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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 , 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 , 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 , 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 , 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 , 1.5. Hg-Ligand Binding Free Energies

Sprache: Englisch

UID:

Umfang: 1 Online-Ressource (xviii, 494 Seiten) , Illustrationen

Ausgabe: First edition

ISBN: 0128111089 , 9780128111086

Serie: Methods in Enzymology volume 578

Inhalt: Computational Approaches for Studying Enzyme Mechanism, Part Bis 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 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

Anmerkung: Description based upon print version of record

Weitere Ausg.: ISBN 9780128111079

Weitere Ausg.: Erscheint auch als Druck-Ausgabe Voth, Gregory Computational Approaches for Studying Enzyme Mechanism Part B San Diego : Elsevier Science,c2016 ISBN 9780128111079

Sprache: Englisch

Schlagwort(e): Enzymologie ; Computational chemistry ; Electronic books ; Aufsatzsammlung

URL: Volltext