jz9b02146_si_001.pdf (14.06 MB)
Extension-Dependent Drift Velocity and Diffusion (DrDiff) Directly Reconstructs the Folding Free Energy Landscape of Atomic Force Microscopy Experiments
journal contribution
posted on 2020-01-17, 14:37 authored by Frederico
Campos Freitas, Ronaldo Junio de OliveiraTwo equilibrium force
microscopy trajectories [q(t)] of
high-precision single-molecule spectroscopy
assays were analyzed: the pulling of an HIV RNA hairpin and of a 3-aa
sequence of the bacteriorhodopsin membrane protein. Both present hundreds
of two-state folding transitions, and their free-energy [F(q)] landscapes were previously obtained by deconvolving
time signals with the inverse Boltzmann and pfold methods. In this letter, the two F profiles
were reconstructed directly from the measured time-series by the drift-diffusion
(DrDiff) framework that characterized the effective conformational
drift-velocity [v(q)] and diffusion
[D(q)] coefficients. The two thermodynamic F profiles reconstructed with DrDiff directly from q(t) were in good agreement with those
previously obtained from the deconvolved time signals. q(t) trajectories simulated with a two-dimensional
framework in which the diffusion coefficient of the pulling setup
(q coordinate) differed from the molecule (x coordinate) were also analyzed by DrDiff. The performance
in reconstructing F was investigated in different
conditions of diffusion anisotropy in the simulated time-series using
Brownian dynamics. In addition, recently developed theories were used
in order to evaluate the quality of the analysis performed in the
experimental time series: the memory effects and the intrinsic biomolecular
dynamic properties after connecting the probe to the molecule. With
the 2-dimensional diffusive models and the additional analyses, it
is proposed that the different physical regimes imposed by the stiffer
probes of the two biomolecules will have an impact in the measured
extension-dependent D and, thus, in the reconstruction
of F by DrDiff. Stiffer AFM probes may reflect the
molecular behavior more faithfully and reconstruction of F might be more successful. The reported quantities extracted directly
from q(t) highlights the current
state of the biomolecule characterization by force spectroscopy experiments:
it is still challenging despite the recent advances, yet it is very
promising.
History
Usage metrics
Categories
Keywords
time-serieHIV RNA hairpinframeworkdeconvolved time signalsF profilesStiffer AFM probesbiomoleculeequilibrium force microscopy trajectoriesExtension-Dependent Drift VelocityFree Energy Landscapehigh-precision single-molecule spectroscopy assaysreconstructioncoefficient3- aa sequencebacteriorhodopsin membrane proteinAtomic Force Microscopy Experimentsdeconvolving time signalsdiffusionforce spectroscopy experimentsDrDiff
Licence
Exports
RefWorks
BibTeX
Ref. manager
Endnote
DataCite
NLM
DC