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Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 3. Relating Solution-Phase to

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Molecular dynamics simulations reveal how peptide ions form conformers during electrospray. Nanodroplet solvent properties significantly alter peptide ion structures compared to bulk solutions.

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Area of Science:

  • Analytical Chemistry
  • Computational Chemistry
  • Physical Chemistry

Background:

  • Electrospray ionization is crucial for analyzing biomolecules.
  • Understanding peptide ion structures in the gas phase is essential for structural biology.
  • Previous studies used ion mobility and HDX to refine gas-phase peptide structures.

Purpose of the Study:

  • To model peptide ion conformer formation during electrospray using molecular dynamics.
  • To investigate the influence of droplet size and charge state on ion structure.
  • To compare simulated gas-phase conformers with experimentally validated structures.

Main Methods:

  • Explicit water molecular dynamics (MD) simulations at 300 K.
  • Modeling nanodroplets with a model peptide and hydronium ions.
  • Simulations focused on ion production and conformer analysis.

Main Results:

  • Ion production modeling supports previous structure refinement based on mobility and HDX.
  • Electrospray modeling accuracy improves with initial droplets near the Rayleigh limit.
  • Peptide ions in nanodroplets adopt different conformers than in bulk solution due to altered solvent properties.

Conclusions:

  • MD simulations provide evidence supporting experimental structure refinement methods.
  • Optimizing initial droplet conditions enhances electrospray modeling fidelity.
  • Confined solvent environments in nanodroplets significantly impact peptide ion conformations.