Quantum tunnelling in enzyme-catalysed reactions /

Quantum tunnelling in enzyme-catalysed reactions /

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Bibliographic Details
Imprint:Cambridge, UK : Royal Society of Chemistry, c2009.
Description:xxv, 385 p. : ill. (some col.) ; 25 cm.
Language:English
Series:RSC biomolecular sciences
RSC biomolecular sciences.
Subject:
Tunneling (Physics)
Quantum biochemistry.
Enzymes.
Catalysis.
Catalysis.
Enzymes.
Quantum biochemistry.
Tunneling (Physics)
Format: Print Book
URL for this record:http://pi.lib.uchicago.edu/1001/cat/bib/7715927
Hidden Bibliographic Details
Other authors / contributors:Allemann, Rudolf K. (Rudolf Konrad)
Scrutton, Nigel S.
ISBN:9780854041220 (hbk.)
0854041222 (hbk.)
Notes:Includes bibliographical references and index.
Summary:Sitting at the interface between biology, chemistry and physics, this introduction to modern theories of enzyme catalysis presents the latest methods used to study quantum tunnelling in biological systems.
Table of Contents:
  • Chapter 1. The Transition-State Theory Description of Enzyme Catalysis for Classically Activated Reactions
  • 1.1. Introduction
  • 1.2. Quantifying the Catalytic Activity of Enzymes
  • 1.3. Free-Energy Analysis of Enzyme Catalysis
  • 1.4. Transition-State Stabilisation or Ground-State Destabilisation?
  • 1.5. Selective Stabilisation of Transition Structures by Enzymes
  • 1.6. Enzyme Flexibility and Dynamics
  • References
  • Chapter 2. Introduction to Quantum Behaviour - A Primer
  • 2.1. Introduction
  • 2.1.1. Classical Mechanics
  • 2.2. Quantum Mechanics
  • 2.2.1. Heisenberg Uncertainty Principle
  • 2.2.2. The Schr&oumlet;dinger Equation
  • 2.3. Electronic-Structure Calculations
  • 2.3.1. Born-Oppenheimer Approximation
  • 2.3.2. Hartree-Fock Theory
  • 2.3.3. Basis Sets
  • 2.3.4. Zero-Point Energy
  • 2.4. Density Functional Theory
  • 2.4.1. DFT Calculations of Free Energies of Activation of Enzyme Models
  • 2.4.2. DFT Calculations of Kinetic Isotope Effects
  • 2.5. Quantum-Mechanics/Molecular-Mechanics Methods
  • 2.6. Summary and Outlook
  • References
  • Chapter 3. Quantum Catalysis in Enzymes
  • 3.1. Introduction
  • 3.2. Theory
  • 3.2.1. Gas-Phase Variational Transition-State Theory
  • 3.2.2. The Transmission Coefficient
  • 3.2.3. Ensemble Averaging
  • 3.3. Examples
  • 3.3.1. Liver Alcohol Dehydrogense - A Workhorse for Studying Hydride Transfer
  • 3.3.2. Dihydrofolate Reductase - A Paradigmatic System
  • 3.3.3. Soybean-Lipoxygenase-1 and Methylmalonyl-CoA Mutase - Enzymes Catalysing Hydrogen Atom Transfer Reactions that Exhibit the Largest KIEs Reported for any Biological System
  • 3.3.4. Other Systems and Perspectives
  • 3.4. Concluding Remarks
  • Appendix - Quantum-Mechanical Rate Theory
  • Acknowledgments
  • References
  • Chapter 4. Selected Theoretical Models and Computational Methods for Enzymatic Tunnelling
  • 4.1. Introduction
  • 4.2. Vibronically Nonadiabatic Reactions: Proton-Coupled Electron Transfer
  • 4.2.1. Theory
  • 4.2.2. Application to Lipoxygenase
  • 4.3. Predominantly Adiabatic Reactions: Proton and Hydride Transfer
  • 4.3.1. Theory
  • 4.3.2. Application to Dihydrofolate Reductase
  • 4.4. Emerging Concepts about Enzyme Catalysis
  • Acknowledgments
  • References
  • Chapter 5. Kinetic Istope Effects from Hybrid Classical and Quantum Path Integral Computations
  • 5.1. Introduction
  • 5.2. Theoretical Background
  • 5.2.1. Path Integral Quantum Transition-State Theory
  • 5.2.2. Centroid Path Integral Simulations
  • 5.2.3. Kinetic Isotope Effects
  • 5.3. Potential-Energy Surface
  • 5.3.1. Combined QM/MM Potentials
  • 5.3.2. The MOVB Potential
  • 5.4. Computational Details
  • 5.5. Illustrative Examples
  • 5.5.1. Proton Transfer between Nitroethane and Acetate Ion
  • 5.5.2. The Decarboxylation of N-Methyl Picolinate
  • 5.5.3. Proton Transfer between Chloroacetic Acid and Substituted ¿-Methoxystyrenes
  • 5.6. Concluding Remarks
  • Acknowledgments
  • References
  • Chapter 6. Beyond Tunnelling Corrections: Full Tunnelling Models for Enzymatic C-H Activation Reactions
