Computational Approaches to Protein Dynamics

Computational Approaches to Protein Dynamics

by Monika Fuxreiter
Released December 2014
Publisher(s): CRC Press
ISBN: 9781482297867

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Book description

The Latest Developments on the Role of Dynamics in Protein Functions

Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, and biology show how these advanced methods provide insights into dynamic aspects of biochemical processes. A particular focus is on intrinsically disordered proteins (IDPs), which lack a well-defined three-dimensional structure and function as dynamic ensembles.

The book covers a wide spectrum of dynamics, from electronic structure-based to coarse-grained techniques via multiscaling at different levels. After an introduction to dynamics and historical overview of basic methodologies, the book addresses the following issues:

  • Is there a quantitative relationship between enzymatic catalysis and protein dynamics?
  • Which are the functionally relevant motions of proteins?
  • How can structural properties and partner recognition mechanisms of IDPs be simulated?
  • How can we speed up molecular dynamics?
  • How can we describe conformational ensembles by the synergistic effort of computations and experiments?

While dynamics is now considered essential for interpreting protein action, it is not yet an integral component in establishing structure–function relationships of proteins. Helping to reshape this classical view in biochemistry, this groundbreaking book explores advances in computational methodology and contributes to the new, ensemble way of studying proteins.

Table of contents

  1. Front Cover (1/2)
  2. Front Cover (2/2)
  3. Contents
  4. Series Preface
  5. Foreword
  6. Preface
  7. Acknowledgments
  8. Editor
  9. Contributors (1/2)
  10. Contributors (2/2)
  11. Chapter 1: Dynamics : A Key to Protein Function (1/8)
  12. Chapter 1: Dynamics : A Key to Protein Function (2/8)
  13. Chapter 1: Dynamics : A Key to Protein Function (3/8)
  14. Chapter 1: Dynamics : A Key to Protein Function (4/8)
  15. Chapter 1: Dynamics : A Key to Protein Function (5/8)
  16. Chapter 1: Dynamics : A Key to Protein Function (6/8)
  17. Chapter 1: Dynamics : A Key to Protein Function (7/8)
  18. Chapter 1: Dynamics : A Key to Protein Function (8/8)
  19. Chapter 2: Adaptive and Accurate Force-Based QM/MM Calculations (1/4)
  20. Chapter 2: Adaptive and Accurate Force-Based QM/MM Calculations (2/4)
  21. Chapter 2: Adaptive and Accurate Force-Based QM/MM Calculations (3/4)
  22. Chapter 2: Adaptive and Accurate Force-Based QM/MM Calculations (4/4)
  23. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (1/14)
  24. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (2/14)
  25. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (3/14)
  26. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (4/14)
  27. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (5/14)
  28. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (6/14)
  29. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (7/14)
  30. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (8/14)
  31. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (9/14)
  32. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (10/14)
  33. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (11/14)
  34. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (12/14)
  35. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (13/14)
  36. Chapter 3: Conformational and Chemical Landscapes of Enzyme Catalysis (14/14)
  37. Chapter 4: Interplay between Enzyme Function and Protein Dynamics : A Multiscale Approach to the Study of the NAG Kinase Family and Two Class II Aldolases (1/6)
