Protein proton-proton dynamics from amide proton spin flip rates

Area of Science:

• Biophysics
• Structural Biology
• Protein Dynamics

Background:

• Calmodulin (CaM) undergoes conformational changes upon peptide binding, crucial for its function.
• Understanding protein dynamics at the residue level is key to elucidating biological mechanisms.

Purpose of the Study:

• To develop and apply a novel method for quantifying local protein dynamics using residue-specific amide proton spin-flip rates.
• To investigate changes in proton network dynamics in Ca(2+)-saturated calmodulin upon binding to the smMLCK peptide.

Main Methods:

• Measurement of residue-specific amide proton spin-flip rates (K).
• Application of a theoretical model for multi-proton relaxation, cross-relaxation, and cross-correlation.
• Definition and calculation of a parameter Q (ratio of experimental to theoretical K-rates) as a measure of local dynamics.

Main Results:

• The parameter Q, reflecting local dynamics, was determined for both free and peptide-bound calmodulin.
• Mean Q values were 0.81 ± 0.02 for free calmodulin and 0.88 ± 0.02 for peptide-bound calmodulin.
• An increase in Q upon peptide binding indicates rigidification of the proton network.

Conclusions:

• The developed methodology provides a sensitive measure of local protein dynamics and interproton disorder.
• Peptide binding to calmodulin leads to a significant rigidification of the surrounding proton network.
• This finding supports the known high entropic cost associated with calmodulin-peptide complex formation.