Identification of complex dynamic modes on prion proteinpeptides using multifrequency ESR with mesoporous materials

Abstract

Identifying protein dynamics is essential for studying protein function. However, the time-scale of dynamic modes varies over domains and segments of a protein. Here we describe an approach using multifrequency ESR with mesoporous materials for protein dynamics in confined nanospace that may mimic the crowded nature within a cell where proteins evolve to fold. While multifrequency ESR permits the separation of dynamic motions in different time-scales, we demonstrate its capability to capture dynamics can still be significantly enhanced by the encapsulation of nitroxide-labeled macromolecule into mesopores. Two mutants of a 26-residue prion protein peptide at temperatures from 2 to 27 °C are studied. The nanochannel provides the peptide with an ordered environment such that the global tumbling of peptide is slow, and ‘frozen’ on the ESR timescale. The local dynamic modes of the peptide in nanochannel are, therefore, distinctly reported on the spectra. The spectra of the peptide in β-hairpin vs. α-helical forms differ markedly, demonstrating the significant improvement of ESR spectroscopic capability due to our methodology. Such distinctly different spectral patterns between the two secondary structures of the peptide cannot be obtained from ESR studies in viscous aqueous solution. The dynamic modes on the peptide are thus unambiguously identified in our multifrequency experiments at the X- and Q-bands. Additionally, the multifrequency spectra for each mutant and temperature are simultaneously fitted to the rigorous models, e.g. the slowly-relaxing-local-structure model, for slow-motion ESR. Marked correlations are revealed and characterized quantitatively for the backbone flexibility between the β-hairpin and α-helical forms of the prion protein peptide. Confirmation of the slow collective dynamic modes extending across the β-hairpin is also provided through the spectral simulations.