  38. Chapter 4: Interplay between Enzyme Function and Protein Dynamics : A Multiscale Approach to the Study of the NAG Kinase Family and Two Class II Aldolases (2/6)
  39. Chapter 4: Interplay between Enzyme Function and Protein Dynamics : A Multiscale Approach to the Study of the NAG Kinase Family and Two Class II Aldolases (3/6)
  40. Chapter 4: Interplay between Enzyme Function and Protein Dynamics : A Multiscale Approach to the Study of the NAG Kinase Family and Two Class II Aldolases (4/6)
  41. Chapter 4: Interplay between Enzyme Function and Protein Dynamics : A Multiscale Approach to the Study of the NAG Kinase Family and Two Class II Aldolases (5/6)
  42. Chapter 4: Interplay between Enzyme Function and Protein Dynamics : A Multiscale Approach to the Study of the NAG Kinase Family and Two Class II Aldolases (6/6)
  43. Chapter 5: Simplified Flexibility Analysis of Proteins (1/6)
  44. Chapter 5: Simplified Flexibility Analysis of Proteins (2/6)
  45. Chapter 5: Simplified Flexibility Analysis of Proteins (3/6)
  46. Chapter 5: Simplified Flexibility Analysis of Proteins (4/6)
  47. Chapter 5: Simplified Flexibility Analysis of Proteins (5/6)
  48. Chapter 5: Simplified Flexibility Analysis of Proteins (6/6)
  49. Chapter 6: ABSINTH Implicit Solvation Model and Force Field Paradigm for Use in Simulations of Intrinsically Disordered Proteins (1/5)
  50. Chapter 6: ABSINTH Implicit Solvation Model and Force Field Paradigm for Use in Simulations of Intrinsically Disordered Proteins (2/5)
  51. Chapter 6: ABSINTH Implicit Solvation Model and Force Field Paradigm for Use in Simulations of Intrinsically Disordered Proteins (3/5)
  52. Chapter 6: ABSINTH Implicit Solvation Model and Force Field Paradigm for Use in Simulations of Intrinsically Disordered Proteins (4/5)
  53. Chapter 6: ABSINTH Implicit Solvation Model and Force Field Paradigm for Use in Simulations of Intrinsically Disordered Proteins (5/5)
  54. Chapter 7: Intrinsically Disordered Protein : A Thermodynamic Perspective (1/6)
  55. Chapter 7: Intrinsically Disordered Protein : A Thermodynamic Perspective (2/6)
  56. Chapter 7: Intrinsically Disordered Protein : A Thermodynamic Perspective (3/6)
  57. Chapter 7: Intrinsically Disordered Protein : A Thermodynamic Perspective (4/6)
  58. Chapter 7: Intrinsically Disordered Protein : A Thermodynamic Perspective (5/6)
  59. Chapter 7: Intrinsically Disordered Protein : A Thermodynamic Perspective (6/6)
  60. Chapter 8: Long Molecular Dynamics Simulations of Intrinsically Disordered Proteins Reveal Preformed Structural Elements for Target Binding (1/5)
  61. Chapter 8: Long Molecular Dynamics Simulations of Intrinsically Disordered Proteins Reveal Preformed Structural Elements for Target Binding (2/5)
  62. Chapter 8: Long Molecular Dynamics Simulations of Intrinsically Disordered Proteins Reveal Preformed Structural Elements for Target Binding (3/5)
  63. Chapter 8: Long Molecular Dynamics Simulations of Intrinsically Disordered Proteins Reveal Preformed Structural Elements for Target Binding (4/5)
  64. Chapter 8: Long Molecular Dynamics Simulations of Intrinsically Disordered Proteins Reveal Preformed Structural Elements for Target Binding (5/5)
  65. Chapter 9: Multiscale Simulations of Large Conformational Changes of Disordered and Ordered Proteins Induced by Their Partners (1/6)
  66. Chapter 9: Multiscale Simulations of Large Conformational Changes of Disordered and Ordered Proteins Induced by Their Partners (2/6)
  67. Chapter 9: Multiscale Simulations of Large Conformational Changes of Disordered and Ordered Proteins Induced by Their Partners (3/6)
  68. Chapter 9: Multiscale Simulations of Large Conformational Changes of Disordered and Ordered Proteins Induced by Their Partners (4/6)
