Journal Article

PUBDB-2023-00346

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble

Kotobi, A.DESY* ; Schwob, L. (Corresponding author)DESY* ; Vonbun-Feldbauer, G. B. ; Rossi, M. ; Piero, G. ; Feiler, C. ; Berden, G. ; Oomens, J. ; Oostenrijk, B. H.Extern*DESY* ; Scuderi, D. ; Bari, S. (Corresponding author)DESY* ; Meißner, R. H. (Corresponding author)

2023
Macmillan Publishers Limited, part of Springer Nature [London]

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Please use a persistent id in citations: doi:10.1038/s42004-023-00835-3  doi:10.3204/PUBDB-2023-00346

Abstract: Leucine enkephalin (LeuEnk), a biologically active endogenous opioid pentapeptide, has been under intense investigation because it is small enough to allow efficient use of sophisticated computational methods and large enough to provide insights into low-lying minima of its conformational space. Here, we reproduce and interpret experimental infrared (IR) spectra of this model peptide in gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. In particular, we evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum that accounts for the corresponding canonical ensemble of the real experimental situation. Representative conformers are identified by partitioning the conformational phase space into subensembles of similar conformers. The IR contribution of each representative conformer is calculated from ab initio and weighted according to the population of each cluster. Convergence of the averaged IR signal is rationalized by merging contributions in a hierarchical clustering and the comparison to IR multiple photon dissociation experiments. The improvements achieved by decomposing clusters containing similar conformations into even smaller subensembles is strong evidence that a thorough assessment of the conformational landscape and the associated hydrogen bonding is a prerequisite for deciphering important fingerprints in experimental spectroscopic data.

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Contributing Institute(s):

1. Biomoleküle in Gasphase (FS-BIG)

Research Program(s):

1. 633 - Life Sciences – Building Blocks of Life: Structure and Function (POF4-633) (POF4-633)
2. HIDSS-0002 - DASHH: Data Science in Hamburg - Helmholtz Graduate School for the Structure of Matter (2019_IVF-HIDSS-0002) (2019_IVF-HIDSS-0002)
3. DFG project 390715994 - EXC 2056: CUI: Advanced Imaging of Matter (390715994) (390715994)
4. DFG project 194651731 - EXC 1074: Hamburger Zentrum für ultraschnelle Beobachtung (CUI): Struktur, Dynamik und Kontrolle von Materie auf atomarer Skala (194651731) (194651731)

Experiment(s):

1. Measurement at external facility

Appears in the scientific report 2023

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