Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations

STAR Protoc. 2021 Feb 3;2(1):100315. doi: 10.1016/j.xpro.2021.100315. eCollection 2021 Mar 19.

Abstract

Here, we describe a generic protocol for monitoring protein-RNA interaction using a cleavable GFP fusion of a recombinant RNA-binding protein. We detail each expression and purification step, including high salt and heparin column for contaminant RNA removal. After the assembly of RNA into the ribonucleoprotein complex, the MicroScale Thermophoresis assay enables the binding affinity to be obtained quickly with a small amount of sample. Further Gaussian accelerated molecular dynamics simulations allow us to analyze protein:RNA interactions in detail. For complete details on the use and execution of this protocol, please refer to Gao et al. (2020).

Keywords: Bioinformatics; Protein biochemistry; Protein expression and purification.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biological Assay
  • Molecular Dynamics Simulation
  • Protein Binding / physiology*
  • RNA / chemistry
  • RNA / isolation & purification*
  • Ribonucleoproteins / isolation & purification*
  • Ribonucleoproteins / metabolism
  • Ribonucleoproteins / physiology
  • Thermodynamics

Substances

  • Ribonucleoproteins
  • RNA