Computational approaches for studying enzyme mecanism

Author(s)

• Voth, Gregory A.

Bibliographic Information

Computational approaches for studying enzyme mecanism

edited by Gregory A. Voth

（Methods in enzymology / editors in chief, Sidney P. Colowick, Nathan O. Kaplan, v. 577-578）

Academic Press, an imprint of Elsevier, 2016

• pt. A
• pt. B

Note

Includes bibliographical references and indexes

Description and Table of Contents

Volume

pt. A ISBN 9780128053478

Description

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.

Table of Contents

1. The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis Yue Yang, Lili Pan, Felice C. Lightstone and Kenneth M. Merz, Jr. 2. Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins Akshaya Kumar Das and Markus Meuwly 3. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways Dongsheng Wu, Mikolai I. Fajer, Liaoran Cao, Xiaolin Cheng and Wei Yang 4. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis Fiona L. Kearns, Phillip S. Hudson, Stefan Boresch and H. Lee Woodcock 5. Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions Yanzi Zhou, Shenglong Wang, Yongle Li and Yingkai Zhang 6. QM/MM Calculations on Proteins Ulf Ryde 7. Enzymatic Cleavage of Glycosidic Bonds: Strategies on how to Setup and Control a QM/MM Metadynamics Simulation Lluis Raich, Alba Nin-Hill, Albert Ardevol and Carme Rovira 8. Towards Determining ATPase Mechanism in ABC-Transporters: Development of the Reaction Path Force Matching QM/MM Method Yan Zhou, Pedro Ojeda-May, Mulpuri Nagaraju and Jingzhi Pu 9. QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes Daniel Roston and Qiang Cui 10. Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions Mudit Dixit, Susanta Das, Anil Ranu Mhashal, Reuven Eitan and Dan Thomas Major 11. Examinations of the Chemical Step in Enzyme Catalysis Priyanka Singh, Zahidul Islam and Amnon Kohen 12. Use of QM/DMD as a Multiscale Approach to Modelling Metalloenzymes Nathan M. Gallup and Anastassia N. Alexandrova 13. Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent Exchange Adam Duster, Christina Garza and Hai Lin 14. Enzymatic Kinetic Isotope Effects from Path Integral Free Energy Perturbation (PI- FEP) Theory Jiali Gao 15. Simulating Nuclear and Electronic Quantum Effects in Enzymes Lu Wang, Christine M. Isborn and Thomas E. Markland 16. Using Molecular Simulation to Study Biocatalysis in Ionic Liquids K. G. Sprenger and Jim Pfaendtner 17. The MoD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes Mikhail Askerka, Junming Ho, Enrique R. Batista, Jose A Gascon and Victor S. Batista

Volume

pt. B ISBN 9780128111079

Description

Computational Approaches for Studying Enzyme Mechanism, Part B is the first of two volumes in the Methods in Enzymology series that focuses 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 the life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, genetics, and other fields of study.

Table of Contents

1. The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis Yue Yang, Lili Pan, Felice C. Lightstone and Kenneth M. Merz, Jr. 2. Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins Akshaya Kumar Das and Markus Meuwly 3. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways Dongsheng Wu, Mikolai I. Fajer, Liaoran Cao, Xiaolin Cheng and Wei Yang 4. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis Fiona L. Kearns, Phillip S. Hudson, Stefan Boresch and H. Lee Woodcock 5. Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions Yanzi Zhou, Shenglong Wang, Yongle Li and Yingkai Zhang 6. QM/MM Calculations on Proteins Ulf Ryde 7. Enzymatic Cleavage of Glycosidic Bonds: Strategies on how to Setup and Control a QM/MM Metadynamics Simulation Lluis Raich, Alba Nin-Hill, Albert Ardevol and Carme Rovira 8. Towards Determining ATPase Mechanism in ABC-Transporters: Development of the Reaction Path Force Matching QM/MM Method Yan Zhou, Pedro Ojeda-May, Mulpuri Nagaraju and Jingzhi Pu 9. QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes Daniel Roston and Qiang Cui 10. Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions Mudit Dixit, Susanta Das, Anil Ranu Mhashal, Reuven Eitan and Dan Thomas Major 11. Examinations of the Chemical Step in Enzyme Catalysis Priyanka Singh, Zahidul Islam and Amnon Kohen 12. Use of QM/DMD as a Multiscale Approach to Modelling Metalloenzymes Nathan M. Gallup and Anastassia N. Alexandrova 13. Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent Exchange Adam Duster, Christina Garza and Hai Lin 14. Enzymatic Kinetic Isotope Effects from Path Integral Free Energy Perturbation (PI- FEP) Theory Jiali Gao 15. Simulating Nuclear and Electronic Quantum Effects in Enzymes Lu Wang, Christine M. Isborn and Thomas E. Markland 16. Using Molecular Simulation to Study Biocatalysis in Ionic Liquids K. G. Sprenger and Jim Pfaendtner 17. The MoD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes Mikhail Askerka, Junming Ho, Enrique R. Batista, Jose A Gascon and Victor S. Batista

by "Nielsen BookData"

Details

• NCID: BB21966188
• ISBN:
  • 9780128053478
  • 9780128111079
• Country Code: ne
• Title Language Code: eng
• Text Language Code: eng
• Place of Publication: Amsterdam
• Pages/Volumes: 2 v.
• Size: 24 cm
• Parent Bibliography ID:
  • BA00197543