Peptide conformation in gas phase probed by collision-induced dissociation and its correlation to conformation in condensed phases

Abstract

A kinetic peptide fragmentation model for quantitative prediction of peptide CID spectra in an ion trap mass spectrometer has been reported recently. When applying the model to predict the CID spectra of large peptides, it was often found that the predicted spectra differed significantly from their experimental spectra, presumably due to noncovalent interactions in these large polypeptides, which are not considered in the fragmentation model. As a result, site-specific quantitative information correlated to the secondary/tertiary structure of an ionized peptide may be extracted from its CID spectrum. To extract this information, the kinetic peptide fragmentation model was modified by incorporating conformation-related parameters. These parameters are optimized for best fit between the predicted and the experimental spectrum. A conformational stability map is then generated from these conformation-related parameters. Analysis of a few bioactive ␣-helical peptides including melittin, glucagon and neuropeptide Y by this technique demonstrated that their stability maps in the gas phase correlate strongly to their secondary structures in the condensed phases. H ow a one-dimensional polypeptide chain folds into a three-dimensional biologically active form is one of the greatest challenges in life science. One approach to understand the role of solvent in this folding process is to study protein conformation in the gas phase, in the absence of solvent. Understanding the relationship between the gas-phase and condensed-phase protein conformations will also help us evaluate mass spectrometry as a tool for studying protein noncovalent interactions.Protein conformation and dynamics in the condensed phases has traditionally been studied by X-ray crystallography [1], nuclear magnetic resonance spectroscopy [2-4], circular dichroism [5], etc., as well as hydrogen exchange [6,7] and its recent combination with mass spectrometry [8 -11]. Compared to the large amount of knowledge about protein conformation in the condensed phases, little is known about the conformation of proteins in gas phase, largely due to the lack of structurally informative techniques to study gasphase proteins [12,13]. Techniques including collision cross-section measurement [14 -21] and hydrogen/deuterium exchange [22][23][24][25][26][27] have been used to study protein gas-phase conformation, but they provide limited structural details. Recently, electron-capture dissociation (ECD) combined with Fourier-transform ion cyclotron resonance mass spectrometry shed some light on the structural details of gaseous proteins [28 -30]. This paper reports a new methodology, based on collisioninduced dissociation (CID) spectra of peptides or proteins, for structural details of gaseous peptides or proteins that compliments the information obtained from ECD and other conventional techniques. Smith and coworkers first demonstrated that CID spectra could be used as a probe for protein conformation [31]. Cassady and Carr also used CID to probe conformation of ubiquitin i...

Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library

“…The greater weight on peak intensities with RDP and RSIM suggests that the accuracy or quality of relative intensities in the simulated spectra might underlie decreased performance. The fragmentation of certain peptides might be modeled poorly by MassAnalyzer because of missing chemical mechanisms and oversimplifying assumptions, resulting in inaccurate relative intensities in simulated MS/MS spectra (28). Another important difference is the increased search space of the TargetSS library, which contains 26-fold more spectra than the NIST reference library.…”

Periodic sequence distribution of product ion abundances in electron capture dissociation of amphipathic peptides and proteins

“…ECD FT-ICR MS of six doubly protonated horse myoglobin tryptic fragments ( [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16], [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31], [32][33][34][35][36][37][38][39][40][41][42] Figure S2) and with vibrational activation ( Figure 5) confirm preferential and sometimes periodic product ion formation from peptides with mainly ␣-helical or ␤-turn secondary structure in solution (before protein digestion). Predominantly z-ions are observed because of preferential charge retention at the C-terminal Lys or Arg basic residue upon electron capture, as expected for doubly charged tryptic peptides.…”

“…The combination of mass spectrometry with gas-phase ultraviolet/infrared (UV/IR) spectroscopy has provided evidence for helical structure in gaseous protein ions [30] and poly-Ala peptides [31]. Collision-induced dissociation of peptide cations in the gas phase has been linked to peptide structure stability and secondary structure elements [32,33].…”

High-Resolution and Tandem Mass Spectrometry – the Indispensable Tools of the XXI Century

“…Furthermore, the product ion abundance distribution is believed to contain information on the peptide and protein secondary and, potentially, tertiary structures in the gas phase. [29][30][31][32][33] The radical nature of the ion-electron interactions is manifested through the influence of amino acid radical stability properties on the product ion abundance. [34,35] Fig.…”