Improved Sugar Puckering Profiles for Nicotinamide Ribonucleoside for Hybrid QM/MM Simulations
| Autor: | Amnon Kohen, Dan Thomas Major, Yaron Pshetitsky, Gilit Verner, Reuven Eitan |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
Stereochemistry
Carbohydrates Nicotinamide adenine dinucleotide Molecular Dynamics Simulation 010402 general chemistry 01 natural sciences Redox Cofactor QM/MM chemistry.chemical_compound Computational chemistry 0103 physical sciences Ribose Physical and Theoretical Chemistry 010304 chemical physics Nicotinamide biology Water Ribonucleoside NAD 0104 chemical sciences Computer Science Applications chemistry biology.protein Quantum Theory NAD+ kinase Gases |
| Zdroj: | Journal of chemical theory and computation. 12(10) |
| ISSN: | 1549-9626 |
| Popis: | The coenzyme nicotinamide adenine dinucleotide (NAD+) and its reduced form (NADH) play ubiquitous roles as oxidizing and reducing agents in nature. The binding, and possibly the chemical redox step, of NAD+/NADH may be influenced by the cofactor conformational distribution and, in particular, by the ribose puckering of its nicotinamide–ribonucleoside (NR) moiety. In many hybrid quantum mechanics–molecular mechanics (QM/MM) studies of NAD+/NADH dependent enzymes, the QM region is treated by semiempirical (SE) methods. Recent work suggests that SE methods do not adequately describe the ring puckering in sugar molecules. In the present work we adopt an efficient and practical strategy to correct for this deficiency for NAD+/NADH. We have implemented a cost-effective correction to a SE Hamiltonian by adding a correction potential, which is defined as the difference between an accurate benchmark density functional theory (DFT) potential energy surface (PES) and the SE PES. In practice, this is implemented via ... |
| Databáze: | OpenAIRE |
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