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Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra

Michaelis, M.; Hildebrand, N.; Meißner, R. H.; Wurzler, N.; Li, Z.; Hirst, J. D.; Micsonai, A.; Kardos, J.; Delle Piane, M.; Colombi Ciacchi, L.

Authors

M. Michaelis

N. Hildebrand

R. H. Meißner

N. Wurzler

Z. Li

J. D. Hirst

A. Micsonai

J. Kardos

M. Delle Piane

L. Colombi Ciacchi



Abstract

Although successful in the structural determination of ordered biomolecules, the spectroscopic investigation of oligopeptides in solution is hindered by their complex and rapidly changing conformational ensemble. The measured circular dichroism (CD) spectrum of an oligopeptide is an ensemble average over all microstates, severely limiting its interpretation, in contrast to ordered biomolecules. Spectral deconvolution methods to estimate the secondary structure contributions in the ensemble are still mostly based on databases of larger ordered proteins. Here, we establish how the interpretation of CD spectra of oligopeptides can be enhanced by the ability to compute the same observable from a set of atomic coordinates. Focusing on two representative oligopeptides featuring a known propensity toward an α-helical and β-hairpin motif, respectively, we compare and cross-validate the structural information coming from deconvolution of the experimental CD spectra, sequence-based de novo structure prediction, and molecular dynamics simulations based on enhanced sampling methods. We find that small conformational variations can give rise to significant changes in the CD signals. While for the simpler conformational landscape of the α-helical peptide de novo structure prediction can already give reasonable

Journal Article Type Article
Publication Date Jul 25, 2019
Journal The Journal of Physical Chemistry B
Print ISSN 1520-6106
Electronic ISSN 1520-5207
Publisher American Chemical Society
Peer Reviewed Peer Reviewed
APA6 Citation Michaelis, M., Hildebrand, N., Meißner, R. H., Wurzler, N., Li, Z., Hirst, J. D., …Colombi Ciacchi, L. (2019). Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra. Journal of Physical Chemistry B, doi:10.1021/acs.jpcb.9b03932
DOI https://doi.org/10.1021/acs.jpcb.9b03932
Keywords Physical and Theoretical Chemistry; Materials Chemistry; Surfaces, Coatings and Films
Publisher URL https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03932
Additional Information This document is the Accepted Manuscript version of a Published Work that appeared in final form in The Journal of Physical Chemistry B, copyright © American Chemical Society after peer review and technical editing by the publisher, To access the final edited and published work see https://doi.org/10.1021/acs.jpcb.9b03932
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