Protein-Ligand Interactions Structure and Spectroscopy

by Harding, Stephen E.; Chowdhry, Babur Z.

ISBN13: 9780199637508

ISBN10: 0199637504

Format: Hardcover

Pub. Date: 2001-03-22

Publisher(s): Oxford University Press

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Summary

The two Practical Approach volumes on protein-ligand interaction do not comprise a comprehensive compilation of all the methods that can be used to investigate protein-ligand interactions. Instead, they are a selection of the most useful and easily applied methods and will be an invaluableguide to the principal techniques used to study the interactions of proteins and ligands. This second volume covers the major spectroscopic methods: FTIR, Raman, and fluorescence spectroscopy; circular dichroism, NMR, mass spectrometry, atomic force microscopy, and the use of paramagnetic probes.There are also chapters on X-ray crystallography and molecular modelling. Hydrodynamic and calorimetric techniques are covered in volume one. Both volumes are available individually, or as a set. Both volumes are written from a practical standpoint to be applicable to both academic and industrialscientists wishing to characterize protein-ligand systems by using a multi-disciplinary approach.

List of protocols

xvii

Abbreviations

xxi

X-ray crystallographic studies of protein-ligand interactions

(98)

Rex A. Palmer

Introduction

(1)

Crystallization of proteins and complexes for X-ray analysis

(18)

Introduction

(3)

Crystallization of proteins

(1)

Practical considerations

(10)

Crystal mounting for X-ray data collection

(1)

Trouble shooting

(1)

Protein-ligand complex crystals

(2)

Crystal geometry and symmetry

(10)

The crystal lattice

(8)

Symmetry elements, crystal systems, and space groups

(2)

X-ray diffraction from crystals

(8)

Bragg's treatment of X-ray diffraction: the location of diffraction maxima

(2)

The reciprocal lattice concept defining the location of diffraction maxima

(2)

The structure factor F(hkl): X-ray intensities I(hkl)

(3)

Calculated structure factors and R-factors

(1)

Recording and measurement of X-ray diffraction patterns

(9)

X-ray sources

(1)

Recording and measuring intensity data

(5)

Image plate data processing

(3)

Preliminary crystal data

(6)

Determination of unit cell and space group

(2)

Resolution

(1)

Number of reflections in the data set

(1)

Completeness of a data set at a given resolution

(1)

Internal consistency

(1)

Number of molecules per unit cell

(3)

Electron density: reconstruction of the molecular structure

(3)

Basic principles

(1)

Properties of the electron density

(1)

Complementarity of the structure factor F(hkl) and electron density p(x, y, x)

(1)

Difference electron density functions

(1)

Patterson's Fourier series: the Patterson function P(uvw)

(2)

Properties of the Patterson function

(1)

Determination of the phases &phis;(hkl) for protein crystals

(19)

Introduction

(1)

Isomorphous replacement (IR)

(1)

Heavy atoms and compounds for isomorphous replacement

(1)

Preparation and screening of heavy atom derivatives

(1)

Phase determination in single isomorphous replacement (SIR)

(1)

Location of the heavy atoms

(1)

Phase determination in multiple isomorphous replacement (MIR)

(2)

Molecular replacement (MR)---the Sledgehammer

(11)

Use of phase information and density modification

(3)

What to do once phasing is acceptable

(1)

Structure refinement, ligand fitting, and geometry verification

(6)

Refinement

(1)

Fourier refinement and simulated annealing

(2)

Least squares refinement

(3)

Examples of protein-ligand complex studies

(13)

N-acetyl-DL-homocysteinyl ribonuclease derivatives: protein-ligand covalent modification

(1)

Environment of the SO42- ion and solvent waters in native bovine RNase A active site at 0.9 A resolution (18)

(1)

Enzyme-inhibitor interactions (non-covalent): r-rat RNase A binding with 2'-5-CpG (85)

(1)

Protein-carbohydrate interactions: the non-covalent sugar binding sites in the lectin MLI

(3)

Glycoproteins: covalently bound sugars and the [... Asn, X, Ser/Thr...] binding site; MLI B-chain Asn 136 sugar binding site (89)

(1)

Protein-steroid interactions: Fab' fragment of antibody DB3 bound to progesterone and progesterone-like steroids

(5)

Protein-nucleic acid interactions: procaryotic recognition of helix-turn-helix motifs in DNA (117)

(2)

Further recommended reading and software

(6)

Protein-peptide interactions: cyclophilin/cyclosporin complexes

(1)

Protein-protein interactions (e.g. protein-antibody): camel VH with lysozyme

(1)

Recommended books

(1)

International tables

(1)

Synchrotrons Web Page

(1)

Space group diagrams

(1)

Software for data processing

(1)

Software for Fourier and structure factor calculations

(1)

Software for MIR

(1)

Software for packing and molecular geometry

(1)

Software for graphics and model building

(1)

Software for molecular graphics and display

(1)

Software for refinement

(1)

Software for molecular dynamics and minimization

(1)

Databases

(1)

References

(4)

Molecular modelling

(24)

Romano T. Kroemer

Introduction

(1)

Protein structure prediction

100

(4)

