Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering.
It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application.
1. Title of Book - p. i 2. Cover image - p. i 3. Title page - p. ii 4. Table of Contents - p. iii 5. Copyright - p. iii 6. Dedicated to - p. iii 7. Contributors - p. xix 8. About the Editors - p. xxii 9. Foreword - p. xxii 10. Preface - p. xxvii 11. Strategies to improve the expression and solubility of recombinant proteins in E. coli - p. 1 12. Chapter 2. Advances in heterologous protein expression strategies in yeast and insect systems - p. 13 13. Chapter 3. Methods for transient expression and purification of monoclonal antibodies in mammalian cells - p. 31 14. Chapter 4. Methods for recombinant production and purification of intrinsically disordered proteins - p. 41 15. Chapter 5. Methods to determine the oligomeric structure of proteins - p. 49 16. Chapter 6. Multimodal methods to study protein aggregation and fibrillation - p. 77 17. Chapter 7. Experimental methods to study the thermodynamics of protein–protein interactions - p. 103 18. Chapter 8. Experimental methods to study the kinetics of protein–protein interactions - p. 115 19. Chapter 9. Computational techniques for studying protein-protein interactions - p. 125 20. Chapter 10. Experimental methods to study protein–nucleic acid interactions - p. 137 21. Chapter 11. Advanced computational tools for quantitative analysis of protein–nucleic acid interfaces - p. 163 22. Chapter 12. Experimental techniques to study protein dynamics and conformations - p. 181 23. Chapter 13. Computational techniques to study protein dynamics and conformations - p. 199 24. Chapter 14. Application of circular dichroism spectroscopy in studying protein folding, stability, and interaction - p. 213 25. Chapter 15. Studying protein-folding dynamics using single-molecule fluorescence methods - p. 225 26. Chapter 16. Advances in liquid-state NMR spectroscopy to study the structure, function, and dynamics of biomacromolecules - p. 237 27. In-cell NMR spectroscopy: A tool to study cellular structure biology - p. 271 28. Chapter 18. Current trends in membrane protein crystallography - p. 277 29. Chapter 19. Advances in sample preparation and data processing for single-particle cryo-electron microscopy - p. 291 30. Chapter 20. Advanced mass spectrometry-based methods for protein molecular-structural biologists - p. 311 31. Chapter 21. Developments, advancements, and contributions of mass spectrometry in omics technologies - p. 327 32. Chapter 22. Role of structural biology methods in drug discovery - p. 360 33. Chapter 23. Prediction, validation, and analysis of protein structures: A beginner’s guide - p. 373 34. Chapter 24. Advances in structure-based virtual screening for drug discovery - p. 387 35. Chapter 25. Methods and applications of machine learning in structure-based drug discovery - p. 409 36. Chapter 26. Molecular dynamics simulations: Principles, methods, and applications in protein conformational dynamics - p. 439 37. Chapter 27. Applications of molecular dynamics simulations in drug discovery - p. 455 38. Chapter 28. Envisaging the conformational space of proteins by coupling machine learning and molecular dynamics - p. 472 39. Chapter 29. Immunoinformatics and reverse vaccinology methods to design peptide-based vaccines - p. 477 40. Chapter 30. Computational methods to study intrinsically disordered proteins - p. 489 41. Chapter 31. Experimental methods to study intrinsically disordered proteins - p. 505 42. Chapter 32. Analysis of structure and dynamics of intrinsically disordered regions in proteins using solution NMR methods - p. 535 43. Chapter 33. Methods to study the effect of solution variables on the conformational dynamics of intrinsically disordered proteins - p. 551 44. Chapter 34. Molecular simulations to study IDP-IDP interactions and their complexes - p. 565 45. Chapter 35. Exploring large-scale protein function using systematic mutant analysis - p. 580 46. Chapter 36. Approaches and methods to study cell signaling: Linguistics of cellular communication - p. 589 47. Chapter 37. Methods to study systems biology of signaling networks: A case study of NSCLC - p. 625 48. Chapter 38. Advancements in the analysis of protein post-translational modifications - p. 635 49. Chapter 39. Protein engineering: Methods and applications - p. 657 50. Chapter 40. Designer 3D-DNA nanodevices: Structures, functions, and cellular applications - p. 669 51. Index - p. 677
Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering.