  69. Chapter 9: Multiscale Simulations of Large Conformational Changes of Disordered and Ordered Proteins Induced by Their Partners (5/6)
  70. Chapter 9: Multiscale Simulations of Large Conformational Changes of Disordered and Ordered Proteins Induced by Their Partners (6/6)
  71. Chapter 10: Coarse-Grained Simulation of Intrinsically Disordered Proteins (1/5)
  72. Chapter 10: Coarse-Grained Simulation of Intrinsically Disordered Proteins (2/5)
  73. Chapter 10: Coarse-Grained Simulation of Intrinsically Disordered Proteins (3/5)
  74. Chapter 10: Coarse-Grained Simulation of Intrinsically Disordered Proteins (4/5)
  75. Chapter 10: Coarse-Grained Simulation of Intrinsically Disordered Proteins (5/5)
  76. Chapter 11: Natural and Directed Evolution of Intrinsically Disordered Proteins (1/7)
  77. Chapter 11: Natural and Directed Evolution of Intrinsically Disordered Proteins (2/7)
  78. Chapter 11: Natural and Directed Evolution of Intrinsically Disordered Proteins (3/7)
  79. Chapter 11: Natural and Directed Evolution of Intrinsically Disordered Proteins (4/7)
  80. Chapter 11: Natural and Directed Evolution of Intrinsically Disordered Proteins (5/7)
  81. Chapter 11: Natural and Directed Evolution of Intrinsically Disordered Proteins (6/7)
  82. Chapter 11: Natural and Directed Evolution of Intrinsically Disordered Proteins (7/7)
  83. Chapter 12: Discrete Molecular Dynamics : Foundations and Biomolecular Applications (1/6)
  84. Chapter 12: Discrete Molecular Dynamics : Foundations and Biomolecular Applications (2/6)
  85. Chapter 12: Discrete Molecular Dynamics : Foundations and Biomolecular Applications (3/6)
  86. Chapter 12: Discrete Molecular Dynamics : Foundations and Biomolecular Applications (4/6)
  87. Chapter 12: Discrete Molecular Dynamics : Foundations and Biomolecular Applications (5/6)
  88. Chapter 12: Discrete Molecular Dynamics : Foundations and Biomolecular Applications (6/6)
  89. Chapter 13: Use of Ensemble Methods to Describe Biomolecular Dynamics by Small Angle X-Ray Scattering (1/8)
  90. Chapter 13: Use of Ensemble Methods to Describe Biomolecular Dynamics by Small Angle X-Ray Scattering (2/8)
  91. Chapter 13: Use of Ensemble Methods to Describe Biomolecular Dynamics by Small Angle X-Ray Scattering (3/8)
  92. Chapter 13: Use of Ensemble Methods to Describe Biomolecular Dynamics by Small Angle X-Ray Scattering (4/8)
  93. Chapter 13: Use of Ensemble Methods to Describe Biomolecular Dynamics by Small Angle X-Ray Scattering (5/8)
  94. Chapter 13: Use of Ensemble Methods to Describe Biomolecular Dynamics by Small Angle X-Ray Scattering (6/8)
  95. Chapter 13: Use of Ensemble Methods to Describe Biomolecular Dynamics by Small Angle X-Ray Scattering (7/8)
  96. Chapter 13: Use of Ensemble Methods to Describe Biomolecular Dynamics by Small Angle X-Ray Scattering (8/8)
  97. Chapter 14: Bridging Experiments and Simulations : Structure Calculations with a Dynamical Touch (1/6)
  98. Chapter 14: Bridging Experiments and Simulations : Structure Calculations with a Dynamical Touch (2/6)
  99. Chapter 14: Bridging Experiments and Simulations : Structure Calculations with a Dynamical Touch (3/6)
  100. Chapter 14: Bridging Experiments and Simulations : Structure Calculations with a Dynamical Touch (4/6)
  101. Chapter 14: Bridging Experiments and Simulations : Structure Calculations with a Dynamical Touch (5/6)
  102. Chapter 14: Bridging Experiments and Simulations : Structure Calculations with a Dynamical Touch (6/6)
  103. Back Cover

Product information

  • Title: Computational Approaches to Protein Dynamics
  • Author(s): Monika Fuxreiter
  • Release date: December 2014
  • Publisher(s): CRC Press
  • ISBN: 9781482297867