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Unfolded protein and peptide dynamics investigated with single-molecule FRET and correlation spectroscopy from picoseconds to seconds.


Nettels, D; Hoffmann, A; Schuler, B (2008). Unfolded protein and peptide dynamics investigated with single-molecule FRET and correlation spectroscopy from picoseconds to seconds. Journal of Physical Chemistry. B, 112(19):6137-6146.

Abstract

Single-molecule fluorescence spectroscopy and correlation methods are finding increasing applications in the investigation of biomolecular dynamics, especially together with Förster resonance energy transfer (FRET). Here, we use the combination of start-stop experiments and classical fluorescence correlation spectroscopy (FCS) to obtain complete intensity auto- and cross-correlation functions from picoseconds to seconds for investigating the dynamics of unfolded proteins and peptides. In combination with distance information from single-molecule transfer efficiency histograms, we can analyze the data in terms of a diffusive process on a potential of mean force to obtain intramolecular diffusion coefficients. This allows us to extend our previous analysis of the time scales of chain dynamics into the low nanosecond range for peptides and into the microsecond range for a small cold shock protein (Csp). Dynamics in short unstructured peptides can be detected down to a time scale of about 10 ns, placing a lower limit on the time scales accessible with correlation methods and currently used dye pairs. We find no evidence for microsecond fluctuations in unfolded Csp, suggesting that its global chain dynamics occur predominantly in the tens of nanosecond range. We further investigate the position dependence of these dynamics by placing donor and acceptor dyes at different positions within the chain and find a decrease in the intramolecular diffusion coefficient by a factor of 3 upon moving one of the dyes toward the center of the polypeptide. Obtaining dynamic information on a wide range of time scales from single-molecule photon statistics will be of increasing importance for the study of unfolded proteins and for biomolecules in general.

Single-molecule fluorescence spectroscopy and correlation methods are finding increasing applications in the investigation of biomolecular dynamics, especially together with Förster resonance energy transfer (FRET). Here, we use the combination of start-stop experiments and classical fluorescence correlation spectroscopy (FCS) to obtain complete intensity auto- and cross-correlation functions from picoseconds to seconds for investigating the dynamics of unfolded proteins and peptides. In combination with distance information from single-molecule transfer efficiency histograms, we can analyze the data in terms of a diffusive process on a potential of mean force to obtain intramolecular diffusion coefficients. This allows us to extend our previous analysis of the time scales of chain dynamics into the low nanosecond range for peptides and into the microsecond range for a small cold shock protein (Csp). Dynamics in short unstructured peptides can be detected down to a time scale of about 10 ns, placing a lower limit on the time scales accessible with correlation methods and currently used dye pairs. We find no evidence for microsecond fluctuations in unfolded Csp, suggesting that its global chain dynamics occur predominantly in the tens of nanosecond range. We further investigate the position dependence of these dynamics by placing donor and acceptor dyes at different positions within the chain and find a decrease in the intramolecular diffusion coefficient by a factor of 3 upon moving one of the dyes toward the center of the polypeptide. Obtaining dynamic information on a wide range of time scales from single-molecule photon statistics will be of increasing importance for the study of unfolded proteins and for biomolecules in general.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Department of Biochemistry
07 Faculty of Science > Department of Biochemistry
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:8 February 2008
Deposited On:24 Oct 2008 14:10
Last Modified:05 Apr 2016 12:28
Publisher:American Chemical Society
ISSN:1520-5207
Publisher DOI:10.1021/jp076971j
Official URL:http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/2008/112/i19/abs/jp076971j.html
PubMed ID:18410159
Permanent URL: http://doi.org/10.5167/uzh-4002

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