  • 6.1. Introduction to Enzymatic C-H Activation Reactions
  • 6.1.1. Methods of Study
  • 6.1.2. The Semiclassical Origin of the Kinetic Isotope Effect
  • 6.2. Detection of Hydrogen Tunnelling in the Context of a "Tunnelling Correction"
  • 6.2.1. The Bell Correction
  • 6.2.2. Implications for Swain-Schaad Relationships
  • 6.2.3. Implication for Arrhenius Behaviour
  • 6.3. Nonclassical Behaviour that Fails to Conform to the Tunnelling Correction
  • 6.3.1. Swain-Schaad Relationships
  • 6.3.2. Arrhenius-Behaviour Deviations
  • 6.4. Full Tunnelling Behaviour under Physiological Conditions
  • 6.4.1. Formalising H-transfer in the Context of Electron Tunnelling
  • 6.4.2. A Simple Physical Model for H-tunnelling
  • 6.5. Soybean Lipoxygenase-1 (SLO-1) as a Prototype of Full Tunnelling in an Enzyme
  • 6.5.1. Overview of the Isotopic Properties of SLO-1 Catalysis
  • 6.5.2. The Temperature Dependence of KIEs in the SLO-1 Reaction
  • 6.6. Conclusions and Implications for Our Understanding of Enzyme Catalysis
  • References
  • Chapter 7. Quantum Effects in Enzyme Kinetics
  • 7.1. Introduction
  • 7.2. Kinetic Isotope Effects: Basic Terms and Concepts
  • 7.2.1. Defining KIEs
  • 7.2.2. Swain-Schaad Relationships for 1° and 2° KIEs
  • 7.2.3. Kinetic Complexity
  • 7.2.4. Coupling and Coupled Motion
  • 7.2.5. Experimental Methods and Design
  • 7.3. KIEs as Probes for Tunnelling
  • 7.3.1. The Size of the KIE
  • 7.3.2. Comparison of 2° KIEs and 2° EIEs
  • 7.3.3. Deviations from Semiclassical 2° Swain-Schaad Relationships
  • 7.3.4. Temperature Dependence of the KIEs
  • 7.4. Test Cases: Alcohol Dehydrogenase, Dihydrofolate Reductase and Thymidylate Synthase
  • 7.4.1. Alcohol Dehydrogenase
  • 7.4.2. Dihydrofolate Reductase
  • 7.4.3. Thymidylate Synthase
  • 7.5. Conclusions
  • References
  • Chapter 8. Direct Methods for the Analysis of Quantum-Mechanical Tunnelling: Dihydrofolate Reductase
  • 8.1. Introduction
  • 8.1.1. The Kinetic Isotope Effect
  • 8.1.2. The Significance of Tunnelling in Enzymatic Reactions
  • 8.1.3. Experimental Methods of Observing the Chemical Step of the Reaction
  • 8.2. Dihydrofolate Reductase: A Case Study
  • 8.2.1. DHFR from Escherichia coli
  • 8.2.2. DHFR from the Thermophile Bacillus stearothermophilus
  • 8.2.3. DHFR from the Hyperthermophile Thermotoga Maritima
  • 8.3. Temperature Dependence of the KIEs for other Homologous Enzymes
  • 8.4. Conclusions
  • References
  • Chapter 9. Probing Coupled Motions in Enzymatic Hydrogen Tunnelling Reactions: Beyond Temperature-Dependence Studies of Kinetic Isotope Effects
  • 9.1. Dynamics and Full Tunnelling Models for Enzymatic H-transfer
  • 9.1.1. Towards a More Detailed Understanding of the Temperature Dependence of KIEs
  • 9.1.2. Identifying a Promoting Motion in AADH and Rationalising the Apparent Temperature Independence of the KIE For Substrate C-H/D Bond Breakage
  • 9.2. Pressure as a Probe of Hydrogen Tunnelling
  • 9.2.1. Steady-State Analysis of the Pressure Dependence of H-Transfer: A Case Study with Alcohol Dehydrogenase
  • 9.2.2. Pressure Variation and Direct Analysis of the Chemical Step: A Case Study with Morphinone Reductase
  • 9.2.3. Modelling the Pressure Dependence of an Environmentally Coupled H-tunnelling Reaction
  • 9.3. Other Probes of Tunnelling: Future Prospects for Experimental Studies
  • 9.3.1. Secondary KIEs
  • 9.3.2. Driving Force
  • 9.3.3. Viscosity
  • 9.3.4. Multiple Reactive Configurations and a Place for Single-Molecule Measurements
  • 9.4. Conclusions
  • References
  • Chapter 10. Computational Simulations of Tunnelling Reactions in Enzymes
  • 10.1. Introduction
  • 10.2. Molecular Mechanical Methods
  • 10.3. Quantum Mechanical Methods
  • 10.4. Combined Quantum Mechanical/Molecular Mechanical Methods
  • 10.5. Improving Semiempirical QM Calculations
  • 10.6. Calculation of Potential Energy Surfaces and Free Energy Surfaces
  • 10.7. Simulation of the H-tunnelling Event
  • 10.8. Calculation of H-tunnelling Rates and Kinetic Isotope Effects
