UID:
almafu_9958130904002883
Umfang:
1 online resource (538 p.)
Ausgabe:
First edition.
ISBN:
9780128111086
,
0128111089
,
9780128111079
,
0128111070
Serie:
Methods in enzymology, Volume 578
Anmerkung:
Description based upon print version of record.
,
Front Cover; Computational Approaches for Studying Enzyme Mechanism Part B; Copyright; Contents; Contributors; Preface; Chapter One: Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins; 1. Introduction; 2. Biomolecular Structure and Flexibility; 3. Solvent Models or: How I Learned to Stop Worrying and Love the Dielectric Coefficient; 4. Modeling Ion-Solute Interactions; 5. Force Field and Parameter Choices; 6. Conclusions; Acknowledgments; References; Chapter Two: Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions; 1. Introduction
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1.1. Established Methods for Computational Calculation of Enzymatic Free Energy Barriers and Rates2. Transition Path Sampling: A New Paradigm for the Study of Enzymatic Mechanism; 2.1. A Statistical Method for Studying Enzymatic Reactions; 2.2. TPS Ensemble Analysis; 3. New Methods for Calculation of Values Relevant to Enzyme Mechanism; 3.1. Free Energy Probes of Nuclear Tunneling; 3.1.1. Application of Work Calculation to Hydride Transfer; 3.2. KIEs of Quantum Particle Transfer from TPS; 3.2.1. Rate Calculation Algorithm; 3.2.2. Application of Modified Algorithm to YADH; 4. Conclusion
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ReferencesChapter Three: Accurate Calculation of Electric Fields Inside Enzymes; 1. Introduction; 2. Theoretical Methods; 2.1. Fragment Approach to Quantum Calculation of Protein-Ligand Interaction; 2.2. Fragment Quantum Calculation of Protein in Solvent; 2.3. EE-GMFCC Method for Calculation of Enzyme Energy; 2.4. Quantum Calculation of Electrostatics Inside Enzyme; 2.5. Electric Field at the Active Site of Enzyme; 2.5.1. Effect of Electronic Polarization on Electrostatics in Proteins; 2.5.2. Effect of Charge Transfer; Acknowledgments; References
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Chapter Four: Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics1. Hydrogenases; 2. Proton Transport; 3. Computational Strategy; 4. Proton Transport in Hydrogenase; 4.1 Classical MD Simulations; 4.2 Classical MD Methodology Used to Study Hydrogenase; 4.2.1 Force Field Parameters; 4.3 Evaluation of the Protein Dynamics; 4.3.1 Error Analysis; 4.4 Hydrogen Bond Analysis; 4.4.1 Hydrogen Bond Interaction in the Proton Pathway; 4.4.2 Hydrogen Bond Interaction with Nearby Residues; 4.4.3 Error Analysis for Hydrogen Bonding
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4.5 The Role of Dynamics in Enzymatic Activity4.5.1 Covariance Analysis; 5. Proton Transport in Hydrogenase Mimics; 5.1 Bottlenecks for Proton Movement in Hydrogenase Mimics; 5.2 Hydrogenase Mimics for H2 Oxidation; 5.2.1 DFT calculations; 5.3 Hydrogenase Mimics for H2 Production; 5.3.1 Outer Coordination Sphere; 5.3.2 Replica Exchange Molecular Dynamics; 6. Summary; Acknowledgments; References; Chapter Five: Modeling Mercury in Proteins; 1. Introduction; 1.1. Mercury Toxicity; 1.2. Inorganic Hg Chemistry; 1.3. Quantum Chemistry; 1.4. Hydration Free Energies
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1.5. Hg-Ligand Binding Free Energies
Sprache:
Englisch