Ab initio predictions

101

(1)

Threading, or fold recognition techniques

101

(1)

Homology (or comparative) modelling

101

(3)

Analysis of protein structures

104

(1)

Docking of ligands to proteins

105

(4)

Ab initio (de novo) ligand design

109

(5)

Active site preparation

110

(1)

Generation of structures

111

(1)

Evaluation of structures

112

(2)

Calculation of binding energies

114

(2)

Statistical analysis of a set of protein ligands

116

(1)

Concluding remarks

117

(6)

Acknowledgements

117

(1)

References

117

(6)

Circular dichroism

123

(46)

Alex F. Drake

Introduction

123

(3)

The ordinary absorption of light

126

(2)

The spectroscopic basis of circular dichroism

128

(4)

The circular dichroism spectrometer

132

(4)

The merits and uses of CD spectroscopy

136

(2)

Protein/peptide conformations as studied by CD spectroscopy

138

(7)

Instrumental measurement factors

143

(1)

Spectroscopic factors

143

(1)

Data analysis methods

144

(1)

Monitoring ligand binding by CD spectroscopy

145

(7)

Measurement conditions and instrumental parameters

146

(1)

Further aspects of the concentration used for absorption and CD measurements

147

(5)

Analysis of CD ligand binding titration studies

152

(12)

Case IA

153

(2)

Case IA'

155

(2)

Case IB

157

(1)

Case IB'

157

(3)

The effect of concentration on binding constant determination

160

(4)

CD kinetics---drug binding to proteins

164

(5)

References

166

(3)

Generic techniques for fluorescence measurements of protein-ligand interactions; real time kinetics and spatial imaging

169

(32)

Josep Cladera

Paul O'Shea

Introduction

169

(2)

Ligand-protein interactions revealed by intrinsic (tryptophan) fluorescence

171

(1)

Tryptophan fluorescence measurements to demonstrate ligand-protein interactions

172

(3)

Steady state tryptophan fluorescence quenching

172

(1)

Time-resolved fluorescence lifetime and anisotropy decay measurements of albumin

172

(3)

The surface electrostatic potential: one of the trinity of electrical membrane potentials

175

(1)

Membrane electrostatics: implementation of fluoresceinphosphatidylethanolamine (FPE) to measure ligand-receptor interactions of membranes

175

(4)

Labelling human cells with FPE

178

(1)

Location of FPE in the membrane

178

(1)

Digital imaging: using CCD fluorescence microscopy and confocal scanning laser fluorescence microscopy (CSLM) of ligand binding reactins of living cells

179

(1)

Fluorescent images corrected for probe disposition and photobleaching

180

(2)

Spatial imaging of the cell surface to identify localized ligand binding

182

(1)

Experimental protocols

182

(7)

Case studies

189

(9)

Ligand (oleate) binding to HAS revealed by tryptophan fluorescenece quenching

189

(1)

Kinetics of oleate-dependent fluorescence changes of HSA

190

(1)

Interactions of a signal peptide (p25) with model membranes

190

(3)

The interactions of serum albumin with B and T lymphocytes

193

(1)

Receptor-mediated membrane binding of albumin

193

(2)

Influence of interleukin-8 (IL-8) on the interaction of the gp41 fusion domain of HIV with T lymphocytes

195

(1)

The interaction of Alzheimer's peptides with B12 microgial cells

196

(2)

Quantitation of spatially localized interactions of ligands (albumin) with living cells

198

(1)

Conclusions

198

(3)

Acknowledgements

199

(1)

References

199

(2)

Stopped-flow techniques

201

(38)

John F. Eccleston

Jon P. Hutchinson

Howard D. White

Introduction

201

(1)

First- and second-order reactions

202

(4)

First-order irreversible reactions

202

(1)

Second-order irreversible reaction

203

(1)

First-order reversible reaction

204

(1)

Second-order reversible reactions

204

(2)

Principle of operation of the stopped-flow instrument

206

(2)

Testing the performance of a stopped-flow instrument

208

(4)

The mixing process

208

(1)

Mixing efficiency

208

(2)

Measurement of dead-time

210

(2)

Optimization of instrument

212

(4)

Lamp selection

212

(1)

Monochromator

212

(1)

Choice of emission filter

213

(1)

Stop volume

214

(1)

Time constant

215

(1)

Probes to monitor stopped-flow reactions

216

(2)

Intrinsic probes

216

(1)

Extrinsic probes

217

(1)

Measurement of association and dissociation rate constants

218

(4)

Initial consideration

218

(1)

Association reactions

219

(1)

Displacement reactions

219

(1)

Example of determination of association and dissociation rate constants

220

(1)

Kinetics of interaction of a non-fluorescent ligand with a protein

220

(2)

Complex binding reactions

222

(1)

Specialized techniques

222

(9)

Double mixing

223

(1)

Variable volume mixing

223

(1)

Logarithmic time base

224

(1)

Diode array detection

224

(2)

Fluorescence anisotropy

226

(5)

Modern continuous flow techniques

231

(1)

Global analysis

231

(8)

Strengths and limitations

232

(1)

Example: myosin-subfragment 1.ADP binding to pyrene-actin

232

(4)

