Computational Approaches for Studying Enzyme Mechanism Part A (Volume 577) (Methods in Enzymology, Volume 577)

__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. * Focuses on computational approaches for studying enzyme mechanism * Continues 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 Part A. 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. -- Empirical Force Fields For Mechanistic Studies Of Chemical Reactions In Proteins / Akshaya Kumar Das And Markus Meuwly -- Generalized Ensemble Sampling Of Enzyme Reaction Free Energy Pathways / Dongsheng Wu, Mikolai I. Fajer, Liaoran Cao, Xiaolin Cheng And Wei Yang -- 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 -- Born-oppenheimer Ab Initio Qm/mm Molecular Dynamics Simulations Of Enzyme Reactions / Yanzi Zhou, Shenglong Wang, Yongle Li And Yingkai Zhang -- Qm/mm Calculations On Proteins / Ulf Ryde --^ Enzymatic Cleavage Of Glycosidic Bonds: Strategies On How To Setup And Control A Qm/mm Metadynamics Simulation / Lluís Raich, Alba Nin-hill, Albert Ardèvol And Carme Rovira -- Toward 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 -- Qm/mm Analysis Of Transition States And Transition State Analogues In Metalloenzymes / Daniel Roston And Qiang Cui -- Practical Aspects Of Multiscale Classical And Quantum Simulations Of Enzyme Reactions / Mudit Dixit, Susanta Das, Anil Ranu Mhashal, Reuven Eitan And Dan Thomas Major -- Examinations Of The Chemical Step In Enzyme Catalysis / Priyanka Singh, Zahidul Islam And Amnon Kohen -- Use Of Qm/dmd As A Multiscale Approach To Modelling Metalloenzymes / Nathan M. Gallup And Anastassia N. Alexandrova --^ Adaptive Partitioning Qm/mm Dynamics Simulations For Substrate Uptake, Product Release, And Solvent Exchange / Adam Duster, Christina Garza And Hai Lin -- Enzymatic Kinetic Isotope Effects From Path-integral Free Energy Perturbation Theory / Jiali Gao -- Simulating Nuclear And Electronic Quantum Effects In Enzymes / Lu Wang, Christine M. Isborn And Thomas E. Markland -- Using Molecular Simulation To Study Biocatalysis In Ionic Liquids / K. G. Sprenger And Jim Pfaendtner -- The Mod-qm/mm Method: Applications To Studies Of Photosystem Ii And Dna G-quadruplexes / Mikhail Askerka, Junming Ho, Enrique R. Batista, Jose A Gascón And Victor S. Batista. Part B. Continuum Electrostatics Approaches To Calculating Pkas And Ems In Proteins / M.r. Gunner, N.a. Baker -- Path Sampling Methods For Enzymatic Quantum Particle Transfer Reactions / M.w. Dzierlenga, M.j. Varga, S.d. Schwartz -- Accurate Calculation Of Electric Fields Inside Enzymes / X. Wang, X. He, J.z.h. Zhang -- Molecular Dynamics Studies Of Proton Transport In Hydrogenase And Hydrogenase Mimics / B. Ginovska, S. Raugei, W.j. Shaw -- Modeling Mercury In Proteins / J.m. Parks, J.c. Smith -- Steered Molecular Dynamics Methods Applied To Enzyme Mechanism And Energetics / C.l. Ramírez, M.a. Martí, A.e. Roitberg -- New Algorithms For Global Optimization And Reaction Path Determination / D. Weber, D. Bellinger, B. Engels -- Simulation Studies Of Protein And Small Molecule Interactions And Reaction / L. Yang, J. Zhang, X. Che, Y.q. Gao -- How To Run Fast Simulations / M.i. Zimmerman, G.r. Bowman --^ Bridging Enzymatic Structure Function Via Mechanics: A Coarse-grain Approach / S. Sacquin-mora -- A Networks Approach To Modeling Enzymatic Reactions / P. Imhof -- Conformational Sub-states And Populations In Enzyme Catalysis / P.k. Agarwal, N. Doucet, C. Chennubhotla, A. Ramanathan, C. Narayanan -- Computation Of Rate Constants For Diffusion Of Small Ligands To And From Buried Protein Active Sites / P.