Investigating conformational changes of protein-nucleic acid and protein-ligand-nucleic acid complexes by tandem mass spectrometry

摘要

Electrospray ionization (ESI) and Fourier transform ion cyclotron resonance (FTICR) mass spectrometry provide a unique platform for studying the dynamics of nucleic acids and ligand-nucleic acid complexes. We have employed this platform to investigate the process of genome dimerization and isomerization in human immunodeficiency virus type 1 (HIV-1), which is mediated by specific interactions between the nucleocapsid (NC) domain of the Gag polyprotein and the dimerization initiation domain (SL1). These structures are critical in the HIV-1 life cycle and, thus, could constitute very favorable targets for the development of new anti-retroviral strategies. In previous work, we have developed a novel approach based on tandem mass spectrometry to study the role played by NC in the isomerization of the metastable kissing-loop (KL) dimer of SL1 into the more stable extended duplex (ED) conformation (Fig.1). This platform has now provided us with a unique tool for screening not only the binding properties of small molecule ligands, but also their ability to disrupt NC's chaperone activity. Interrogating the conformational state of species produced by multiple simultaneous equilibria in solution affords an additional level of information for evaluating possible lead compounds in the development of new therapeutic strategies for containing the AIDS pandemic.