A computational model for protein ionization by electrospray based on gas-phase basicity

J Am Soc Mass Spectrom. 2012 Nov;23(11):1903-10. doi: 10.1007/s13361-012-0449-0. Epub 2012 Sep 20.

Abstract

Identifying the key factor(s) governing the overall protein charge is crucial for the interpretation of electrospray-ionization mass spectrometry data. Current hypotheses invoke different principles for folded and unfolded proteins. Here, first we investigate the gas-phase structure and energetics of several proteins of variable size and different folds. The conformer and protomer space of these proteins ions is explored exhaustively by hybrid Monte-Carlo/molecular dynamics calculations, allowing for zwitterionic states. From these calculations, the apparent gas-phase basicity of desolvated protein ions turns out to be the unifying trait dictating protein ionization by electrospray. Next, we develop a simple, general, adjustable-parameter-free model for the potential energy function of proteins. The model is capable to predict with remarkable accuracy the experimental charge of folded proteins and its well-known correlation with the square root of protein mass.

MeSH terms

  • Animals
  • Cattle
  • Gases / chemistry*
  • Humans
  • Molecular Dynamics Simulation*
  • Proteins / chemistry*
  • Spectrometry, Mass, Electrospray Ionization / methods*

Substances

  • Gases
  • Proteins