Enzyme Engineering: Methods and Protocols

ISBN-13: 9781071618257 / Angielski / Twarda / 2021 / 396 str.

Francesca Magnani; Chiara Marabelli; Francesca Paradisi

Spis treści

Part I: Enzyme Libraries Preparation and Screening

 

1. Preparation of Soil Metagenome Libraries and Screening for Gene Specific Amplicons

            Luke J. Stevenson, David F. Ackerley, and Jeremy G. Owen

 

2. Ultrahigh-Throughput Screening of Metagenomic Libraries Using Droplet Microfluidics

            Davide Agostino Cecchini, Mercedes Sánchez-Costa, Alejandro H. Orrego, Jesús Fernández-Lucas, and Aurelio Hidalgo

 

3. Synthetic DNA Libraries for Protein Engineering toward Process Improvement in Drug Synthesis

            Michele Tavanti

 

Part II: Directed Evolution

 

4. In Silico Prediction Methods for Site-Saturation Mutagenesis

            Ge Qu and Zhoutong Sun

 

5. Recombination of Compatible Substitutions by 2GenReP and InSiReP

            Haiyang Cui, Mehdi D. Davari, and Ulrich Schwaneberg

 

Part III: Semi-Rational and De Novo Design

 

6. Using the Evolutionary History of Proteins to Engineer Insertion-Deletion Mutants from Robust, Ancestral Templates Using Graphical Representation of Ancestral Sequence Predictions (GRASP)

            Connie M. Ross, Gabriel Foley, Mikael Boden, and Elizabeth M.J. Gillam

 

7. Resurrecting Enzymes by Ancestral Sequence Reconstruction

            Maria Laura Mascotti

 

8. Expression and In Vivo Loading of De Novo Proteins with Tetrapyrrole Cofactors

            Paul Curnow and J.L. Ross Anderson

 

Part IV: Rational Design

 

9. Rational-Design Engineering to Improve Enzyme Thermostability

            Vinutsada Pongsupasa, Piyanuch Anuwan, Somchart Maenpuen, and Thanyaporn Wongnate

 

10. Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents

            Haiyang Cui, Markus Vedder, Ulrich Schwaneberg, and Mehdi D. Davari

 

11. In Silico Engineering of Enzyme Access Tunnels

            Alfonso Gautieri, Federica Rigoldi, Archimede Torretta, Alberto Redaelli, and Emilio Parisini

 

12. Quantum-Mechanical/Molecular-Mechanical (QM/MM) Simulations for Understanding Enzyme Dynamics

            Rimsha Mehmood and Heather J. Kulik

 

13. Computational Enzyme Design at Zymvol

            Emanuele Monza, Victor Gil, and Maria Fatima Lucas

 

Part V: Biocatalytic Process Development

 

14. Advanced Enzyme Immobilization Technologies: An Eco-Friendly Support, a Polymer-Stabilizing Immobilization Strategy, and an Improved Cofactor Co-Immobilization Technique

            Ana I. Benítez-Mateos and Francesca Paradisi

 

15. Chemical Reaction Engineering to Understand Applied Kinetics in Free Enzyme Homogeneous Reactors

            Alvaro Lorente-Arevalo, Alberto Garcia-Martin, Miguel Ladero, and Juan M. Bolivar

 

16. Enzymatic Oxidative Cascade for Oxofunctionalization of Fatty Acids in One-Pot

            Somayyeh Gandomkar and Mélanie Hall

 

17. CRISPR-Cas9 Editing of the Synthesis of Biodegradable Polyesters Polyhydroxyalkanaotes (PHA) in Pseudomonas putida KT2440

            Si Liu, Tanja Narancic, Chris Davis, and Kevin E. O’Connor

Blurb

This book provides comprehensive methods and protocols about enzyme design. The chapters are grouped by main topic, starting with methodologies describing library preparation and screening, state of the art techniques in directed evolution and rational design, followed by examples of immobilization of enzymes on sustainable polymers, as well as biocatalytic conversions mediated by homogenous enzymatic preparations or whole cells. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and timely, Enzyme Engineering: Methods and Protocols is an ideal guide for both the novice and the veteran researcher interested in biocatalysis.

Chapter 13 is available open access under a CC BY 4.0 license.