Biocalorimetry 2 Applications of Calorimetry

Following the success of the first edition, this latest book covers all the latest advances in biocalorimetry. High sensitivity calorimeters are now common in most laboratories that require measurement of thermodynamic parameters associated with biomolecular interactions and stability. They are used to investigate interactions among drugs, proteins and nucleic acids as well as DNA and protein stability. Biocalorimetry is being applied increasingly to high-throughput compound screening and kinetic analysis. Written by leading experts in the field, this indispensable reference covers advances in instrumentation, applications and methodology, and features new developments in the measurement of small samples and in high-throughput screening. The book also includes sections with clearly described protocols for experiments and will therefore be of interest not only to researchers in the field, but also to undergraduate students.

John Edward Simon Durham Ladbury

Welcome Trust Senior Research Fellow/Honorary Senior Lecturer, Department of Biochemistry & Molecular Biology, University College London

Preface

xi

List of Contributors

xiii

Part I General Introduction

1

(34)

Applications of Biocalorimetry: Binding, Stability and Enzyme Kinetics

3

(32)

Ronan O'Brien

Ihtshamul Haq

Introduction

3

(4)

Principles of isothermal titration calorimetry (ITC)

7

(1)

Applications of ITC in the life sciences

8

(2)

Thermodynamic signatures of non-covalent interactions

10

(1)

Thermodynamic discrimination (TD)

10

(3)

ITC as a tool for studying drug-DNA interactions

13

(2)

ITC as a tool for studying protein-DNA interactions

15

(2)

The application of calorimetry for examining hydration effects

17

(1)

The use of ITC for studying the kinetics and thermodynamics of enzyme catalysis

18

(3)

Principles of differential scanning calorimetry (DSC)

21

(1)

Applications of DSC in the life sciences

22

(1)

Thermodynamic stability

23

(1)

Shelf life versus thermodynamic stability

24

(1)

Specific and non-specific binding

25

(1)

Intrinsic and extrinsic macromolecular stability

25

(1)

Oligomerization

25

(1)

The use of DSC for examining nucleic acid helix → coil transitions

26

(4)

Summary

30

(5)

Acknowledgements

30

(1)

References

31

(4)

Part II Isothermal Titration Calorimetry

35

(152)

Isothermal Titration Calorimetry: A Tutorial

37

(22)

James A. Thomson

John E. Ladbury

Introduction

37

(1)

Thermodynamic characterization

38

(2)

Instrumentation

40

(2)

Raw data

42

(1)

Basic considerations for experimental set-up

43

(7)

Data analysis

50

(3)

Summary

53

(6)

Application notes

53

(4)

Acknowledgement

57

(1)

References

57

(2)

The Application of Isothermal Titration Calorimetry to Drug Discovery

59

(22)

Geoff Holdgate

Stewart Fisher

Walter Ward

Introduction

59

(1)

Overview of the drug discovery process

60

(3)

Experimental measurement of thermodynamic binding parameters

63

(4)

ITC in drug discovery

67

(11)

Summary

78

(3)

References

78

(3)

Dissecting the Thermodynamics of DNA--Protein Interactions

81

(12)

Torleif Hard

Introduction

81

(1)

Model systems

82

(1)

Comparison with the hydrophobic effect

83

(1)

Protonation and charged-charged hydrogen bonds

84

(2)

Dissection of the binding entropy

86

(1)

Entropy contributions to the Sso7d-DNA interaction

87

(1)

Entropy contributions to the GCN4-DNA interaction

88

(2)

Discussion

90

(3)

Acknowledgements

90

(1)

References

90

(3)

Salt Effects in Ribonuclease-Ligand Interactions: Screening or Competitive Binding?

93

(14)

Kenneth P. Murphy

Travis T. Waldron

Greta L. Schrift

Introduction

93

(1)

Anion binding to a protein-protein complex

94

(2)

Charge-charge interactions in ribonuclease binding

96

(7)

Conclusions

103

(4)

Acknowledgement

104

(1)

References

104

(3)

Thermodynamics-Structure Correlations of Sulfonamide Inhibitor Binding to Carbonic Anhydrase

107

(26)

Daumantas Matulis

Matthew Todd

Introduction

107

(1)

Identification of protonation reactions occurring upon binding

108

(3)

Observed thermodynamics of inhibitor binding to CA

111

(8)

Energetics of inhibitor protonation

119

(4)