It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application.
1. Title of Book - p. i 2. Cover image - p. i 3. Title page - p. ii 4. Table of Contents - p. iii 5. Copyright - p. iii 6. Dedicated to - p. iii 7. Contributors - p. xix 8. About the Editors - p. xxii 9. Foreword - p. xxii 10. Preface - p. xxvii 11. Strategies to improve the expression and solubility of recombinant proteins in E. coli - p. 1 12. Chapter 2. Advances in heterologous protein expression strategies in yeast and insect systems - p. 13 13. Chapter 3. Methods for transient expression and purification of monoclonal antibodies in mammalian cells - p. 31 14. Chapter 4. Methods for recombinant production and purification of intrinsically disordered proteins - p. 41 15. Chapter 5. Methods to determine the oligomeric structure of proteins - p. 49 16. Chapter 6. Multimodal methods to study protein aggregation and fibrillation - p. 77 17. Chapter 7. Experimental methods to study the thermodynamics of protein–protein interactions - p. 103 18. Chapter 8. Experimental methods to study the kinetics of protein–protein interactions - p. 115 19. Chapter 9. Computational techniques for studying protein-protein interactions - p. 125 20. Chapter 10. Experimental methods to study protein–nucleic acid interactions - p. 137 21. Chapter 11. Advanced computational tools for quantitative analysis of protein–nucleic acid interfaces - p. 163 22. Chapter 12. Experimental techniques to study protein dynamics and conformations - p. 181 23. Chapter 13. Computational techniques to study protein dynamics and conformations - p. 199 24. Chapter 14. Application of circular dichroism spectroscopy in studying protein folding, stability, and interaction - p. 213 25. Chapter 15. Studying protein-folding dynamics using single-molecule fluorescence methods - p. 225 26. Chapter 16. Advances in liquid-state NMR spectroscopy to study the structure, function, and dynamics of biomacromolecules - p. 237 27. In-cell NMR spectroscopy: A tool to study cellular structure biology - p. 271 28. Chapter 18. Current trends in membrane protein crystallography - p. 277 29. Chapter 19. Advances in sample preparation and data processing for single-particle cryo-electron microscopy - p. 291 30. Chapter 20. Advanced mass spectrometry-based methods for protein molecular-structural biologists - p. 311 31. Chapter 21. Developments, advancements, and contributions of mass spectrometry in omics technologies - p. 327 32. Chapter 22. Role of structural biology methods in drug discovery - p. 360 33. Chapter 23. Prediction, validation, and analysis of protein structures: A beginner’s guide - p. 373 34. Chapter 24. Advances in structure-based virtual screening for drug discovery - p. 387 35. Chapter 25. Methods and applications of machine learning in structure-based drug discovery - p. 409 36. Chapter 26. Molecular dynamics simulations: Principles, methods, and applications in protein conformational dynamics - p. 439 37. Chapter 27. Applications of molecular dynamics simulations in drug discovery - p. 455 38. Chapter 28. Envisaging the conformational space of proteins by coupling machine learning and molecular dynamics - p. 472 39. Chapter 29. Immunoinformatics and reverse vaccinology methods to design peptide-based vaccines - p. 477 40. Chapter 30. Computational methods to study intrinsically disordered proteins - p. 489 41. Chapter 31. Experimental methods to study intrinsically disordered proteins - p. 505 42. Chapter 32. Analysis of structure and dynamics of intrinsically disordered regions in proteins using solution NMR methods - p. 535 43. Chapter 33. Methods to study the effect of solution variables on the conformational dynamics of intrinsically disordered proteins - p. 551 44. Chapter 34. Molecular simulations to study IDP-IDP interactions and their complexes - p. 565 45. Chapter 35. Exploring large-scale protein function using systematic mutant analysis - p. 580 46. Chapter 36. Approaches and methods to study cell signaling: Linguistics of cellular communication - p. 589 47. Chapter 37. Methods to study systems biology of signaling networks: A case study of NSCLC - p. 625 48. Chapter 38. Advancements in the analysis of protein post-translational modifications - p. 635 49. Chapter 39. Protein engineering: Methods and applications - p. 657 50. Chapter 40. Designer 3D-DNA nanodevices: Structures, functions, and cellular applications - p. 669 51. Index - p. 677