  • 10.9. Analysing Molecular Dynamics Trajectories
  • 10.10. A Case Study: Aromatic Amine Dehydrogenase (AADH)
  • 10.10.1. Preparation of the System
  • 10.10.2. Analysis of the H-tunnelling Step in AADH
  • 10.10.3. Analysis of the Role of Promoting Motions in Driving Tunnelling
  • 10.10.4. Comparison of Short-Range Motions in AADH with Long-Range Motions in Dihydrofolate Reductase
  • 10.11. Summary
  • References
  • Chapter 11. Tunnelling does not Contribute Significantly to Enzyme Catalysis, but Studying Temperature Dependence of Isotope Effects is Useful
  • 11.1. Introduction
  • 11.2. Methods
  • 11.3. Simulating Temperature Dependence of KIEs in Enzymes
  • 11.4. Concluding Remarks
  • Acknowledgement
  • References
  • Chapter 12. The Use of X-ray Crystallography to Study Enzymic H-tunnelling
  • 12.1. Introduction
  • 12.2. X-ray Crystallography: A Brief Overview
  • 12.2.1. Accuracy of X-ray Diffraction Structures
  • 12.2.2. Dynamic Information from X-ray Crystallography
  • 12.3. Examples of H-tunnelling Systems Studied by Crystallography
  • 12.3.1. Crystallographic Studies of AADH Catalytic Mechanism
  • 12.3.2. Crystallographic Studies of MR
  • 12.4. Conclusions
  • References
  • Chapter 13. The Strengths and Weaknesses of Model Reactions for the Assessment of Tunnelling in Enzymic Reactions
  • 13.1. Model Reactions for Biochemical Processes
  • 13.2. Model Reactions Relevant to Enzymic Tunnelling
  • 13.3. Isotope Effect Temperature Dependences and the Configurational-Search Framework (CSF) for their Interpretation
  • 13.3.1. The Traditionally Dependent Category
  • 13.3.2. The Underdependent Tunnelling Category
  • 13.3.3. The Overdependent Tunnelling Category
  • 13.4. Example 1. Hydride Transfer in a Thermophilic Alcohol Dehydrogenase
  • 13.4.1. The Kirby-Walwyn Intramolecular Model Reaction
  • 13.4.2. The Powell-Bruice Tunnelling Model Reaction
  • 13.4.3. Enzymic Tunnelling in Alcohol Dehydrogenases
  • 13.4.4. Model Reactions and the Catalytic Power of Alcohol Dehydrogenase
  • 13.5. Example 2. Hydrogen-Atom Transfer in Methylmalonyl Coenzyme A Mutase (MCM)
  • 13.5.1. Nonenzymic Tunnelling in the Finke Model Reactions for MCM
  • 13.5.2. Enzymic Tunnelling in MCM
  • 13.5.3. Model Reactions and MCM Catalytic Power
  • 13.6. The Roles of Theory in the Comparison of Model and Enzymic Reactions
  • 13.7. Model Reactions, Enzymic Accelerations, and Quantum Tunnelling
  • References
  • Chapter 14. Long-Distance Electron Tunnelling in Proteins
  • 14.1. Introduction
  • 14.2. Electronic Coupling and Tunnelling Pathways
  • 14.2.1. Direct Method
  • 14.2.2. Avoided Crossing
  • 14.2.3. Application of Koopmans' Theorem
  • 14.2.4. Generalised Mulliken-Hush Method
  • 14.2.5. The Propagator Method
  • 14.2.6. Protein Pruning
  • 14.2.7. Tunnelling Pathways
  • 14.3. The Method of Tunnelling Currents
  • 14.3.1. General Relations
  • 14.3.2. Many-Electron Picture
  • 14.4. Many-Electron Aspects
  • 14.4.1. One Tunnelling Orbital (OTO) Approximation and Polarisation Effects
  • 14.4.2. The Limitation of the SCF Description of Many-Electron Tunnelling
  • 14.4.3. Correlation Effects. Polarisation Cloud Dynamics. Beyond Hartree-Fock Methods
  • 14.4.4. Quantum Interference Effects. Quantised Vertices
  • 14.4.5. Electron Transfer or Hole Transfer? Exchange Effects
  • 14.5. Dynamical Aspects
  • Acknowledgments
  • References
  • Chapter 15. Proton-Coupled Electron Transfer: The Engine that Drives Radical Transport and Catalysis in Biology
  • 15.1. Introduction
  • 15.2. PCET Model Systems
  • 15.2.1. Unidirectional PCET Networks
  • 15.2.2. Bidirectional PCET Networks
  • 15.2.3. PCET Biocatalysis
  • 15.3. PCET in Enzymes: A Study of Ribonucleotide Reductase
  • 15.3.1. The PCET Pathway in RNR
  • 15.3.2. PCET in the ¿2 Subunit of RNR
  • 15.3.3. PCET in ¿2 Subunit of RNR: PhotoRNRs
  • 15.3.4. A Model for PCET in RNR
  • 15.4. Concluding Remarks
  • Acknowledgements
  • References
  • Subject Index
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