Literature DB >> 23020428

Auto- and cross-power spectral analysis of dual trap optical tweezer experiments using Bayesian inference.

Yann von Hansen1, Alexander Mehlich, Benjamin Pelz, Matthias Rief, Roland R Netz.   

Abstract

The thermal fluctuations of micron-sized beads in dual trap optical tweezer experiments contain complete dynamic information about the viscoelastic properties of the embedding medium and-if present-macromolecular constructs connecting the two beads. To quantitatively interpret the spectral properties of the measured signals, a detailed understanding of the instrumental characteristics is required. To this end, we present a theoretical description of the signal processing in a typical dual trap optical tweezer experiment accounting for polarization crosstalk and instrumental noise and discuss the effect of finite statistics. To infer the unknown parameters from experimental data, a maximum likelihood method based on the statistical properties of the stochastic signals is derived. In a first step, the method can be used for calibration purposes: We propose a scheme involving three consecutive measurements (both traps empty, first one occupied and second empty, and vice versa), by which all instrumental and physical parameters of the setup are determined. We test our approach for a simple model system, namely a pair of unconnected, but hydrodynamically interacting spheres. The comparison to theoretical predictions based on instantaneous as well as retarded hydrodynamics emphasizes the importance of hydrodynamic retardation effects due to vorticity diffusion in the fluid. For more complex experimental scenarios, where macromolecular constructs are tethered between the two beads, the same maximum likelihood method in conjunction with dynamic deconvolution theory will in a second step allow one to determine the viscoelastic properties of the tethered element connecting the two beads.

Entities:  

Mesh:

Year:  2012        PMID: 23020428     DOI: 10.1063/1.4753917

Source DB:  PubMed          Journal:  Rev Sci Instrum        ISSN: 0034-6748            Impact factor:   1.523


  16 in total

1.  Folding and assembly of the large molecular machine Hsp90 studied in single-molecule experiments.

Authors:  Markus Jahn; Johannes Buchner; Thorsten Hugel; Matthias Rief
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-19       Impact factor: 11.205

2.  Ultrafast folding kinetics and cooperativity of villin headpiece in single-molecule force spectroscopy.

Authors:  Gabriel Žoldák; Johannes Stigler; Benjamin Pelz; Hongbin Li; Matthias Rief
Journal:  Proc Natl Acad Sci U S A       Date:  2013-10-21       Impact factor: 11.205

3.  Capturing transition paths and transition states for conformational rearrangements in the ribosome.

Authors:  Jeffrey K Noel; Jorge Chahine; Vitor B P Leite; Paul Charles Whitford
Journal:  Biophys J       Date:  2014-12-16       Impact factor: 4.033

4.  From mechanical folding trajectories to intrinsic energy landscapes of biopolymers.

Authors:  Michael Hinczewski; J Christof M Gebhardt; Matthias Rief; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2013-03-04       Impact factor: 11.205

5.  α-Actinin/titin interaction: A dynamic and mechanically stable cluster of bonds in the muscle Z-disk.

Authors:  Marco Grison; Ulrich Merkel; Julius Kostan; Kristina Djinović-Carugo; Matthias Rief
Journal:  Proc Natl Acad Sci U S A       Date:  2017-01-17       Impact factor: 11.205

6.  Multiplexing molecular tension sensors reveals piconewton force gradient across talin-1.

Authors:  Pia Ringer; Andreas Weißl; Anna-Lena Cost; Andrea Freikamp; Benedikt Sabass; Alexander Mehlich; Marc Tramier; Matthias Rief; Carsten Grashoff
Journal:  Nat Methods       Date:  2017-09-18       Impact factor: 28.547

7.  Nanomechanics of the substrate binding domain of Hsp70 determine its allosteric ATP-induced conformational change.

Authors:  Soumit Sankar Mandal; Dale R Merz; Maximilian Buchsteiner; Ruxandra I Dima; Matthias Rief; Gabriel Žoldák
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-22       Impact factor: 11.205

8.  Spectral Rate Theory for Two-State Kinetics.

Authors:  Jan-Hendrik Prinz; John D Chodera; Frank Noé
Journal:  Phys Rev X       Date:  2014-02       Impact factor: 15.762

9.  Unraveling the Mechanics of a Repeat-Protein Nanospring: From Folding of Individual Repeats to Fluctuations of the Superhelix.

Authors:  Marie Synakewicz; Rohan S Eapen; Albert Perez-Riba; Pamela J E Rowling; Daniela Bauer; Andreas Weißl; Gerhard Fischer; Marko Hyvönen; Matthias Rief; Laura S Itzhaki; Johannes Stigler
Journal:  ACS Nano       Date:  2022-03-08       Impact factor: 15.881

10.  Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK.

Authors:  Daniela Bauer; Dale R Merz; Benjamin Pelz; Kelly E Theisen; Gail Yacyshyn; Dejana Mokranjac; Ruxandra I Dima; Matthias Rief; Gabriel Žoldák
Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-03       Impact factor: 11.205

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