Exploring the conformational preferences of 20-residue peptides in isolation: Ac-Ala19-Lys + H(+)vs. Ac-Lys-Ala19 + H(+) and the current reach of DFT.

Reliable, quantitative predictions of the structure of peptides based on their amino-acid sequence information are an ongoing challenge. We here explore the energy landscapes of two unsolvated 20-residue peptides that result from a shift of the position of one amino acid in otherwise the same sequence. Our main goal is to assess the performance of current state-of-the-art density-functional theory for predicting the structure of such large and complex systems, where weak interactions such as dispersion or hydrogen bonds play a crucial role. For validation of the theoretical results, we employ experimental gas-phase ion mobility-mass spectrometry and IR spectroscopy. While unsolvated Ac-Ala19-Lys + H(+) will be shown to be a clear helix seeker, the structure space of Ac-Lys-Ala19 + H(+) is more complicated. Our first-principles structure-screening strategy using the dispersion-corrected PBE functional (PBE + vdW(TS)) identifies six distinctly different structure types competing in the low-energy regime (≈16 kJ mol(-1)). For these structure types, we analyze the influence of the PBE and the hybrid PBE0 functional coupled with either a pairwise dispersion correction (PBE + vdW(TS), PBE0 + vdW(TS)) or a many-body dispersion correction (PBE + MBD*, PBE0 + MBD*). We also take harmonic vibrational and rotational free energy into account. Including this, the PBE0 + MBD* functional predicts only one unique conformer to be present at 300 K. We show that this scenario is consistent with both experiments.

Amide-I and -II vibrations of the cyclic beta-sheet model peptide gramicidin S in the gas phase.

In the condensed phase, the peptide gramicidin S is often considered as a model system for a beta-sheet structure. Here, we investigate gramicidin S free of any influences of the environment by measuring the mid-IR spectra of doubly protonated (deuterated) gramicidin S in the gas phase. In the amide I (i.e., C=O stretch) region, the spectra show a broad split peak between 1580 and 1720 cm(-1). To deduce structural information, the conformational space has been searched using molecular dynamics methods and several structural candidates have been further investigated at the density functional level. The calculations show the importance of the interactions of the charged side-chains with the backbone, which is responsible for the lower frequency part of the amide I peak. When this interaction is inhibited via complexation with two 18-crown-6 molecules, the amide I peak narrows and shows two maxima at 1653 and 1680 cm(-1). A comparison to calculations shows that for this complexed ion, four C=O groups are in an antiparallel beta-sheet arrangement. Surprisingly, an analysis of the calculated spectra shows that these beta-sheet C=O groups give rise to the vibrations near 1680 cm(-1). This is in sharp contrast to expectations based on values for the condensed phase, where resonances of beta-sheet sections are thought to occur near 1630 cm(-1). The difference between those values might be caused by interactions with the environment, as the condensed phase value is mostly deduced for beta-sheet sections that are embedded in larger proteins, that interact strongly with solvent or that are part of partially aggregated species.

Catching proteins in liquid helium droplets.

An experimental approach is presented that allows for the incorporation of large mass-to-charge ratio selected ions in liquid helium droplets. It is demonstrated that droplets can be efficiently doped with a mass-to-charge ratio selected amino acid as well as with the much bigger m ≈ 12,000 amu protein cytochrome C in selected charge states. The sizes of the ion-doped droplets are determined via electrostatic deflection. Under the experimental conditions employed, the observed droplet sizes are very large and range, depending on the incorporated ion, from 10¹° helium atoms for protonated phenylalanine to 10¹² helium atoms for cytochrome C. As a possible explanation, a simple model based on the size and internal energy dependence of the pickup efficiency is given.

IR spectroscopy of gas-phase C60-.

We present the IR spectrum of the gas-phase C60(-) anion. The C60(-) anions are mass-selected and trapped in an ion cyclotron mass spectrometer cell. The spectrum is obtained by recording the yield of electrons following infrared multiple photon absorption and subsequent electron detachment of the anions. Two bands are observed that correlate to two of the four IR-allowed transitions in neutral C60. The results show that the higher frequency band is strongly shifted from its position in neutral C60 and is a sensitive marker for the charge state. The band positions and intensities are compared to results obtained by theory as well as to known bands in solid samples and good agreement is found.