Kinetic and Thermodynamic Analyses of RNA-Protein Interactions

Ryo Amano; Taiichi Sakamoto

doi:10.1007/978-1-0716-0231-7_8

Kinetic and Thermodynamic Analyses of RNA-Protein Interactions

Methods Mol Biol. 2020:2106:137-150. doi: 10.1007/978-1-0716-0231-7_8.

Authors

Ryo Amano¹, Taiichi Sakamoto²

Affiliations

¹ The Institute of Medical Science, Project Division of RNA Medical Science, The University of Tokyo, Tokyo, Japan.
² Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba, Japan. taiichi.sakamoto@p.chibakoudai.jp.

PMID: 31889255
DOI: 10.1007/978-1-0716-0231-7_8

Abstract

Recently created biophysical methods, such as surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC), have been widely used to quantitatively study biomolecule interactions. The dissociation constant of the interaction with kinetic parameters, such as association rate constant and dissociation rate constant, can be obtained using SPR analysis. With thermodynamic parameters, such as enthalpy change and entropy change, the dissociation constant can be obtained by ITC analysis. Both methods differ not only in the type of information obtained but also in throughput and sample concentration. Analyzing the biophysical parameters of RNA-protein interactions will help us understand their functions in biological processes. In this chapter, we describe step-by-step SPR and ITC protocols suitable to study the kinetics and thermodynamics of RNA-protein interactions.

Keywords: Dissociation constant; Enthalpy; Entropy; Protein; RNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Calorimetry / methods*
Entropy
Kinetics
Protein Binding
RNA / chemistry
RNA / metabolism*
RNA-Binding Proteins / chemistry
RNA-Binding Proteins / metabolism*
Surface Plasmon Resonance / methods*

Substances

RNA-Binding Proteins
RNA