Exploring Conformational Landscapes Using Trap and Release Tandem Ion Mobility Spectrometry

Area of Science:

• Biophysical Chemistry
• Mass Spectrometry
• Computational Chemistry

Background:

• Understanding protein conformational dynamics is crucial for deciphering biological function.
• Isolated peptide ions provide a simplified system to study fundamental principles of protein folding and stability.
• Ion mobility spectrometry (IMS) is a powerful technique for separating and characterizing gas-phase ion conformers.

Purpose of the Study:

• To investigate the dynamics and thermodynamics of structural changes in isolated glu-fibrinopeptide B (GluFib).
• To determine isomerization rates and equilibrium populations of different GluFib conformers as a function of temperature.
• To compare experimental thermodynamic data with results from molecular dynamics simulations.

Main Methods:

• Tandem ion mobility spectrometry (IMS) was employed to select and store doubly protonated GluFib ions.
• Temperature-induced conformational changes were monitored by IMS as a function of trapping time.
• Replica-exchange molecular dynamics simulations using the AMOEBA force field and weighted histogram analysis method were performed for comparison.

Main Results:

• Isomerization rates and equilibrium populations of GluFib conformers were determined across a range of temperatures.
• Good qualitative agreement was observed between experimental thermodynamic quantities and simulated observables.
• The balance between Coulomb repulsion and charge solvation was identified as a key factor in conformational bistability.

Conclusions:

• The study highlights differences between kinetically driven and thermodynamically driven conformational distributions.
• Experimental measurements allow for the determination of Arrhenius activation energies and relative enthalpy/entropy changes.
• The findings provide a foundation for understanding peptide conformational landscapes and their thermodynamic underpinnings.