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.

Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Schubert, F; Rossi, M; Baldauf, C; Pagel, K; Warnke, S; von Helden, G; Filsinger, F; Kupser, P; Meijer, G; Salwiczek, M; Koksch, B; Scheffler, M; Blum, V

Published Date

  • March 2015

Published In

Volume / Issue

  • 17 / 11

Start / End Page

  • 7373 - 7385

PubMed ID

  • 25700010

Electronic International Standard Serial Number (EISSN)

  • 1463-9084

International Standard Serial Number (ISSN)

  • 1463-9076

Digital Object Identifier (DOI)

  • 10.1039/c4cp05541a

Language

  • eng