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Protein Engineering

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Cover of 'Protein Engineering'

Table of Contents

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    Book Overview
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    Chapter 1 Protein Engineering: Past, Present, and Future
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    Chapter 2 Rational and Semirational Protein Design
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    Chapter 3 Computational Analysis of Protein Tunnels and Channels
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    Chapter 4 YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations
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    Chapter 5 A Computational Library Design Protocol for Rapid Improvement of Protein Stability: FRESCO
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    Chapter 6 Directed Evolution of Proteins Based on Mutational Scanning
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    Chapter 7 A Brief Guide to the High-Throughput Expression of Directed Evolution Libraries
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    Chapter 8 Library Growth and Protein Expression: Optimal and Reproducible Microtiter Plate Expression of Recombinant Enzymes in E. coli Using MTP Shakers
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    Chapter 9 Normalized Screening of Protein Engineering Libraries by Split-GFP Crude Cell Extract Quantification
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    Chapter 10 Functional Analysis of Membrane Proteins Produced by Cell-Free Translation
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    Chapter 11 Practical Considerations Regarding the Choice of the Best High-Throughput Assay
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    Chapter 12 High-Throughput Screening Assays for Lipolytic Enzymes
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    Chapter 13 Continuous High-Throughput Colorimetric Assays for α -Transaminases
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    Chapter 14 Colorimetric High-Throughput Screening Assays for the Directed Evolution of Fungal Laccases
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    Chapter 15 Directed Coevolution of Two Cellulosic Enzymes in Escherichia coli Based on Their Synergistic Reactions
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    Chapter 16 Program-Guided Design of High-Throughput Enzyme Screening Experiments and Automated Data Analysis/Evaluation
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    Chapter 17 Solid-Phase Agar Plate Assay for Screening Amine Transaminases
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    Chapter 18 Ultrahigh-Throughput Screening of Single-Cell Lysates for Directed Evolution and Functional Metagenomics
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    Chapter 19 Isolation of pH-Sensitive Antibody Fragments by Fluorescence-Activated Cell Sorting and Yeast Surface Display
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    Chapter 20 Library Generation and Auxotrophic Selection Assays in Escherichia coli and Thermus thermophilus
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    Chapter 21 Erratum to: Functional Analysis of Membrane Proteins Produced by Cell-Free Translation
Attention for Chapter 3: Computational Analysis of Protein Tunnels and Channels
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Chapter title
Computational Analysis of Protein Tunnels and Channels
Chapter number 3
Book title
Protein Engineering
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7366-8_3
Pubmed ID
Book ISBNs
978-1-4939-7364-4, 978-1-4939-7366-8
Authors

Jan Brezovsky, Barbora Kozlikova, Jiri Damborsky, Brezovsky, Jan, Kozlikova, Barbora, Damborsky, Jiri

Abstract

Protein tunnels connecting the functional buried cavities with bulk solvent and protein channels, enabling the transport through biological membranes, represent the structural features that govern the exchange rates of ligands, ions, and water solvent. Tunnels and channels are present in a vast number of known proteins and provide control over their function. Modification of these structural features by protein engineering frequently provides proteins with improved properties. Here we present a detailed computational protocol employing the CAVER software that is applicable for: (1) the analysis of tunnels and channels in protein structures, and (2) the selection of hot-spot residues in tunnels or channels that can be mutagenized for improved activity, specificity, enantioselectivity, or stability.

Mendeley readers

The data shown below were compiled from readership statistics for 36 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 36 100%

Demographic breakdown

Readers by professional status Count As %
Student > Bachelor 9 25%
Researcher 8 22%
Student > Ph. D. Student 7 19%
Student > Master 3 8%
Lecturer 2 6%
Other 2 6%
Unknown 5 14%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 17 47%
Agricultural and Biological Sciences 6 17%
Chemistry 4 11%
Computer Science 1 3%
Unknown 8 22%