Methods in Protein Design

Contributors

Preface

Methods in Enzymology

Chapter One. Computational Design of Novel Protein Binders and Experimental Affinity Maturation

Abstract

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

References

Chapter Two. Mining Tertiary Structural Motifs for Assessment of Designability

Abstract

1 Introduction

2 MaDCaT

3 Quantifying Designability

4 Further Developments

5 Summary

Acknowledgments

References

Chapter Three. Computational Methods for Controlling Binding Specificity

Abstract

1 Introduction

2 Narrowing Down Binding Specificity

3 Broadening Binding Specificity

4 Summary

Acknowledgments

References

Chapter Four. Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations

Abstract

1 Introduction

2 Rosetta Moves to Model Alternative Conformations in X-Ray Density

3 Sequence Plasticity and Conformational Plasticity are Intertwined

4 Future Challenges

Acknowledgments

References

Chapter Five. OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms

Abstract

1 Introduction

2 OSPREY Design Principles

3 Applications of OSPREY

4 Protein Design in OSPREY

5 Example: Predicting Drug Resistance Mutations Using OSPREY

6 Future Directions and Availability

Acknowledgments

References

Chapter Six. Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement

Abstract

1 Introduction

2 Energy Function Model

3 Feature Analysis

4 Maximum Likelihood Parameter Estimation with optE

5 Large-Scale Benchmarks

6 Three Proposed Changes to the Rosetta Energy Function

7 Conclusion

Acknowledgments

References

Chapter Seven. Molecular Dynamics Simulations for the Ranking, Evaluation, and Refinement of Computationally Designed Proteins

Abstract

1 Introduction

2 Inside-Out Computational Enzyme Design

3 Filtering, Ranking, and Evaluation of Final Designs

4 Discerning Active from Inactive Designs with MD

5 MD Evaluation Examples

6 MD Refinement Examples

7 Molecular Dynamics Simulations: Preparation and Setup

8 Conclusions

Acknowledgments

References

Chapter Eight. Multistate Protein Design Using CLEVER and CLASSY

Abstract

1 Introduction: Accomplishments and Limitations of Structure-Based Design

2 Theory

3 Benefits Offered by Cluster Expansion in Protein Modeling and Design

4 How to Run a Cluster Expansion with CLEVER 1.0

5 GenSeqs

6 CETrFILE

7 CEEnergy

8 Cluster Expansion Case Study

9 Using Cluster Expansion with Integer Linear Programming

10 CLASSY Applied to Multistate Design

11 Conclusion

Acknowledgments

References

Chapter Nine. Using Analyses of Amino Acid Coevolution to Understand Protein Structure and Function

Abstract

1 Introduction

2 Predicting Specificity Determining Residues Using MI

3 Concluding Remarks

Acknowledgments

References

Chapter Ten. Evolution-Based Design of Proteins

Abstract

1 Introduction

2 SCA: The Pattern of Evolutionary Constraint in Proteins

3 SCA-Based Protein Design

4 SCA-Based Parsing of Protein Stability and Function

5 Future Monte Carlo Strategies for Exploring Sequence Space

6 Conclusion

Acknowledgments

References

Chapter Eleven. Protein Engineering and Stabilization from Sequence Statistics: Variation and Covariation Analysis

Abstract

1 Introduction

2 Case Study: BPTI

3 Acquiring an MSA

4 Relative Entropies: Quantifying the Degree of Positional Variation

5 Mutual Information: Quantifying the Degree of Covariation

6 Protocol for Predicting Stabilizing Mutations

7 Summary

References

Chapter Twelve. Enzyme Engineering by Targeted Libraries

Abstract

1 Introduction

2 Screening Versus Selection

3 The Merits of a Direct Screen: The Nerve Agent-Detoxifying Enzymes

4 Hedging the Bets: Mutational Spiking Approaches

5 Rational and Analytical Library Designs

6 Summary

References

Chapter Thirteen. Generation of High-Performance Binding Proteins for Peptide Motifs by Affinity Clamping

Abstract

1 Introduction

2 The Affinity Clamping Concept

3 Design of Affinity Clamps

4 Production and Characterization of Affinity Clamps

5 Applications of Affinity Clamps

6 Conclusion

Acknowledgments

References

Chapter Fourteen. Engineering Fibronectin-Based Binding Proteins by Yeast Surface Display

Abstract

1 Introduction

2 Engineering and Screening Approach of Fn3s

3 Analysis of Individual Clones

4 Summary

Acknowledgments

References

Chapter Fifteen. Engineering and Analysis of Peptide-Recognition Domain Specificities by Phage Display and Deep Sequencing

Abstract

1 Introduction

2 Directed Evolution of PDZ Variants

3 Peptide Profiling of PDZ Variants

4 Summary

Acknowledgment

References

Chapter Sixteen. Efficient Sampling of SCHEMA Chimera Families to Identify Useful Sequence Elements

Abstract

1 Introduction

2 SCHEMA Chimera Family Design Overview

3 Prediction of Thermostable Chimeras by Linear Regression Modeling

4 Summary

Acknowledgments

References

Chapter Seventeen. Protein Switch Engineering by Domain Insertion

Abstract

1 Introduction

2 Creation of Random Double-Stranded Breaks in Plasmids Containing the Acceptor DNA

3 Repair, Purification and Dephosphorylation of Acceptor DNA

4 Preparation of Insert DNA

5 Ligation, Transformation, Recovery, and Storage of the Library

6 Characterization of the Library

Acknowledgments

References

Chapter Eighteen. Design of Chimeric Proteins by Combination of Subdomain-Sized Fragments

Abstract

1 Introduction

2 Selecting the Starting Structures for Chimera Design

3 Evaluation and Optimization of the Chimera

4 Summary and Final Considerations

References

Chapter Nineteen. α-Helix Mimicry with α/β-Peptides

Abstract

1 Introduction

2 Helical Secondary Structures from β-Peptides and α/β-Peptides

3 Biological Function from Helical β-Peptides

4 α-Helix Mimicry with α/β-Peptides

5 Toward a General Approach for α-Helix Mimicry with Protease-Resistant α/β-Peptides

Acknowledgments

References

Author Index

Subject Index