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Computational approaches for studying enzyme mechanism. Part A /
| Clasificación: | Libro Electrónico |
|---|---|
| Otros Autores: | |
| Formato: | Electrónico eBook |
| Idioma: | Inglés |
| Publicado: |
Cambridge, MA :
Academic Press is an imprint of Elsevier,
2016.
|
| Colección: | Methods in enzymology ;
v. 577. |
| Temas: | |
| Acceso en línea: | Texto completo Fulltext Pt. B |
MARC
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| 245 | 0 | 0 | |a Computational approaches for studying enzyme mechanism. |n Part A / |c edited by Gregory A. Voth. |
| 264 | 1 | |a Cambridge, MA : |b Academic Press is an imprint of Elsevier, |c 2016. | |
| 300 | |a 1 online resource : |b color illustrations. | ||
| 336 | |a text |b txt |2 rdacontent | ||
| 337 | |a computer |b c |2 rdamedia | ||
| 338 | |a online resource |b cr |2 rdacarrier | ||
| 347 | |a data file |2 rda | ||
| 490 | 1 | |a Methods in enzymology ; |v volume 577 | |
| 504 | |a Includes bibliographical references and indexes. | ||
| 588 | 0 | |a Online resource; title from PDF title page (ScienceDirect, viewed August 12, 2016). | |
| 505 | 0 | |a Front Cover; Computational Approaches for Studying Enzyme Mechanism Part A; Copyright; Contents; Contributors; Preface; Chapter One: The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis; 1. Introduction; 2. Method; 2.1. Umbrella Sampling; 2.2. Steered MD; 3. Applications; 3.1. Protein Farnesyltransferase; 3.1.1. Understanding the Conformational Activation of FPP; 3.1.2. Identification of the Mg2+ Binding Site in FTase; 3.1.3. Simulating the Farnesylation Reaction; 3.2. Aromatic Prenyltransferase NphB | |
| 505 | 8 | |a 3.2.1. Identifying the Product Regioselectivity Associated with NphB Catalysis3.2.2. Elucidating the Reaction Mechanism with QM/MM PMF Simulations; 3.3. Aspergillus Fumigatus Prenyltransferase; 3.3.1. Regioselectivity of WT FtmPT1; 3.3.2. Regioselectivity of G115T Mutant; 3.4. Cytochrome P450s; 4. Summary; Acknowledgments; References; Chapter Two: Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins; 1. Introduction; 2. Computational Approaches; 2.1. Adiabatic Reactive Molecular Dynamics; 2.2. Multisurface ARMD; 2.3. Empirical Valence Bond; 3. Applications | |
| 505 | 8 | |a 3.1. Rebinding Dynamics in MbNO3.2. NO Detoxification Reaction in trHbN; 3.3. Competitive Ligand Binding in trHbN; 4. Outlook; Acknowledgments; References; Chapter Three: Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways; 1. Introduction; 2. Collective Variable and Reaction Order Parameter; 3. Traditional Importance Sampling vs GE Sampling; 4. Dimensionality Limit; 5. One of the First Metadynamics-Based Enzyme Reaction Studies; 6. GE-Based String Optimization: The OTPRW Method; 7. OTPRW Study of a Substrate-Assisted Glycosylation Reaction; 8. Final Remarks; Acknowledgments | |
| 505 | 8 | |a 2.1. The Pseudobond Approach to Describe the QM/MM Boundary Across Covalent Bonds2.2. A Dual Focal aiQM/MM-PME Potential with the Periodic Boundary Condition; 2.3. Microiterative Optimization and Reaction Coordinate Driving; 2.4. Born-Oppenheimer aiQM/MM-MD with Umbrella Sampling; 2.5. Implementation; 3. Examples; 3.1. Dissociation of tert-Butyl Chloride in Water; 3.2. First Step of Acylation Reaction for a Serine Protease; 4. Enzyme Simulation Protocol; 5. Conclusion; Acknowledgments; References; Chapter Six: QM/MM Calculations on Proteins; 1. Introduction; 2. Methods; 2.1. QM Methods | |
| 650 | 0 | |a Enzymology. | |
| 650 | 0 | |a Enzymes |x Analysis. | |
| 650 | 0 | |a Enzymes |x Synthesis. | |
| 650 | 2 | |a Computational Biology |x methods |0 (DNLM)D019295Q000379 | |
| 650 | 2 | |a Enzymes |x analysis |0 (DNLM)D004798Q000032 | |
| 650 | 2 | |a Enzymes |x chemical synthesis |0 (DNLM)D004798Q000138 | |
| 650 | 6 | |a Enzymologie. |0 (CaQQLa)201-0269407 | |
| 650 | 6 | |a Enzymes |x Analyse. |0 (CaQQLa)201-0090075 | |
| 650 | 6 | |a Enzymes |x Synth�ese. |0 (CaQQLa)201-0070003 | |
| 650 | 7 | |a SCIENCE / Life Sciences / Biochemistry |2 bisacsh | |
| 650 | 7 | |a Enzymes |x Analysis |2 fast |0 (OCoLC)fst00913606 | |
| 650 | 7 | |a Enzymes |x Synthesis |2 fast |0 (OCoLC)fst00913628 | |
| 650 | 7 | |a Enzymology |2 fast |0 (OCoLC)fst00913635 | |
| 655 | 4 | |a Internet Resources. | |
| 700 | 1 | |a Voth, Gregory A., |e editor. | |
| 776 | 0 | 8 | |i Print version: |z 012805347X |z 9780128053478 |w (OCoLC)946605486 |
| 830 | 0 | |a Methods in enzymology ; |v v. 577. | |
| 856 | 4 | 0 | |u https://sciencedirect.uam.elogim.com/science/bookseries/00766879/577 |z Texto completo |
| 856 | 4 | 0 | |u https://sciencedirect.uam.elogim.com/science/bookseries/00766879/578 |y Fulltext Pt. B |z Texto completo |