Protein Design and Structure

Cover image

Title page

Table of Contents

Copyright

Contributors

Chapter One: Algorithms for protein design

Abstract

1: Introduction

2: Applications of protein design

3: Design goals

4: Target function design

5: Algorithms for protein design

6: Software

7: Discussion

8: Conclusion

Acknowledgments

References

Chapter Two: Computational prediction of protein functional sites—Applications in biotechnology and biomedicine

Abstract

1: Introduction

2: Sequence-based approaches

3: Structure-based approaches

4: Machine learning

5: Conclusions and future trends

Acknowledgments

References

Chapter Three: Structure and chemistry of enzymatic active sites that play a role in the switch and conformation mechanism

Abstract

1: Introduction

2: Proteins as drug targets

3: Protein conformations

4: Enzymes in reaction mechanism

5: Enzymes active site

6: Metal and ion oriented active site

7: Substrate binding models

8: Understanding allosteric site and active site

9: Role of charges in active site

10: Reported proteins with active site switches

11: Open and closed conformation in active sites

12: Conformational changes in active sites

13: Role of water in active site

14: Future prospectus

Acknowledgment

References

Chapter Four: Accelerating therapeutic protein design

Abstract

1: Introduction

2: Computational design of protein drugs

3: Advances in computational design of therapeutic proteins

4: Outstanding challenges in protein design

5: Perspectives on accelerating therapeutic protein design

6: Conclusions

Acknowledgments

References

Chapter Five: Aromatic interactions directing peptide nano-assembly

Abstract

1: Introduction

2: Aromatic interactions in biomolecules

3: History of aromatic stacking

4: Mechanism of amyloid formation through aromatic π–π stacking

5: Strategies adopted and types of building blocks for the construction of bioorganic nanoassemblies

6: Nanostructures formed through aromatic π–π interactions

7: Factors controlling stimulus-response and the formation of nanoassemblies

8: Physical properties of Nanoassemblies

9: Applications

10: Conclusions and future directions

References

Chapter Six: Understanding binding affinity and specificity of modular protein domains: A focus in ligand design for the polyproline-binding families

Abstract

1: Modular domains for protein recognition

2: Modular domains for the recognition of proline-rich sequences

3: High-throughput screening strategies for the design of binding partners for polyproline-binding domains

4: Rational design of ligands for polyproline-binding domains

References

Chapter Seven: The structural basis of histone modifying enzyme specificity and promiscuity: Implications for metabolic regulation and drug design

Abstract

1: The structure of histone modifying enzymes

2: Small molecule inhibitors of histone modifying enzymes

3: Discovery of small molecule and metabolite inhibitors of histone modifying enzymes

4: Discussion

References

Chapter Eight: Designing synthetic transcription factors: A structural perspective

Abstract

1: Introduction

2: General principles of de novo protein designing

3: Synthetic structural biology

4: General grammar for the structural assembly of STFs

5: STF designs involving zinc fingers

6: STF designs involving basic leucine zippers

7: STF designs involving helix-turn-helix

8: STF designs involving homeodomains

9: Applications of TFs in genetic circuit design

10: Conclusion

References

Chapter Nine: Recent advances in structural studies of 14-3-3 protein complexes

Abstract

1: Introduction

2: Nomenclature, structure, and functioning of 14-3-3

3: Approaches to obtain 14-3-3 complexes for structural studies

4: Crystal structures of 14-3-3 complexes with partner proteins

5: Cryoelectron microscopy structures of 14-3-3 complexes

6: The protein-peptide binding approach in studying 14-3-3 complexes

7: Chimeric 14-3-3 proteins with phosphorylated peptides

8: 14-3-3 studies by nuclear magnetic resonance

9: Conclusions

Acknowledgments

References

Chapter Ten: Immunosafe(r)-by-design nanoparticles: Molecular targets and cell signaling pathways in a next-generation model proxy for humans

Abstract

1: Safe(r)-by-design concept for nanoparticle development: Immunological point of view

2: Bio-corona: An important issue in nano-immune interactions

3: Nanoparticle surface functionalization for biomedical use

4: The innate immunity of the sea urchin from the human perspective

5: The sea urchin Paracentrotus lividus: A next-generation model to study the immunosafety of nanoparticles

6: Insights into the molecular targets and cell signaling pathways involved in immune-nanoparticle recognition/interaction of the sea urchin Paracentrotus lividus

7: Concluding remarks

References

Chapter Eleven: Mutations in G6PC2 gene with increased risk for development of type 2 diabetes: Understanding via computational approach

Abstract

1: Introduction

2: Materials and methods

3: Results and discussion

4: Conclusion

References

Chapter Twelve: Computational structural assessment of BReast CAncer type 1 susceptibility protein (BRCA1) and BRCA1-Associated Ring Domain protein 1 (BARD1) mutations on the protein-protein interface

Abstract

1: Introduction

2: Materials and methods

3: Results

4: Discussion

5: Conclusion

References

Chapter Thirteen: Evolutionary aspect of Miltefosine transporter proteins in Leishmania major

Abstract

1: Introduction

2: Methodology

3: Results

4: Discussion

References