Methods in enzymology. Volume five hundred and twenty three, Methods in protein design / edited by Amy E. Keating, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.

Format:

Book

Contributor:

Keating, Amy E., editor.

Series:

Methods in enzymology ; v. 523.

Methods in enzymology, 0076-6879 ; v. 523

Methods in enzymology ; volume five hundred and twenty three

Gale eBooks

Language:

English

Subjects (All):

Protein engineering.

Enzymology.

Physical Description:

1 online resource (liv, 464 pages, 20 unnumbered pages of plates) : illustrations (some color).

Edition:

1st ed.

Place of Publication:

San Diego, Calif. : Academic Press, 2013.

San Diego, CA : Academic Press, 2013.

Language Note:

English

Summary:

This new volume of Methods in Enzymology continues the legacy of this premier serial by containing quality chapters authored by leaders in the field. This volume covers methods in protein design and it has chapters on such topics as protein switch engineering by domain insertion, evolution based design of proteins, and computationally designed proteins. Continues the legacy of this premier serial with quality chapters authored by leaders in the fieldCovers methods in protein designContains chapters with such topics as protein switch engineering by

Contents:

Front Cover; Methods in Protein Design; Copyright; Contents; Contributors; Preface; Methods in Enzymology; Chapter One: Computational Design of Novel Protein Binders and Experimental Affinity Maturation; 1. Introduction; 2. Computational Design of Binders Using Novel Scaffolds; 3. Target Selection; 4. Generating an Idealized Concept of the Hotspot; 5. Selecting Shape Complementary Scaffold Surfaces for Design; 6. Interface Design; 7. Yeast Cell-Surface Display as a Screening Method for Designed Binders; 8. Affinity Maturation; 9. What Works, What Fails, and What It Means; Acknowledgments

ReferencesChapter Two: Mining Tertiary Structural Motifs for Assessment of Designability; 1. Introduction; 2. MaDCaT; 2.1. Similarity score; 2.2. The algorithm; 2.2.1. Single-segment queries; 2.2.2. Multisegment queries; 2.2.3. Interfacial searches; 2.2.4. Dali versus MaDCaT; 2.2.5. Obtaining MaDCaT; 3. Quantifying Designability; 3.1. Motif usage in nature varies significantly; 3.2. Connection between structure and sequence; 4. Further Developments; 5. Summary; Acknowledgments; References; Chapter Three: Computational Methods for Controlling Binding Specificity; 1. Introduction

1.1. Positive and negative design in manipulating binding specificity2. Narrowing Down Binding Specificity; 2.1. Optimizing a large number of residues with positive design; 2.1.1. Structure preparation; 2.1.2. Set up the design calculation; 2.1.3. Perform the design calculation; 2.1.4. Analyze the results; 2.1.5. Example: Enhancing binding specificity of CaM to CaM-dependent protein kinase II (CaMKII) relative to calcineurin ...; 2.2. Designing single specificity-enhancing mutations with positive and negative design; 2.2.1. Structure preparation; 2.2.2. Define the design problem

2.2.3. Perform the design calculation2.2.4. Identify specificity-enhancing mutations; 2.2.5. Examples: Specificity-enhancing mutations identified by the saturated mutagenesis protocol; 3. Broadening Binding Specificity; 3.1. Structure preparation for multistate design; 3.2. Set up the design calculation for each of the selected design states; 3.3. Design of multispecific binding interface sequences; 3.4. Design sequences with single specificity; 3.5. Analyze the results; 3.6. Example: Multistate protein design in CaM-target interactions; 4. Summary; Acknowledgments; References

Chapter Four: Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations1. Introduction; 2. Rosetta Moves to Model Alternative Conformations in X-Ray Density; 2.1. Modeling the Richardson backrub in Rosetta; 2.2. Modeling the response to mutations; 2.3. Discovering and modeling alternative conformations from X-ray data; 2.4. Sampling functional alternative conformations in Cyclophilin A; 3. Sequence Plasticity and Conformational Plasticity are Intertwined; 3.1. Modeling peptide binding specificity; 3.2. Covariation and interface design in two-component signaling

Backrub ensemble generation

Notes:

Includes bibliographical references and indexes.

"ISSN: 0076-6879."

ISBN:

9780123946294

0123946298

9781299160071

1299160077

OCLC:

881096601