Chapter 12 - Experimental techniques to study protein dynamics and conformations

Abstract

Proteins are flexible biomolecules and can adopt a wide range of structural conformations such that they can have their whole conformational ensemble. Understanding of protein function is not complete without proper knowledge of protein dynamics. The nature of these structural transitions, their probabilities, and the time span for each conformation is decided by the relative free energy landscape. Protein dynamics and conformational transitions have become a research hotspot for many human diseases. Many biological phenomena like the interaction between proteins, protein, and DNA, and protein and ligand, require detailed information on protein dynamics and conformations. Various biophysical techniques such as nuclear magnetic resonance, cryo-EM, small-angle X-ray scattering, mass spectrometry, atomic force microscopy and single-molecule fluorescence resonance energy transfer, etc., are used to study the pH, temperature, or ligand-induced conformational modulations. Some of these have emerged and advanced as major tools to study molecular interactions; however, certain limitations still exist in detailing the atomic level information. In this chapter, experimental methods to study protein conformational dynamics along with specific case studies are described. These techniques offer an overall view of what happens to the structure of a protein when it performs its biological function.