New mass spectrometric methods for the study of noncovalent associations of biopolymers

Abstract

The use of electrospray ionization–mass spectrometry(ESI–MS) for the characterization of noncovalent complexes of biomacromolecules in solution is based upon the gentle nature of the electrospray process that allows a wide range of associations to be transferred intact to the gas phase as fully desolvated complexes. Examples include multimeric proteins, oligonucleotide duplexes, DNA–drug complexes and enzyme-inhibitor complexes. Various studies have indicated that at least some qualities of the three-dimensional solution structures are retained in the gas phase. Recent investigations have also shown the relative stabilities of complexes in the gas phase can be very different than the same complexes in solution. In spite of this, the use of very gentle electrospray interface conditions can provide a direct reflection of relative solution abundances for similar complexes. Competitive binding experiments using sets of ligands have been shown to yield insights regarding relative binding affinities in solution. The potential for high throughput affinity screening of combinatorial libraries using ESI–MS is described based upon the multi-stage MS capability of Fourier transform ion cyclotron resonance instrumentation and involving the characterization of components (after dissociation) of the library constituents initially present as complexes with a target biopolymer in the ion trap. This approach combines, in one rapid experiment, both affinity selection by complex formation with a biopolymer and the identification of the ligands selected from combinatorial mixtures, thus providing information on the relative binding affinities of the library constituents. The present status, limitations and promise of these methods are discussed.