Acknowledgements

236

(1)

References

237

(2)

Protein-ligand interactions studied by FTIR spectroscopy: methodological aspects

239

(26)

Michael Jackson

Henry H. Mantsch

Introduction

239

(1)

Protein structure determination by FTIR spectroscopy

240

(2)

Experimental design

242

(14)

Experimental technique

242

(5)

Experimental conditions: choice of solvent

247

(3)

Solvent and water vapour subtraction

250

(3)

Derivation and deconvolution

253

(3)

Thermal and solvent manipulation techniques for assessing protein-ligand interactions

256

(4)

Difference spectroscopy

260

(1)

Isotope edited difference spectroscopy

260

(1)

Reaction-induced difference spectroscopy

261

(4)

References

262

(3)

Protein-ligand interactions studied by Raman and resonance Raman spectroscopy

265

(46)

Robert Withnall

Introduction

265

(3)

Raman experiments

268

(24)

Visible/near infrared Raman spectroscopy

268

(7)

FT Raman spectroscopy

275

(2)

Difference Raman spectroscopy

277

(2)

Resonance Raman spectroscopy

279

(6)

Ultra-violet Raman and ultra-violet resonance Raman (UVRR) spectroscopy

285

(1)

Raman optical activity (ROA)

286

(2)

Time-resolved resonance Raman (TR3) spectroscopy

288

(1)

Surface-enhanced Raman spectroscopy (SERS) and surface-enhanced resonance Raman spectroscopy (SERRS)

289

(2)

Coherent anti-Stokes Raman spectroscopy (CARS)

291

(1)

Interpretation of protein spectra and band assignments

292

(3)

Amide group frequencies

292

(3)

Group frequencies of side groups

295

(1)

Specific information on proteins and their interactions with ligands

295

(16)

Secondary structure

295

(3)

Solvent exposure of aromatic side chains

298

(1)

pKD's of protein-ligand complexes

299

(1)

pKa's of specific protein groups

299

(1)

Entropic and enthalpic changes on ligand binding

300

(2)

Binding rate constants

302

(4)

Acknowledgements

306

(1)

References

307

(4)

Electrospray ionization mass spectrometry

311

(36)

T. J. Hill

D. Lafitte

P. J. Derrick

Introduction

311

(1)

Mass spectrometry

311

(2)

Electrospray ionization

313

(14)

Principle

313

(4)

Sample preparation

317

(1)

Sample injection

318

(2)

Creating a vacuum

320

(1)

Mass analysis---selection and detection

320

(3)

Data analysis

323

(4)

Data storage

327

(1)

Protein-ligand interactions of calmodulin

327

(20)

Preparation of calmodulin

327

(1)

ESI mass spectrometry of calmodulin

328

(16)

References

344

(3)

Nitroxide spin labels as paramagnetic probes

347

(36)

David A. Middleton

Introduction

347

(1)

Origin of the EPR spectrum

348

(10)

Magnetic resonance

348

(1)

Instrumentation

349

(1)

Phase-sensitive detection and the first derivative spectrum

350

(1)

Obtaining a spectrum

351

(2)

EPR spectroscopy of nitroxide spin labels

353

(5)

Conventional EPR spectroscopy

358

(12)

Sample requirements

358

(2)

Modification of protein side groups

360

(8)

Analysis of multiple component spectra

368

(2)

Saturation transfer EPR

370

(7)

Aims

370

(1)

Theory

371

(1)

Recording a spectrum

372

(3)

Interpretation of ST-EPR spectra

375

(2)

Protein-ligand interactions

377

(6)

Experimental design

377

(3)

Time-resolved spectroscopy

380

(1)

References

380

(3)

NMR studies of protein-ligand interactions

383

(24)

Lu-Yun Lian

Introduction

383

(1)

Preparation of sample and preliminary binding studies

384

(1)

Chemical exchange and analysing the NMR spectra for protein-ligand complexes

385

(3)

Screening for ligand interactions

388

(2)

Overview of NMR techniques used to study protein-ligand interactions

390

(2)

Exchange rate measurements

392

(3)

Assignment of resonances

395

(2)

Protein resonance assignments

395

(1)

Ligand resonance assignments

396

(1)

Structural information

397

(10)

Chemical shift changes

398

(2)

Nuclear Overhauser effects and structure calculations

400

(1)

Determination of ionization states

401

(1)

Protein ionization states

402

(3)

References

405

(2)

Quantification and mapping of protein-ligand interactions at the single molecule level by atomic force microscopy

407

(18)

Clive J. Roberts

Stephanie Allen

Martyn C. Davies

Saul J. B. Tendler

Philip M. Williams

Introduction

407

(3)

Applications

410

(1)

Quantification of the adhesion forces of individual protein-ligand complexes

410

(11)

General guidelines

410

(2)

Measurement of antibody-antigen interactions

412

(9)

Spatial mapping of protein-ligand interactions

421

(1)

Conclusions

421

(4)

References

422

(3)

List of suppliers

425

(8)

Index

433

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Protein-Ligand Interactions Structure and Spectroscopy

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Protein-Ligand Interactions Structure and Spectroscopy

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