Calcium-binding protein protocols. / Volume 2, Methods and techniques

Dedication .........................................................................................................v Preface ........................................................................................................... vii Contents of Companion Volume ................................................................... xiii Contributors..................................................................................................xv PART III. METHODS AND TECHNIQUES TO STUDY CALCIUM-BINDING PROTEINS 1 Quantitative Analysis of Ca2+-Binding by Flow Dialysis Michio Yazawa ........................................................................................ 3 2 Calcium Binding to Proteins Studied via Competition with Chromophoric Chelators Sara Linse ............................................................................................. 15 3 Deconvolution of Calcium-Binding Curves: Facts and Fantasies Jacques Haiech and Marie-Claude Kilhoffer .................................... 25 4 Absorption and Circular Dichroism Spectroscopy Stephen R. Martin and Peter M. Bayley ............................................ 43 5 Fourier Transform Infrared Spectroscopy of Calcium-Binding Proteins Heinz Fabian and Hans J. Vogel ........................................................ 57 6 Steady-State Fluorescence Spectroscopy Aalim M. Weljie and Hans J. Vogel .................................................... 75 7 Fluorescence Methods for Measuring Calcium Affinity and Calcium Exchange with Proteins J. David Johnson and Svetlana B. Tikunova ................................... 89 8 Surface Plasmon Resonance of Calcium-Binding Proteins Karin Julenius .................................................................................... 103 9 Differential Scanning Calorimetry Maria M. Lopez and George I. Makhatadze .................................... 113 10 Isothermal Titration Calorimetry Maria M. Lopez and George I. Makhatadze .................................... 121 11 Multiangle Laser Light Scattering and Sedimentation Equilibrium Leslie D. Hicks, Jean-René Alattia, Mitsuhiko Ikura, and Cyril M. Kay ............................................................................. 127 x Contents 12 Small-Angle Solution Scattering Reveals Information on Conformational Dynamics in Calcium-Binding Proteins and in their Interactions with Regulatory Targets Jill Trewhella and Joanna K. Krueger ............................................. 137 13 Investigation of Calcium-Binding Proteins Using Electrospray Ionization Mass Spectrometry Amanda L. Doherty-Kirby and Gilles A. Lajoie .............................. 161 14 Synthetic Calcium-Binding Peptides Gary S. Shaw ...................................................................................... 175 15 Proteolytic Fragments of Calcium-Binding Proteins Richard D. Brokx and Hans J. Vogel ............................................... 183 16 Electron Magnetic Resonance Studies of Calcium-Binding Proteins Lawrence J. Berliner ......................................................................... 195 17 Cadmium-113 and Lead-207 NMR Spectroscopic Studies of Calcium-Binding Proteins Teresa E. Clarke and Hans J. Vogel ................................................ 205 18 Calcium-43 of NMR of Calcium-Binding Proteins Torbjörn Drakenberg ......................................................................... 217 19 Exploring Familial Relationships Using Multiple Sequence Alignment Aalim M. Weljie and Jaap Heringa ................................................... 231 20 Structure Determination by NMR: Isotope Labeling Monica X. Li, David C. Corson, and Brian D. Sykes ...................... 255 21 Protein Structure Calculation from NMR Data Tapas K. Mal, Stefan Bagby, and Mitsuhiko Ikura ........................ 267 22 Shape and Dynamics of a Calcium-Binding Protein Investigated by Nitrogen-15 NMR Relaxation Jörn M. Werner, Iain D. Campbell, and A. Kristina Downing ....... 285 23 The Use of Dipolar Couplings for the Structure Refinement of a Pair of Calcium-Binding EGF Domains Jonathan Boyd, Iain D. Campbell, and A. Kristina Downing ....... 301 24 Vector Geometry Mapping: A Method to Characterize the Conformation of Helix-Loop-Helix Calcium-Binding Proteins Kyoko L. Yap, James B. Ames, Mark B. Swindells, and Mitsuhiko Ikura ...................................................................... 317 25 Use of Calmodulin Antagonists and S-100 Protein Interacting Drugs for Affinity Chromatography Ryoji Kobayashi ................................................................................. 325 26 Enzymatic Assays to Compare Calmodulin Isoforms, Mutants, and Chimeras Michael P. Walsh, Jacquelyn E. Van Lierop, Cindy Sutherland, Ritsu Kondo, and J. David Johnson ........................................... 339 27 Gene Expression in Transfected Cells Kate Hughes, Juha Saarikettu, and Thomas Grundström ........... 355 28 Monitoring the Intracellular Free Ca2+-Calmodulin Concentration with Genetically-Encoded Fluorescent Indicator Proteins Anthony Persechini ........................................................................... 365 29 Studying the Spatial Distribution of Ca2+-Binding Proteins: How Does it Work for Calmodulin? Katalin Török, Richard Thorogate, and Steven Howell ................ 383 Index ............................................................................................................ 409