Electrostatics of hydrogen exchange for analyzing protein flexibility

Area of Science:

• Biophysics
• Protein Dynamics
• Computational Biology

Background:

• Protein backbone amide hydrogen exchange (HX) is a fundamental process.
• Electrostatic interactions at the protein-solvent interface significantly impact HX.
• Understanding these interactions is crucial for predicting protein structure and dynamics.

Purpose of the Study:

• To investigate the role of electrostatic interactions in modulating protein backbone amide reactivity.
• To assess the predictability of experimental HX rates using continuum dielectric methods.
• To establish electrostatic analysis of HX rates as a tool for validating protein structural models.

Main Methods:

• Experimental measurement of hydroxide-catalyzed amide HX rates.
• Application of continuum dielectric methods for rate prediction.
• Electrostatic analysis of experimental HX rates in relation to protein structure.

Main Results:

• Electrostatic interactions can modulate amide reactivity by over a billion-fold.
• The short lifetime of the peptide anion intermediate allows for robust prediction of HX rates.
• Experimental HX rates correlate strongly with electrostatic potential at the protein-aqueous interface.

Conclusions:

• Continuum dielectric methods accurately predict HX rates for solvent-exposed amides.
• Electrostatic analysis of HX rates provides a reliable method for assessing the validity of protein structural ensembles.
• This approach helps determine if a model ensemble represents the correct Boltzmann conformational distribution of the protein native state.