Conformation of Polyalanine and Polyglycine Dications in the Gas Phase: Insight from Ion Mobility Spectrometry and Replica-Exchange Molecular Dynamics

Abstract

The conformation of model [Arg(Ala)(4)X(Ala)(4)Lys+2H](2+) and [Arg(Gly)(4)X(Gly)(4)Lys+2H](2+) peptides has been systematically investigated as a function of the central amino acid X through a combined experimental and theoretical approach. Mass spectrometry-based ion mobility measurements have been performed together with conformational sampling using replica-exchange molecular dynamics to probe the influence of each amino acid on the stable peptide conformation. Satisfactory agreement is obtained between measured and calculated diffusion cross section distributions. The results confirm the propensity of alanine-based peptides to form alpha-helices in the gas phase, differences between peptides arising from the local arrangement of the central side chain with respect to the charged ends. More generally, we find that charge solvation plays a major role in secondary structure stabilization, especially in the case of glycine-based peptides. The rich variety of conformations exhibited by the latter is qualitatively captured by the simulations. This work illustrates the potentiality of such combined experimental/theoretical strategy to determine peptide secondary structures. The present polyalanine and polyglycine peptides also offer a series of benchmark systems for future conformation-resolved studies.

Action-FRET: Probing the Molecular Conformation of Mass-Selected Gas-Phase Peptides with Förster Resonance Energy Transfer Detected by Acceptor-Specific Fragmentation

“…Ion mobility measurements were performed using a custom-built ion mobility spectrometer already described elsewhere. 41 Briefly, a 1 m long drift tube is inserted between an electrospray ionization source and a time-of-flight (TOF) mass spectrometer. Helium at a Analytical Chemistry pressure of 15 Torr is maintained in the drift tube, and the temperature of the whole setup is kept at 300 K. Ions are periodically injected in the drift tube from an hourglass funnel ion trap.…”

Statistical Analysis of Ion Mobility Spectrometry. I. Unbiased and Guided Replica-Exchange Molecular Dynamics

“…By reproducing the shape of the experimental ATDs, the REMD simulations quantitatively account for the extent of conformational flexibility consistent with the observed peaks. As already shown in reference [28], different conformers may actually all lie within a single IMS peak. However, the width alone is compatible with the prediction from the Fick's law, hence the contribution of isomer spreading to the calculated distribution cannot be inferred and the diffusion broadening appears as the limiting factor for the resolving power of the instrument.…”

“…IM-MS measurements were carried out using a custom-built ion mobility spectrometer, the experimental setup of which is described elsewhere [28]. Briefly, the ions are formed in an electrospray ion source and transferred to a cylindrical ion trap [29] via an ion funnel.…”

“…We chose the two systems as representatives of the two main structural families identified in reference [28] upon a series of variants of the sequence RA 4 XA 4 K, X standing for one of the 20 naturally occuring amino acids. Most of the variants were found to form α-helices at room temperature, and shorter helices were assigned to the peptides for which the central amino acid side chain is involved in the solvation of the charges, as for X=D (further denoted AlaD).…”

“…Most of the variants were found to form α-helices at room temperature, and shorter helices were assigned to the peptides for which the central amino acid side chain is involved in the solvation of the charges, as for X=D (further denoted AlaD). Most of the other variants, including X=V (further denoted AlaV) form longer helices [28]. Figure 1 displays the ATDs recorded at room temperature for AlaV and AlaD using a drift field of 770 V.m -1 and a drift gas pressure of 12 Torr.…”