PART IV NUCLEOTIDE BINDING AND HYDROLYSIS
12 A Quick Primer in Fluorescence-Based Equilibrium and Pre-steady
State Methods for Determining Protein–Nucleotide Affinities . . . . . . . . . . . . . . . . 273
Harland E. Brandon and Hans-Joachim Wieden
13 Measurement of Nucleotide Hydrolysis Using Fluorescent
Biosensors for Phosphate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289
Simone Kunzelmann
PART V BINDING NUCLEIC ACIDS
14 Gel-Based Analysis of Protein–Nucleic Acid Interactions. . . . . . . . . . . . . . . . . . . . . 321
James A. W. Stowell, Terence T. L. Tang, Maximilian Seidel,
and Lori A. Passmore
15 Biophysical Studies of the Binding of Viral RNA with the 80S
Ribosome Using switchSENSE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341
Emma Schenckbecher, Guillaume Bec, Taiichi Sakamoto,
Benoit Meyer, and Eric Ennifar
16 Biolayer Interferometry: Protein–RNA Interactions . . . . . . . . . . . . . . . . . . . . . . . . . 351
Stephen R. Martin, Andres Ramos, and Laura Masino
17 Analysis of Protein–DNA Interactions Using Surface Plasmon
Resonance and a ReDCaT Chip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369
Clare E. M. Stevenson and David M. Lawson
18 Characterization of Protein–Nucleic Acid Complexes by Size-Exclusion
Chromatography Coupled with Light Scattering, Absorbance,
and Refractive Index Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381
Ewa Folta-Stogniew
19 Analytical Ultracentrifugation for Analysis of Protein–Nucleic
Acid Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397
Andrea Bogutzki and Ute Curth
20 Studying RNA–Protein Complexes Using X-Ray Crystallography. . . . . . . . . . . . . 423
Andrew P. Turnbull and Xiaoqiu Wu
PART VI MEMBRANE BINDING
21 Flow Linear Dichroism of Protein–Membrane Systems . . . . . . . . . . . . . . . . . . . . . . 449
Matthew R. Hicks, Sarah R. Dennison, Adewale Olamoyesan,
and Alison Rodger
22 Probing Protein–Membrane Interactions and Dynamics Using
Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) . . . . . . . . . . . . . 465
Jordan T. B. Stariha, Reece M. Hoffmann, David J. Hamelin,
and John E. Burke
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 487
viii
Contents
12 A Quick Primer in Fluorescence-Based Equilibrium and Pre-steady
State Methods for Determining Protein–Nucleotide Affinities . . . . . . . . . . . . . . . . 273
Harland E. Brandon and Hans-Joachim Wieden
13 Measurement of Nucleotide Hydrolysis Using Fluorescent
Biosensors for Phosphate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289
Simone Kunzelmann
PART V BINDING NUCLEIC ACIDS
14 Gel-Based Analysis of Protein–Nucleic Acid Interactions. . . . . . . . . . . . . . . . . . . . . 321
James A. W. Stowell, Terence T. L. Tang, Maximilian Seidel,
and Lori A. Passmore
15 Biophysical Studies of the Binding of Viral RNA with the 80S
Ribosome Using switchSENSE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341
Emma Schenckbecher, Guillaume Bec, Taiichi Sakamoto,
Benoit Meyer, and Eric Ennifar
16 Biolayer Interferometry: Protein–RNA Interactions . . . . . . . . . . . . . . . . . . . . . . . . . 351
Stephen R. Martin, Andres Ramos, and Laura Masino
17 Analysis of Protein–DNA Interactions Using Surface Plasmon
Resonance and a ReDCaT Chip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369
Clare E. M. Stevenson and David M. Lawson
18 Characterization of Protein–Nucleic Acid Complexes by Size-Exclusion
Chromatography Coupled with Light Scattering, Absorbance,
and Refractive Index Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381
Ewa Folta-Stogniew
19 Analytical Ultracentrifugation for Analysis of Protein–Nucleic
Acid Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397
Andrea Bogutzki and Ute Curth
20 Studying RNA–Protein Complexes Using X-Ray Crystallography. . . . . . . . . . . . . 423
Andrew P. Turnbull and Xiaoqiu Wu
PART VI MEMBRANE BINDING
21 Flow Linear Dichroism of Protein–Membrane Systems . . . . . . . . . . . . . . . . . . . . . . 449
Matthew R. Hicks, Sarah R. Dennison, Adewale Olamoyesan,
and Alison Rodger
22 Probing Protein–Membrane Interactions and Dynamics Using
Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) . . . . . . . . . . . . . 465
Jordan T. B. Stariha, Reece M. Hoffmann, David J. Hamelin,
and John E. Burke
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 487
viii
Contents