-h. Wang, D. De Sancho, R.b. Best, J. Blumberger -- Calculation Of Enzyme Fluctuograms From All-atom Molecular Dynamics Simulation / T.h. Click, N. Raj, J.-w. Chu -- Constructing Kinetic Network Models To Elucidate Mechanisms Of Functional Conformational Changes Of Enzymes And Their Recognition With Ligands / L. Zhang, H. Jiang, F.k. Sheong, F. Pardo-avila, P.p.-h. Cheung, X. Huang --^ Microscopic Characterization Of Membrane Transporter Function By In Silico Modeling And Simulation / J.v. Vermaas, N. Trebesch, C.g. Mayne, S. Thangapandian, M. Shekhar, P. Mahinthichaichan, J.l. Baylon, T. Jiang, Y. Wang, M.p. Muller, E. Shinn, Z. Zhao, P.-c. Wen, E. Tajkhorshid -- Detecting Allosteric Networks Using Molecular Dynamics Simulation / S. Bowerman, J. Wereszczynski. Edited By Gregory A. Voth. Includes Bibliographical References And Indexes. Content: Series Page Page ii Copyright Page iv Contributors Pages xi-xiv Preface Pages xv-xvi G.A. Voth Chapter One - The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis Pages 1-29 Y. Yang, L. Pan, F.C. Lightstone, K.M. Merz Jr. Chapter Two - Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins Pages 31-55 A.K. Das, M. Meuwly Chapter Three - Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways Pages 57-74 D. Wu, M.I. Fajer, L. Cao, X. Cheng, W. Yang Chapter Four - Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis Pages 75-104 F.L. Kearns, P.S. Hudson, S. Boresch, H.L. Woodcock Chapter Five - Born–Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions Pages 105-118 Y. Zhou, S. Wang, Y. Li, Y. Zhang Chapter Six - QM/MM Calculations on Proteins Pages 119-158 U. Ryde Chapter Seven - Enzymatic Cleavage of Glycosidic Bonds: Strategies on How to Set Up and Control a QM/MM Metadynamics Simulation Pages 159-183 L. Raich, A. Nin-Hill, A. Ardèvol, C. Rovira Chapter Eight - Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path–Force Matching QM/MM Method Pages 185-212 Y. Zhou, P. Ojeda-May, M. Nagaraju, J. Pu Chapter Nine - QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes Pages 213-250 D. Roston, Q. Cui Chapter Ten - Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions Pages 251-286 M. Dixit, S. Das, A.R. Mhashal, R. Eitan, D.T. Major Chapter Eleven - Examinations of the Chemical Step in Enzyme Catalysis Pages 287-318 P. Singh, Z. Islam, A. Kohen Chapter Twelve - Use of QM/DMD as a Multiscale Approach to Modeling Metalloenzymes Pages 319-339 N.M. Gallup, A.N. Alexandrova Chapter Thirteen - Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent Exchange Pages 341-357 A. Duster, C. Garza, H. Lin Chapter Fourteen - Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory Pages 359-388 J. Gao Chapter Fifteen - Simulating Nuclear and Electronic Quantum Effects in Enzymes Pages 389-418 L. Wang, C.M. Isborn, T.E. Markland Chapter Sixteen - Using Molecular Simulation to Study Biocatalysis in Ionic Liquids Pages 419-441 K.G. Sprenger, J. Pfaendtner Chapter Seventeen - The MOD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes Pages 443-481 M. Askerka, J. Ho, E.R. Batista, J.A. Gascón, V.S. Batista Author Index Pages 483-511 Subject Index Pages 513-522

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.

• Focuses on computational approaches for studying enzyme mechanism
• Continues 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

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. Focuses on computational approaches for studying enzyme mechanism Continues 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