Conformations of Prolyl-Peptide Bonds in the Bradykinin 1-5 Fragment in Solution and in the Gas Phase.

The dynamic nature of intrinsically disordered peptides makes them a challenge to characterize by solution-phase techniques. In order to gain insight into the relation between the disordered state and the environment, we explore the conformational space of the N-terminal 1-5 fragment of bradykinin (BK[1-5](2+)) in the gas phase by combining drift tube ion mobility, cold-ion spectroscopy, and first-principles simulations. The ion-mobility distribution of BK[1-5](2+) consists of two well-separated peaks. We demonstrate that the conformations within the peak with larger cross-section are kinetically trapped, while the more compact peak contains low-energy structures. This is a result of cis-trans isomerization of the two prolyl-peptide bonds in BK[1-5](2+). Density-functional theory calculations reveal that the compact structures have two very different geometries with cis-trans and trans-cis backbone conformations. Using the experimental CCSs to guide the conformational search, we find that the kinetically trapped species have a trans-trans configuration. This is consistent with NMR measurements performed in a solution, which show that 82% of the molecules adopt a trans-trans configuration and behave as a random coil.

Native like helices in a specially designed ß peptide in the gas phase.

In the natural peptides, helices are stabilized by hydrogen bonds that point backward along the sequence direction. Until now, there is only little evidence for the existence of analogous structures in oligomers of conformationally unrestricted ß amino acids. We specifically designed the ß peptide Ac-(ß(2)hAla)6-LysH(+) to form native like helical structures in the gas phase. The design follows the known properties of the peptide Ac-Ala6-LysH(+) that forms a α helix in isolation. We perform ion-mobility mass-spectrometry and vibrational spectroscopy in the gas phase, combined with state-of-the-art density-functional theory simulations of these molecular systems in order to characterize their structure. We can show that the straightforward exchange of alanine residues for the homologous ß amino acids generates a system that is generally capable of adopting native like helices with backward oriented H-bonds. By pushing the limits of theory and experiments, we show that one cannot assign a single preferred structure type due to the densely populated energy landscape and present an interpretation of the data that suggests an equilibrium of three helical structures.

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.

Infrared photodissociation spectroscopy of microhydrated nitrate-nitric acid clusters NO3(-)(HNO3)(m)(H2O)(n).

Infrared multiple photon dissociation (IRMPD) spectra of NO3(-)(HNO3)m(H2O)n(H2)z with m = 1-3, up to n = 8 and z ≥ 1, are measured in the fingerprint region (550-1880 cm(-1)), directly probing the NO-stretching modes, as well as bending and other lower frequency modes. The assignment of the spectra is aided by electronic structure calculations. The IRMPD spectrum of the m = 1, n = 0 cluster is distinctly different from all the other measured spectra as a result of strong hydrogen bonding, leading to an equally shared proton in between two nitrate moieties (O2NO(-)···H(+)···ONO2(-)). It exhibits a strong absorption at 877 cm(-1) and lacks the characteristic NO2-antisymmetric stretching/NOH-bending mode absorption close to 1650 cm(-1). Addition of at least one more nitric acid molecule or two more water molecules weakens the hydrogen bond network, breaking the symmetry of this arrangement and leading to localization of the proton near one of the nitrate cores, effectively forming HNO3 hydrogen-bonded to NO3(-). Not all IR active modes are observed in the IRMPD spectra of the bare nitrate-nitric acid clusters. Addition of a water or a hydrogen molecule lowers the dissociation limit of the complexes and relaxes (H2O) or lifts (H2) this IRMPD transparency.

Comparison of Aspiration Catheters with Modified Standard Catheters for Treatment of Large Pulmonary Embolism Using an In-vitro Patho-Physiological Model.

PURPOSE: The presented in-vitro study provides a comparison of various catheters for mechanical treatment of large-burden pulmonary embolism (PE) under standardized conditions, using a new test rig. Dedicated aspiration catheters (JETi®, Penumbra Indigo®, Aspirex®) were compared with standard catheters (Pigtail, Multi-Purpose, Balloon Catheter) applied for embolus fragmentation. MATERIALS AND METHODS: Emboli prepared from porcine blood were washed into the test rig which consists of anatomical models of the pulmonary artery (PA) and of the right heart in combination with a pulsatile drive system. For all catheters, the duration of the recanalization procedure and the weight percentage (wt%) of the remaining, removed and washed-down clot fractions were evaluated. For aspiration catheters, the aspirated volume was measured. RESULTS: All catheters achieved full or partial recanalization. The aspiration catheters showed a significantly (p < 0.05) lower procedure time (3:15 min ± 4:26 min) than the standard fragmentation catheters (7:19 min ± 4:40 min). The amount of thrombus removed by aspiration was significantly (p < 0.001) higher than that by fragmentation, averaging 86.1 wt% ± 15.6 wt% and 31.7 wt% ± 3.8 wt%, respectively. Nonetheless, most of the residue was fragmented into pieces of ≥ 1 mm and washed down. Only in 2 of 36 tests, a residual thrombus of 11.9 wt% ± 5.1 wt% remained in the central PA. CONCLUSION: Comparison under standardized in-vitro patho-physiological conditions showed that embolus fragmentation with standard catheters is clearly inferior to aspiration with dedicated catheters in the treatment of large-burden PE, but can still achieve considerable success. LEVEL OF EVIDENCE: No level of evidence, experimental study.