Protein-Ligand Interactions A Practical Approach Volume 2: Structure and Spectroscopy

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

• ISBN13: 9780199637478
• ISBN10: 0199637474
• Edition: 1st
• Format: Paperback
• Copyright: 2001-03-22
• Publisher: Oxford University Press

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.

Table of Contents

List of protocols	xvii
Abbreviations	xxi
X-ray crystallographic studies of protein-ligand interactions	1	(98)
Rex A. Palmer
Introduction	1	(1)
Crystallization of proteins and complexes for X-ray analysis	1	(18)
Introduction	1	(3)
Crystallization of proteins	4	(1)
Practical considerations	5	(10)
Crystal mounting for X-ray data collection	15	(1)
Trouble shooting	16	(1)
Protein-ligand complex crystals	17	(2)
Crystal geometry and symmetry	19	(10)
The crystal lattice	19	(8)
Symmetry elements, crystal systems, and space groups	27	(2)
X-ray diffraction from crystals	29	(8)
Bragg's treatment of X-ray diffraction: the location of diffraction maxima	29	(2)
The reciprocal lattice concept defining the location of diffraction maxima	31	(2)
The structure factor F(hkl): X-ray intensities I(hkl)	33	(3)
Calculated structure factors and R-factors	36	(1)
Recording and measurement of X-ray diffraction patterns	37	(9)
X-ray sources	37	(1)
Recording and measuring intensity data	38	(5)
Image plate data processing	43	(3)
Preliminary crystal data	46	(6)
Determination of unit cell and space group	46	(2)
Resolution	48	(1)
Number of reflections in the data set	48	(1)
Completeness of a data set at a given resolution	48	(1)
Internal consistency	49	(1)
Number of molecules per unit cell	49	(3)
Electron density: reconstruction of the molecular structure	52	(3)
Basic principles	52	(1)
Properties of the electron density	52	(1)
Complementarity of the structure factor F(hkl) and electron density p(x, y, x)	53	(1)
Difference electron density functions	53	(1)
Patterson's Fourier series: the Patterson function P(uvw)	53	(2)
Properties of the Patterson function	55	(1)
Determination of the phases &phis;(hkl) for protein crystals	55	(19)
Introduction	55	(1)
Isomorphous replacement (IR)	56	(1)
Heavy atoms and compounds for isomorphous replacement	56	(1)
Preparation and screening of heavy atom derivatives	56	(1)
Phase determination in single isomorphous replacement (SIR)	57	(1)
Location of the heavy atoms	58	(1)
Phase determination in multiple isomorphous replacement (MIR)	58	(2)
Molecular replacement (MR)---the Sledgehammer	60	(11)
Use of phase information and density modification	71	(3)
What to do once phasing is acceptable	74	(1)
Structure refinement, ligand fitting, and geometry verification	74	(6)
Refinement	74	(1)
Fourier refinement and simulated annealing	75	(2)
Least squares refinement	77	(3)
Examples of protein-ligand complex studies	80	(13)
N-acetyl-DL-homocysteinyl ribonuclease derivatives: protein-ligand covalent modification	80	(1)
Environment of the SO42- ion and solvent waters in native bovine RNase A active site at 0.9 A resolution (18)	81	(1)
Enzyme-inhibitor interactions (non-covalent): r-rat RNase A binding with 2'-5-CpG (85)	82	(1)
Protein-carbohydrate interactions: the non-covalent sugar binding sites in the lectin MLI	83	(3)
Glycoproteins: covalently bound sugars and the [... Asn, X, Ser/Thr...] binding site; MLI B-chain Asn 136 sugar binding site (89)	86	(1)
Protein-steroid interactions: Fab' fragment of antibody DB3 bound to progesterone and progesterone-like steroids	86	(5)
Protein-nucleic acid interactions: procaryotic recognition of helix-turn-helix motifs in DNA (117)	91	(2)
Further recommended reading and software	93	(6)
Protein-peptide interactions: cyclophilin/cyclosporin complexes	93	(1)
Protein-protein interactions (e.g. protein-antibody): camel VH with lysozyme	93	(1)
Recommended books	93	(1)
International tables	93	(1)
Synchrotrons Web Page	93	(1)
Space group diagrams	93	(1)
Software for data processing	94	(1)
Software for Fourier and structure factor calculations	94	(1)
Software for MIR	94	(1)
Software for packing and molecular geometry	94	(1)
Software for graphics and model building	94	(1)
Software for molecular graphics and display	94	(1)
Software for refinement	94	(1)
Software for molecular dynamics and minimization	94	(1)
Databases	94	(1)
References	95	(4)
Molecular modelling	99	(24)
Romano T. Kroemer
Introduction	99	(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