine (CAS: 39180-83-1)?

The market for N-Ethyl-3,4-dimethylbenzylamine (CAS: 39180-83-1) remains steady,...

39180-83-1N-Ethyl-3,4-dimethyl...
Compound Q&A

What is Tert-butyl 3-(pyrrolidin-1-yl)azetidine-1-carboxylate (CAS: 1019008-21-9)?

Tert-butyl 3-(pyrrolidin-1-yl)azetidine-1-carboxylate is a chemical compound wit...

1019008-21-9Tert-butyl 3-(pyrrol...
Compound Q&A

What regulatory guidelines apply to 1-Bromo-3-chloro-2,4-dimethoxybenzene (CAS: 1228956-93-1)?

1-Bromo-3-chloro-2,4-dimethoxybenzene (CAS: 1228956-93-1) falls under the classi...

1228956-93-11-Bromo-3-chloro-2,4...
Compound Q&A

Is 8-Bromo-2-methyl-3,4-dihydroisoquinolin-1(2H)-one (CAS: 1368622-07-4) safe?

The safety of 8-Bromo-2-methyl-3,4-dihydroisoquinolin-1(2H)-one (CAS: 1368622-07...

1368622-07-48-Bromo-2-methyl-3,4...
Compound Q&A

Is Benzyl [(3S)-2,6-dioxo-3-piperidinyl]carbamate (CAS: 22785-43-9) safe?

Benzyl [(3S)-2,6-dioxo-3-piperidinyl]carbamate is generally safe when handled wi...

22785-43-9Benzyl [(3S)-2,6-dio...
Compound Q&A

How should 1-{[4-(4,4,5,5-Tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]sulfonyl}pyrrolidine (CAS: 928657-21-0) be stored?

1-{[4-(4,4,5,5-Tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]sulfonyl}pyrrolidine s...

928657-21-01-{[4-(4,4,5,5-Tetra...

Source Journal

Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
Articles per Year: 3036

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.

Recommended Suppliers

Disclaimer
This page provides academic journal information for reference and research purposes only. We are not affiliated with any journal publishers and do not handle publication submissions. For publication-related inquiries, please contact the respective journal publishers directly.
If you notice any inaccuracies in the information displayed, please contact us at support@chemtradehub.com. We will promptly review and address your concerns.