Berlin 2012 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 7: Posters: Proteins
BP 7.20: Poster
Montag, 26. März 2012, 17:30–19:30, Poster A
Probing peptide structure prototypes with first-principles replica exchange: Ac-Ala19-LysH+ vs. Ac-LysH+-Ala19 — •Franziska Schubert, Mariana Rossi, Carsten Baldauf, Volker Blum, and Matthias Scheffler — Fritz-Haber-Institut der MPG, D-14195 Berlin
Predicting the structure of peptides requires a method with high accuracy for “weak” interactions. We here focus on the predominant structure types of two alanine-based peptides under “clean-room” conditions in the gas phase from first principles and in comparison to experimental IR spectroscopy [1]: Ac-Ala19-LysH+, which is α-helical [2,3], in contrast to Ac-LysH+-Ala19, where mostly globular monomers and a small amount of helical dimers and helices with non-standard protonation sites are expected [3]. Despite supposedly very different conformers, Ac-LysH+-Ala19 and Ac-Ala19-LysH+ yield very similar experimental IR spectra in the ≈1000-2000 cm−1 wavenumber range. We suggest plausible candidates for all likely structure prototypes generated by a two-step structure search: On top of force-field based replica exchange molecular dynamics (REMD) scans we follow up with further REMD scans based on density functional theory with the van der Waals corrected [4] PBE functional. Helix-turn-helix motifs emerge as the most likely candidates and explain a subtle peak shift in experiment. [1] IRMPD experiments: G. von Helden, P. Kupser, K. Pagel, F. Filsinger, G. Meijer, Department of Molecular Physics, Fritz-Haber-Institut; [2] M. Rossi et al., JPCL 1, 3465 (2010); [3] M. Jarrold, PCCP 9, 1659 (2007); [4] A. Tkatchenko, M. Scheffler, PRL 102, 073005 (2009).