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Correlation between Labeling Yield and Surface Accessibility in Covalent Labeling Mass Spectrometry.

Daniel S Ziemianowicz1,2, Justin L MacCallum3, David C Schriemer1,2,3

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Covalent labeling mass spectrometry (CL-MS) shows local protein surface correlations but not global ones. Protein dynamics and chemistry, not just solvent exposure, influence labeling yields, suggesting a "chemical accessibility" view.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Chemical Biology

Background:

  • Protein functional properties depend on surface topography.
  • Covalent labeling mass spectrometry (CL-MS) measures surface accessibility but has inconsistent labeling yields.
  • CL-MS is useful for protein interaction studies but requires better structural analysis.

Purpose of the Study:

  • To evaluate the relationship between labeling yield and surface exposure in CL-MS.
  • To improve CL-MS for structural analysis by understanding labeling inconsistencies.
  • To apply new diazirine reagents for deep coverage of protein surfaces.

Main Methods:

  • Applied novel diazirine reagents for covalent labeling of the Eg5 motor domain.
  • Utilized computational methods to correlate labeling yields with accessibility data.
  • Analyzed labeling patterns across the protein structure.

Main Results:

  • Observed local structural correlations between labeling and accessibility.
  • Found that correlations do not extend globally across the protein structure.
  • Identified protein dynamics and chemical composition as key factors influencing labeling yield.

Conclusions:

  • CL-MS data reflects "chemical accessibility" rather than solely "solvent accessibility".
  • Protein dynamics and local chemical environment significantly impact labeling outcomes.
  • CL-MS is a valuable tool for studying protein-solute interactions, with data interpreted through a chemical accessibility lens.