Methods for Analysis of Protein‑protein and Protein‑ligand Interactions

Czech version

Authors: M. Ďurech; F. Trčka; B. Vojtěšek; P. Müller
Authors‘ workplace: Regionální centrum aplikované molekulární onkologie, Masarykův onkologický ústav, Brno
Published in: Klin Onkol 2014; 27(Supplementum): 75-81

Overview

In order to maintain cellular homeostasis, cellular proteins coexist in complex and variable molecular assemblies. Therefore, understanding of major physiological processes at molecular level is based on analysis of protein‑protein interaction networks. Firstly, composition of the molecular assembly has to be qualitatively analyzed. In the next step, quantitative biochemical properties of the identified protein‑protein interactions are determined. Detailed information about the protein‑protein interaction interface can be obtained by crystallographic methods. Accordingly, the insight into the molecular architecture of these protein‑protein complexes allows us to rationally design new synthetic compounds that specifically influence various physiological or pathological processes by targeted modulation of protein interactions. This review is focused on description of the most used methods applied in both qualitative and quantitative analysis of protein‑protein interactions. Co‑ immunoprecipitation and affinity co‑ precipitation are basic methods designed for qualitative analysis of protein binding partners. Further biochemical analysis of the interaction requires definition of kinetic and thermodynamic parameters. Surface plasmon resonance (SPR) is used for description of affinity and kinetic profile of the interaction, fluorescence polarization (FP) method for fast determination of inhibition potential of inhibitors and isothermal titration calorimetry (ITC) for definition of thermodynamic parameters of the interaction (∆G, ∆H and ∆S). Besides the importance of uncovering the molecular basis of protein interactions for basic research, the same methodological approaches open new possibilities in rational design of novel therapeutic agents.

Key words:
protein interaction networks – co‑ immunoprecipitation – pull‑ down analysis – surface plasmon resonance – fluorescence polarization – isothermal titration calorimetry

This work was supported by the European Regional Development Fund and the State Budget of the Czech Republic (RECAMO, CZ.1.05/2.1.00/03.0101) and by MH CZ – DRO (MMCI, 00209805).

The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.

The Editorial Board declares that the manuscript met the ICMJE “uniform requirements” for biomedical papers.

Submitted:
31. 1. 2014

Accepted:
10. 3. 2014

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