Hierarchical features of the energy landscape of the folding/unfolding behavior of adenylate kinase, including its dependence on denaturant concentration, are elucidated in terms of single-molecule fluorescence resonance energy transfer (smFRET) measurements in which the proteins are encapsulated in a lipid vesicle. The core in constructing the energy landscape from single-molecule time-series across different denaturant concentrations is the application of rate-distortion theory (RDT), which naturally considers the effects of measurement noise and sampling error, in combination with change-point detection and the quantification of the FRET efficiency-dependent photobleaching behavior. Energy landscapes are constructed as a function of observation time scale, revealing multiple partially folded conformations at small time scales that are situated in a superbasin. As the time scale increases, these denatured states merge into a single basin, demonstrating the coarse-graining of the energy landscape as observation time increases. Because the photobleaching time scale is dependent on the conformational state of the protein, possible nonequilibrium features are discussed, and a statistical test for violation of the detailed balance condition is developed based on the state sequences arising from the RDT framework.
Skip Nav Destination
Deciphering hierarchical features in the energy landscape of adenylate kinase folding/unfolding
Article navigation
28 March 2018
Research Article|
January 24 2018
Deciphering hierarchical features in the energy landscape of adenylate kinase folding/unfolding
Special Collection:
Single Molecule Biophysics
J. Nicholas Taylor;
J. Nicholas Taylor
1
Research Institute for Electronic Science, Hokkaido University
, Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020, Japan
Search for other works by this author on:
Menahem Pirchi;
Menahem Pirchi
2
Weizmann Institute of Science
, Rehovot 76100, Israel
Search for other works by this author on:
Gilad Haran
;
Gilad Haran
2
Weizmann Institute of Science
, Rehovot 76100, Israel
Search for other works by this author on:
Tamiki Komatsuzaki
Tamiki Komatsuzaki
1
Research Institute for Electronic Science, Hokkaido University
, Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020, Japan
3
Graduate School of Life Science
, Hokkaido University, Sapporo 001-0020, Japan
Search for other works by this author on:
J. Chem. Phys. 148, 123325 (2018)
Article history
Received:
November 20 2017
Accepted:
January 05 2018
Citation
J. Nicholas Taylor, Menahem Pirchi, Gilad Haran, Tamiki Komatsuzaki; Deciphering hierarchical features in the energy landscape of adenylate kinase folding/unfolding. J. Chem. Phys. 28 March 2018; 148 (12): 123325. https://doi.org/10.1063/1.5016487
Download citation file:
Sign in
Don't already have an account? Register
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Sign in via your Institution
Sign in via your InstitutionPay-Per-View Access
$40.00