Sulfonamide `anion' binding thermodynamics

123

(2)

Correlations between structures and the thermodynamics of sulfonamide binding to CA

125

(6)

Conclusions

131

(2)

References

132

(1)

Energetics of the Interaction of Human Acidic Fibroblast Growth Factor with Heparin and the Functional Analogue Myo-Inositol Hexasulfate

133

(18)

Mercedes Guzman-Casado

Maria M. Garcia-Mira

Pedro Cano-Soldado

Guillermo Gimenez-Gallego

Jose M. Sanchez-Ruiz

Antonio Parody-Morreale

Introduction

133

(4)

Thermodynamic parameter derived from ITC experiments

137

(5)

Discussion

142

(9)

Acknowledgement

148

(1)

References

148

(3)

Thermodynamics of SH2 Domain Binding

151

(24)

Gabriel Waksman

Sangaralingam Kumaran

Olga Lubman

Introduction

151

(1)

SH2 domains and human pathologies

152

(3)

Structure and ligand binding

155

(11)

SH2-domain-binding inhibitors

166

(2)

Conclusions

168

(7)

References

169

(6)

Titration Calorimetry as a Tool to Determine Thermodynamic and Kinetic Parameters of Enzymes

175

(12)

M. Lucia Bianconi

Introduction

175

(2)

1CT of enzyme catalysed reactions

177

(7)

Summary

184

(3)

Acknowledgements

184

(1)

References

184

(3)

Part III Differential Scanning Calorimetry

187

(66)

Energetics of Site-Specific DNA Recognition by Integrase Tn916

189

(14)

Stoyan Milev

Hans Rudolf Bosshard

Ilian Jelesarov

Introduction

189

(1)

Conformational stability of INT-DBD and the target DNA duplex

190

(4)

Thermodynamics of complex formation measured by titration calorimetry

194

(1)

Thermal dissociation and unfolding of the protein-DNA complex

195

(3)

The heat capacity change of protein-DNA association

198

(3)

Discussion

201

(2)

References

202

(1)

Linkage Between Temperature and Chemical Denaturant Effects on Protein Stability: the Interpretation of Calorimetrically-Determined m Values

203

(12)

Beatriz Ibarra-Molero

Raul Perez-Jimenez

Raquel Godoy-Ruiz

Jose M. Sanchez-Ruiz

Introduction

203

(2)

Linkage between temperature and chemical denaturant effects on protein stability

205

(3)

Calorimetrically determined urea m values

208

(2)

Calorimetrically determined guanidine m values

210

(2)

Concluding remarks

212

(3)

Acknowledgement

212

(1)

References

212

(3)

Thermodynamic Indications of the Molten Globule State of Cytochrome c Induced by Hydrophobic Salts

215

(16)

Ali A. Moosavi-Mohavedi

Jamshid Chamani

Introduction

215

(3)

Thermodynamic description of molten globule state

218

(3)

Molten globule structure detection by isothermal titration calorimetry (ITC)

221

(2)

Enthalpic relationship with electronic transfer of molten globule state

223

(2)

Indication of molten globule state by differential scanning calorimetry (DSC)

225

(6)

Acknowledgement

227

(1)

References

227

(4)

Microcalorimetry as Applied to Psychrophilic Enzymes

231

(10)

Salvino D'Amico

Daphne Georlette

Tony Collins

Georges Feller

Charles Gerday

Introduction

231

(1)

Cold adaptation

231

(2)

Uniformly unstable enzymes

233

(1)

Enzymes with local flexibility

234

(2)

Thermal inactivation recorded by isothermal titration calorimetry

236

(2)

Microcalorimetric determination of enzyme kinetic parameters

238

(1)

Conclusion

239

(2)

References

240

(1)

An Autosampling Differential Scanning Calorimeter for Study of Biomolecular Interactions

241

(12)

Valerian Plotnikov

Andrew Rochalski

Michael Brandts

John F. Brandts

Samuel Williston

Verna Frasca

Lung-Nan Lin

Introduction to DSC

241

(1)

Description of instrument

242

(3)

Materials and methods

245

(1)

Results for ribonuclease binding to anionic inhibitors

246

(2)

Discussion

248

(5)

References

249

(1)

Appendix. Data analysis (reprinted from reference 10)

250

(3)

Index

253

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Biocalorimetry 2 Applications of Calorimetry in the Biological Sciences

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