The determination of high-affinity protein/inhibitor binding constants by electrospray ionization hydrogen/deuterium exchange mass spectrometry

QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure

Background

Hydrogen/deuterium exchange (HDX) coupled to mass spectrometry permits analysis of structure, dynamics, and molecular interactions of proteins. HDX mass spectrometry is confounded by deuterium exchange-associated peaks overlapping with peaks of heavy, natural abundance isotopes, such as carbon-13. Recent studies demonstrated that high-performance mass spectrometers could resolve isotopic fine structure and eliminate this peak overlap, allowing direct detection and quantification of deuterium incorporation.

Results

Here, we present a graphical tool that allows for a rapid and automated estimation of deuterium incorporation from a spectrum with isotopic fine structure. Given a peptide sequence (or elemental formula) and charge state, the mass-to-charge ratios of deuterium-associated peaks of the specified ion is determined. Intensities of peaks in an experimental mass spectrum within bins corresponding to these values are used to determine the distribution of deuterium incorporated. A theoretical spectrum can then be calculated based on the estimated distribution of deuterium exchange to confirm interpretation of the spectrum. Deuterium incorporation can also be detected for ion signals without a priori specification of an elemental formula, permitting detection of exchange in complex samples of unidentified material such as natural organic matter. A tool is also incorporated into QUDeX-MS to help in assigning ion signals from peptides arising from enzymatic digestion of proteins. MATLAB-deployable and standalone versions are available for academic use at qudex-ms.sourceforge.net and agarlabs.com.

Conclusion

Isotopic fine structure HDX-MS offers the potential to increase sequence coverage of proteins being analyzed through mass accuracy and deconvolution of overlapping ion signals. As previously demonstrated, however, the data analysis workflow for HDX-MS data with resolved isotopic fine structure is distinct. QUDeX-MS we hope will aid in the adoption of isotopic fine structure HDX-MS by providing an intuitive workflow and interface for data analysis.

Energetics-based methods for protein folding and stability measurements

Over the past 15 years, a series of energetics-based techniques have been developed for the thermodynamic analysis of protein folding and stability. These techniques include Stability of Unpurified Proteins from Rates of amide H/D Exchange (SUPREX), pulse proteolysis, Stability of Proteins from Rates of Oxidation (SPROX), slow histidine H/D exchange, lysine amidination, and quantitative cysteine reactivity (QCR). The above techniques, which are the subject of this review, all utilize chemical or enzymatic modification reactions to probe the chemical denaturant- or temperature-induced equilibrium unfolding properties of proteins and protein-ligand complexes. They employ various mass spectrometry-, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE)-, and optical spectroscopy-based readouts that are particularly advantageous for high-throughput and in some cases multiplexed analyses. This has created the opportunity to use protein folding and stability measurements in new applications such as in high-throughput screening projects to identify novel protein ligands and in mode-of-action studies to identify protein targets of a particular ligand.

Studies on the non-covalent interactions between cyclodextrins and aryl alkanol piperazine derivatives by mass spectrometry and fluorescence spectroscopy

The non-covalent complexes of alpha- and beta-cyclodextrins (alpha-, beta-CDs) with two aryl alkanol piperazine derivatives (Pipe I and Pipe II) have been studied by electrospray ionization mass spectrometry (ESI-MS) and fluorescence spectroscopy. The ESI-MS experimental results demonstrated that Pipe I can conjugate to beta-CD and form 1:1 or 1:2 stoichiometric non-covalent complexes, and Pipe II can only form 1:1 complexes with alpha- or beta-CD. Fluorescence spectra indicated that the fluorescence intensities of Pipe I and Pipe II can be enhanced by increasing the content of beta-CD. The mass spectrometric titration experiments showed that the dissociation constants K(d1) were 5.77 and 9.52 x 10(-4) mol L(-1) for the complexes of alpha-CD with Pipe I and Pipe II, respectively, revealing that the binding of alpha-CD-Pipe I was stronger than alpha-CD-Pipe II. The K(d1) and K(d2) values were 9.81 x 10(-4) mol L(-1) and 1.11 x 10(-7) (mol L(-1))(2) for 1:1 and 1:2 complexes of Pipe I with beta-CD, respectively. The K(d) values obtained from fluorescence spectroscopy were in agreement with those from ESI-MS titration.

Binding constant determination of high-affinity protein-ligand complexes by electrospray ionization mass spectrometry and ligand competition

We describe an approach for the determination of binding constants for protein-ligand complexes with electrospray ionization mass spectrometry, based on the observation of unbound ligands competing for binding to a protein target. For the first time, dissociation constants lower than picomolar could be determined with good accuracy by electrospray ionization mass spectrometry. The presented methodology relies only on the determination of signal intensity ratios for free ligands in the low mass region. Therefore, all the advantages of measuring low masses with mass spectrometry, such as high resolution are preserved. By using a reference ligand with known binding affinity, the affinity of a second ligand can be determined. Since no noncovalently bound species are observed, assumptions about response factors are not necessary. The method is validated with ligands binding to avidin and applied to ligands binding to p38 mitogen-activated protein kinase.