Structure Characterization of a Disordered Peptide Using In-Droplet Hydrogen/Deuterium Exchange Mass Spectrometry and...

Area of Science:

• Biochemistry
• Structural Biology
• Computational Chemistry

Background:

• Hydrogen/deuterium exchange (HDX) coupled with mass spectrometry (MS) is a powerful technique for studying protein structure and dynamics.
• Intrinsically disordered regions (IDRs) lack stable structures, making their conformational flexibility and interactions challenging to characterize.
• Understanding the structural dynamics of peptides is crucial for elucidating biological mechanisms and developing therapeutics.

Purpose of the Study:

• To develop a predictive model correlating peptide structural flexibility with hydrogen/deuterium exchange (HDX) reactivity.
• To elucidate the relationship between structural flexibility and HDX reactivity across diverse peptide conformations.
• To apply the model to characterize the conformational flexibility and structural bias of the disease-relevant Nt17 peptide.

Main Methods:

• In-droplet hydrogen/deuterium exchange (HDX)-mass spectrometry (MS) experiments were performed on peptides with varied conformational types.
• A novel model was developed integrating protection factors (PF) from molecular dynamics (MD) simulations with intrinsic HDX rates (k_int).
• This model generated a structure-to-reactivity calibration curve to analyze peptide behavior.

Main Results:

• The study established a structure-to-reactivity calibration curve using the developed model.
• The model successfully elucidated the relationship between peptide structural flexibility and HDX reactivity.
• For the Nt17 peptide, the model revealed significant HDX protection despite its inherent flexibility, attributed to α-helical conversion upon binding.

Conclusions:

• The developed model provides a quantitative link between peptide structure and HDX reactivity.
• HDX reactivity can serve as a predictor for the degree of structural flexibility and secondary structure propensity in IDRs.
• This approach holds potential for high-throughput screening of IDR structural transformations upon ligand binding, aiding drug candidate identification.