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Journal of Chemical Physics / Volume 133 / Issue 1 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 133, 015101 (2010); http://dx.doi.org/10.1063/1.3456552 (6 pages)

Fluctuation power spectra reveal dynamical heterogeneity of peptides

Bhavin Khatri1, Zu Thur Yew2, Sergei Krivov2, Tom McLeish3, and Emanuele Paci4

1Institute for Condensed Matter and Complex Systems, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3JZ, United Kingdom
2Institute of Molecular and Cell Biology, University of Leeds, Leeds LS2 9JTUnited Kingdom
3Departments of Physics and Chemistry, Durham University, Durham DH1 3HP, United Kingdom
4Institute of Molecular and Cell Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom

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(Received 7 April 2010; accepted 2 June 2010; published online 7 July 2010)

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.

© 2010 American Institute of Physics

Article Outline

  1. MODELS AND SIMULATION
  2. RESULTS
    1. Static properties
    2. Characterizing dynamic properties
    3. Comparison of power spectra
    4. Power spectra from atomic level simulations
  3. DISCUSSION

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KEYWORDS and PACS

Keywords

biochemistry, biomechanics, fluctuations, free energy, molecular biophysics, polymers, proteins, simulation, spectral analysis

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3456552

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

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