Quantitative protein topography analysis and high-resolution structure prediction using hydroxyl radical labeling and tandem-ion mass spectrometry.

Feb. 16, 2015

Hydroxyl radical footprinting (HRF) based mass spectrometry (MS) for protein structure assessment has the goal of understanding ligand induced conformational changes and macromolecular interactions, e.g. protein tertiary and quaternary structure, but the structural resolution provided by typical peptide-level quantification is limiting. In this work, we present experimental strategies using tandem-MS fragmentation to increase the spatial resolution of the technique to the single residue level to provide a high precision tool for molecular biophysics research. Overall, in this study we demonstrated an eight-fold increase in structural resolution compared to peptide level assessments. In addition, to provide a quantitative analysis of residue based solvent accessibility and protein topography as a basis for high-resolution structure prediction; we illustrate strategies of data transformation using the relative reactivity of side chains as a normalization strategy and predict side-chain surface area from the footprinting data. We tested the methods by examination of Ca+2-calmodulin showing highly significant correlations between surface area and side-chain contact predictions for individual side chains and the crystal structure. Tandem ion based HRF-MS provides quantitative high-resolution protein topology information in solution that can fill existing gaps in structure determination for large proteins and macromolecular complexes.

Figure: Workflow steps for (a) Setting up the MS experimental method (b) Data analysis. DR: dose response, MS: mass spectrometry, m/z: mass-to-charge ratio, RC: rate constant, RT: retention time, SIC: selected ion chromatogram

Results from: Kaur P, Kiselar J, Yang S, Chance MR.Mol Cell Proteomics. 2015 Feb 16. pii: mcp.O114.044362. [Epub ahead of print]