Protein–Protein and Protein–Ligand Interactions

Authored by: Marilyn D. Yoder

Handbook of Molecular and Cellular Methods in Biology and Medicine

Print publication date:  December  2011
Online publication date:  April  2016

Print ISBN: 9781420069389
eBook ISBN: 9781439881958
Adobe ISBN:

10.1201/b11351-23

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Abstract

Biological processes are dependent on interactions of proteins with other proteins, carbohydrates, nucleic acids, lipids, or smaller molecule ligands. Two fundamental problems exist: the determination of what molecules interact with a given protein, and characterization and quantification of the interaction once it is known. This chapter focuses on the latter. Methodologies to quantify protein interactions with other molecules are numerous. Two methods that provide fundamental thermodynamic and kinetic parameters are calorimetry and surface plasmon resonance (SPR). There are two general calorimetric techniques used in studying biological processes: differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). DSC measures heat capacity and enthalpy during denaturation processes; ITC measures heat evolved or absorbed during molecular association. ITC has a wide range of applications and can be used to measure free energy change, enthalpy change, entropy change, stoichiometry of binding, and heat capacity change (Perozzo et al. 2004). SPR measures in real time changes in refractive index upon binding of a molecule to another molecule, and therefore, can be a useful technique to analyze the kinetics of protein interactions including on and off rates.

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