Confirming differences in conformation: Infrared Multiphoton Dissociation Spectroscopy of isomeric dipeptides AlaDap and DapAla
Poster Number
5
Introduction/Abstract
Our studies have shown that isomeric dipeptides exhibit significantly different proton affinities and gas-phase basicities. The only difference between the two peptides is the order for which the two residues are placed. For the case of this research, a basic residue is placed closest to the N-terminus or closest to the C-terminus. Molecular modeling shows that one protonated isomer is more compact than the other, allowing efficient internal solvation of the charged site, thereby increasing its proton affinity and gas-phase basicity. Although theory suggests differences in conformation, these differences have not been confirmed experimentally.
Purpose
To apply in-depth conformational analysis via molecular modeling using varying levels of theory and to compare experimentally acquired Infrared Multiphoton Dissociation (IRMPD) spectra data to validate the accuracy of our modeling.
Method
The peptides analyzed contained Alanine (Ala) and 2,3-diaminoburitic acid (Dap) and were synthesized in-house using standard solid-phase peptide synthesis. IRMPD spectra were obtained using a Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR MS) coupled to the Free Electron Laser for Infrared eXperiments (FELIX Facility) in Nijmegen, The Netherlands. Molecular modeling results were acquired using a sequential approach where 10,000 initial conformers were generated and sequentially optimized using progressively higher levels of theory until the 10 lowest energy conformers and their vibrational modes were determined using B3LYP/6-311+g(d) and ωB97X-D/6-311+g(d) levels of theory. MP2/6- 311++g(2d,p) level calculations were carried out on the final conformers to obtain a more accurate energy ladder. Lastly, calculated infrared spectra for each conformer was compared to IRMPD spectra to determine the most likely conformers represented by the experimental spectrum.
Results
The IRMPD spectra of AlaDap and DapAla were acquired and are shown to exhibit completely different spectra. Calculated IR spectra and IRMPD spectra were directly compared. The results show that for both peptides the IRMPD spectrum contains features present in IR spectra of several calculated conformers. This indicates that the experimental spectrum represents a population of different conformers existing in the gas phase. Application of a Boltzmann weighted average for calculated IR spectra intensities and frequencies provides better matching to the IRMPD spectrum.
Significance
Comparing calculated infrared spectra to experimentally acquired IRMPD results provide essential benchmarking of the accuracy of our theoretical models. Also, by understanding sequence dependent conformation effects on model systems we can gain critical insight into the form and function of biologically relevant peptides and proteins.
Location
DeRosa University Center, Stockton campus, University of the Pacific
Format
Poster Presentation
Confirming differences in conformation: Infrared Multiphoton Dissociation Spectroscopy of isomeric dipeptides AlaDap and DapAla
DeRosa University Center, Stockton campus, University of the Pacific
Our studies have shown that isomeric dipeptides exhibit significantly different proton affinities and gas-phase basicities. The only difference between the two peptides is the order for which the two residues are placed. For the case of this research, a basic residue is placed closest to the N-terminus or closest to the C-terminus. Molecular modeling shows that one protonated isomer is more compact than the other, allowing efficient internal solvation of the charged site, thereby increasing its proton affinity and gas-phase basicity. Although theory suggests differences in conformation, these differences have not been confirmed experimentally.
