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Fluctuation power spectra reveal dynamical heterogeneity of peptides.

Khatri, Bhavin and Yew, Zu Thur and Krivov, Sergei and McLeish, Tom and Paci, Emanuele (2010) 'Fluctuation power spectra reveal dynamical heterogeneity of peptides.', Journal of chemical physics., 133 (1). 015101.

Abstract

Characterizing the conformational properties and dynamics of biopolymers and their relation to biological activity and function is an ongoing challenge. Single molecule techniques have provided a rich experimental window on these properties, yet they have often relied on simple one-dimensional projections of a multidimensional free energy landscape for a practical interpretation of the results. Here, we study three short peptides with different structural propensity (α helical, β hairpin, and random coil) in the presence (or absence) of a force applied to their ends using Langevin dynamics simulation and an all-atom model with implicit solvation. Each peptide produces fluctuation power spectra with a characteristic dynamic fingerprint consistent with persistent structural motifs of helices, hairpins, and random coils. The spectra for helix formation shows two well-defined relaxation modes, corresponding to local relaxation and cooperative coil to uncoil interconversion. In contrast, both the hairpin and random coil are polymerlike, showing a broad and continuous range of relaxation modes giving characteristic power laws of ω−5/4 and ω−3/2, respectively; the −5/4 power law for hairpins is robust and has not been previously observed. Langevin dynamics simulations of diffusers on a potential of mean force derived from the atomistic simulations fail to reproduce the fingerprints of each peptide motif in the power spectral density, demonstrating explicitly that such information is lacking in such one-dimensional projections. Our results demonstrate the yet unexploited potential of single molecule fluctuation spectroscopy to probe more fine scaled properties of proteins and biological macromolecules and how low dimensional projections may cause the loss of relevant information.

Item Type:Article
Keywords:Biochemistry, Biomechanics, Fluctuations, Free energy, Molecular biophysics, Polymers, Proteins, Simulation, Spectral analysis.
Full text:PDF - Published Version (246Kb)
Status:Peer-reviewed
Publisher Web site:http://dx.doi.org/10.1063/1.3456552
Publisher statement:Copyright 2010 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in Khatri, Bhavin and Yew, Zu Thur and Krivov, Sergei and McLeish, Tom and Paci, Emanuele (2010) 'Fluctuation power spectra reveal dynamical heterogeneity of peptides.', Journal of chemical physics., 133 (1). 015101 and may be found at http://dx.doi.org/10.1063/1.3456552
Record Created:11 Jan 2012 15:35
Last Modified:12 Jan 2012 16:44

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