Computational Approaches for Studying Enzyme Mechanism Part A, is the first of two volumes in the Methods in Enzymology series, focusses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, and genetics to name a few. Focusses on computational approaches for studying enzyme mechanismContinues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers INDICE: 1. Conformational sub-states and populations associated with enzyme catalysis2. QM/MM sampling in mechanistic studies of metalloenzymes3. Quantum Mechanics/Molecular Mechanics Studies of Photosystem II4. Ligand Transport to Protein Active Sites from Markov State Modelling5. How to run FAST simulations6. Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics Simulation7. Investigation of enzyme catalysis with DFTB/MM and free energy simulations8. New Algorithms for global optimization and reaction path determination9. Accurate computation of enzymatic kinetic isotope effects from integrated path integral and free energy perturbation simulations10. Simulation studies of protein and small molecule interactions and reaction11. Classical Monte Carlo Approaches to Calculating Protein and Ligand pKas and Ems in Proteins12. Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and their Recognition with Ligands13. A networks approach to modelling enzymatic reactions14. Computational and Experimental Interplay in the Examinations of the Chemical Step in Enzyme Catalysis15. Adaptive partitioning QM/MM dynamics simulations for substrate uptake, product release, and solvent exchange16. Multiscale quantum and classical simulations of enzyme reactions using CHARMM17. Probing nuclear and electronic quantum effects in enzymes with ab initio path integral molecular dynamics simulations18. Uncovering Enzymatic Mechanisms by Transition Path Sampling19. The role of molecular dynamics potential of mean force calculations in the investigation of enzyme catalysis20. Empirical force fields for mechanistic studies of chemical reactions in proteins21. Using molecular simulation to study biocatalysis in ionic liquid22. Towards Determining ATPase Mechanism in ABC-Transporters: Development of the Reaction Path Force Matching QM/MM Method23. Steered molecular dynamics methods applied to enzyme mechanism and energetics24. Ab initio QM/MM metadynamics simulations of enzymatic glycosidic bond cleavage25. QM/MM calculations of enzyme reactions26. Bridging enzymatic structure and function via mechanics: a coarse-grain approach27. Computational Methods applied to analysis and prediction of genetic cardiac disease28. Proton transport in hydrogenases29. Modeling Mercury in Proteins30. Microscopic Characterization of Functional Motions of Membrane Proteins31. Detecting Allosteric Networks in Enzyme Systems32. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis33. Generalized Ensemble Simulation of Biomolecular Minimum Free Energy Pathways34. Accurate calculation of electric fields inside enzymes35. Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions
- ISBN: 978-0-12-805347-8
- Editorial: Academic Press
- Encuadernacion: Cartoné
- Páginas: 412
- Fecha Publicación: 01/08/2016
- Nº Volúmenes: 1
- Idioma: Inglés