Gas Phase Protein Folding Triggered by Proton Stripping Generates Inside-Out Structures: A Molecular Dynamics...

Area of Science:

• Mass Spectrometry
• Computational Chemistry
• Structural Biology

Background:

• Electrosprayed protein ions' gas-phase structures are poorly understood due to limited high-resolution methods.
• Existing evidence suggests ions may retain solution-like conformations, but these may not reflect intrinsic gas-phase preferences.

Purpose of the Study:

• To investigate the intrinsic structural preferences of gaseous protein ions.
• To simulate and characterize the gas-phase conformations of ubiquitin ions after proton stripping.

Main Methods:

• Utilized microsecond-scale molecular dynamics (MD) simulations of gaseous ubiquitin.
• Employed a mobile-proton algorithm to model proton migration in gas-phase proteins.
• Simulated proton stripping to induce folding of ubiquitin ions.

Main Results:

• Proton stripping induced ubiquitin folding into heterogeneous "inside-out" structures.
• These conformers featured hydrophilic cores stabilized by charge-charge and polar interactions.
• Hydrophobic residues were predominantly located on the protein surface, contrasting with solution behavior.
• Simulated collision cross-sections aligned well with experimental data.

Conclusions:

• Gaseous protein ions exhibit intrinsically preferred "inside-out" architectures, distinct from solution-phase structures.
• Kinetically trapped native-like conformers do not represent true intrinsic gas-phase preferences.
• This study provides the first detailed insights into intrinsically preferred gas-phase protein structures.