TY - JOUR A1 - Santos de Freitas, M. A1 - Araghi, R. R. A1 - Brandenburg, E. A1 - Leiterer, Jork A1 - Emmerling, Franziska A1 - Folmert, K. A1 - Gerling-Driessen, U. I. M. A1 - Bardiaux, B. A1 - Böttcher, C. A1 - Pagel, K. A1 - Diehl, A. A1 - v. Berlepsch, H. A1 - Oschkinat, H. A1 - Koksch, B. T1 - The protofilament architecture of a de novo designed coiled coil-based amyloidogenic peptide N2 - Amyloid fibrils are polymers formed by proteins under specific conditions and in many cases they are related to pathogenesis, such as Parkinson’s and Alzheimer’s diseases. Their hallmark is the presence of a β-sheet structure. High resolution structural data on these systems as well as information gathered from multiple complementary analytical techniques is needed, from both a fundamental and a pharmaceutical perspective. Here, a previously reported de novo designed, pH-switchable coiled coil-based peptide that undergoes structural transitions resulting in fibril formation under physiological conditions has been exhaustively characterized by transmission electron microscopy (TEM), cryo-TEM, atomic force microscopy (AFM), wide-angle X-ray scattering (WAXS) and solid-state NMR (ssNMR). Overall, a unique 2-dimensional carpet-like assembly composed of large coexisiting ribbon-like, tubular and funnel-like structures with a clearly resolved protofilament substructure is observed. Whereas electron microscopy and scattering data point somewhat more to a hairpin model of β-fibrils, ssNMR data obtained from samples with selectively labelled peptides are in agreement with both, hairpin structures and linear arrangements. KW - Amyloid KW - Elektronenmikroskopie PY - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-458713 UR - https://www.sciencedirect.com/science/article/pii/S1047847718301333 SN - 1047-8477 VL - 203 IS - 3 SP - 263 EP - 272 PB - Elsevier AN - OPUS4-45871 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ickert, Stefanie A1 - Schwaar, Timm A1 - Springer, A. A1 - Grabarics, M. A1 - Riedel, Jens A1 - Beck, S. A1 - Pagel, K. A1 - Linscheid, M. W. T1 - Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes N2 - DNA and locked nucleic acid (LNA) were characterized as single strands, as well as double stranded DNA-DNA duplexes and DNA-LNA hybrids using tandem mass spectrometry with collision-induced dissociation. Additionally, ion mobility spectrometry was carried out on selected species. Oligonucleotide duplexes of different sequences – bearing mismatch positions and abasic sites of complementary DNA 15-mers – were investigated to unravel general trends in their stability in the gas phase. Single stranded LNA oligonucleotides were also investigated with respect to their gas phase behavior and fragmentation upon collision-induced dissociation. In contrast to the collision-induced dissociation of DNA, almost no base loss was observed for LNAs. Here, backbone cleavages were the dominant dissociation pathways. This finding was further underlined by the need for higher activation energies. Base losses from the LNA strand were also absent in fragmentation experiments of the investigated DNA-LNA hybrid duplexes. While DNA-DNA duplexes dissociated easily into single stranded fragments, the high stability of DNA-LNA hybrids resulted in predominant fragmentation of the DNA part rather than the LNA, while base losses were only observed from the DNA single strand of the hybrid. KW - Oligonucleotide fragmentation KW - Locked nucleic acids KW - Collision induced dissociation (CID) KW - Double strands KW - Ion mobility spectrometry PY - 2019 U6 - https://doi.org/10.1002/jms.4344 VL - 54 IS - 5 SP - 402 EP - 411 PB - Wiley AN - OPUS4-47485 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ickert, Stefanie A1 - Hofmann, J. A1 - Riedel, Jens A1 - Beck, S. A1 - Pagel, K. A1 - Linscheid, M. W. T1 - Charge-induced geometrical reorganization of DNA oligonucleotides studied by tandem mass spectrometry and ion mobility N2 - Mass spectrometry is applied as a tool for the elucidation of molecular structures. This premises that gas-phase structures reflect the original geometry of the analytes, while it requires a thorough understanding and investigation of the forces controlling and affecting the gas-phase structures. However, only little is known about conformational changes of oligonucleotides in the gas phase. In this study, a series of multiply charged DNA oligonucleotides (n¼15–40) has been subjected to a comprehensive tandem mass spectrometric study to unravel transitions between different ionic gas-phase structures. The nucleobase sequence and the chain length were varied to gain insights into their influence on the geometrical oligonucleotide organization. Altogether, 23 oligonucleotides were analyzed using collision-induced fragmentation. All sequences showed comparable correlation regarding the characteristic collision energy. This value that is also a measure for stability, strongly correlates with the net charge density of the precursor ions. With decreasing charge of the oligonucleotides, an increase in the fragmentation energy was observed. At a distinct charge density, a deviation from linearity was observed for all studied species, indicating a structural reorganization. To corroborate the proposed geometrical change, collisional cross-sections of the oligonucleotides at different charge states were determined using ion mobility-mass spectrometry. The results clearly indicate that an increase in charge density and thus Coulomb repulsion results in the transition from a folded, compact form to elongated structures of the precursor ions. Our data show this structural transition to depend mainly on the charge density, whereas sequence and size do not have an influence. KW - Ion mobility KW - Collision-induced dissociation KW - Mass spectrometry KW - Oligonucleotide KW - Fragmentation KW - Tandem-MS PY - 2018 U6 - https://doi.org/10.1177/1469066717746896 SN - 1469-0667 SN - 1751-6838 VL - 24 IS - 2 SP - 225 EP - 230 PB - Sage AN - OPUS4-44429 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -