Extracting intrinsic dynamic parameters of biomolecular folding from single-molecule force spectroscopy experiments (Q35667903)

9 August 2017

Extracting intrinsic dynamic parameters of biomolecular folding from single-molecule force spectroscopy experiments (English)

1 reference

9 August 2017

Gi-Moon Nam

1

1 reference

PubMed ID

26088347

9 August 2017

Dmitrii E Makarov

series ordinal

2

1 reference

9 August 2017

19 June 2015

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9 August 2017

1 reference

9 August 2017

25

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9 August 2017

1

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9 August 2017

123-134

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

9 August 2017

1 reference

Communication: Does force spectroscopy of biomolecules probe their intrinsic dynamic properties?

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Multidimensional reaction rate theory with anisotropic diffusion.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Perspective: Markov models for long-timescale biomolecular dynamics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Reconstructing folding energy landscapes by single-molecule force spectroscopy

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Analyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

How long does it take to equilibrate the unfolded state of a protein?

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Rigid DNA beams for high-resolution single-molecule mechanics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Atomic-level description of ubiquitin folding

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE Parallelization

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Rate limit of protein elastic response is tether dependent

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Protein folding kinetics and thermodynamics from atomistic simulation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Direct observation of multiple misfolding pathways in a single prion protein molecule

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Single-molecule fluorescence experiments determine protein folding transition path times

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

How fast-folding proteins fold

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Deconvolution of dynamic mechanical networks

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Free energy profiles from single-molecule pulling experiments

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Taming the complexity of protein folding

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Everything you wanted to know about Markov State Models but were afraid to ask

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Theory, analysis, and interpretation of single-molecule force spectroscopy experiments

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Protein folding studied by single-molecule FRET.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Ultrafast dynamics of protein collapse from single-molecule photon statistics.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Finding mechanochemical pathways and barriers without transition state search.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Force-clamp experiments reveal the free-energy profile and diffusion coefficient of the collapse of protein molecules.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

From mechanical folding trajectories to intrinsic energy landscapes of biopolymers.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Interplay of non-Markov and internal friction effects in the barrier crossing kinetics of biopolymers: insights from an analytically solvable model

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Failure of one-dimensional Smoluchowski diffusion models to describe the duration of conformational rearrangements in floppy, diffusive molecular systems: a case study of polymer cyclization.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Biomolecules under mechanical stress: a simple mechanism of complex behavior

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Atomic-level characterization of the structural dynamics of proteins

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

How the diffusivity profile reduces the arbitrariness of protein folding free energies.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Reaction-rate theory: fifty years after Kramers

25 September 2018

1 reference

Transition-Path Probability as a Test of Reaction-Coordinate Quality Reveals DNA Hairpin Folding Is a One-Dimensional Diffusive Process

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815315

Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments

25 September 2018

1 reference

Multiple Probes are Required to Explore and Control the Rugged Energy Landscape of RNA Hairpins

21 January 2018

1 reference

Unfolded Protein and Peptide Dynamics Investigated with Single-Molecule FRET and Correlation Spectroscopy from Picoseconds to Seconds†

21 January 2018

1 reference

Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories

21 January 2018

1 reference

12 December 2020

Concerted dihedral rotations give rise to internal friction in unfolded proteins

1 reference

12 December 2020

Locating the Barrier for Folding of Single Molecules under an External Force

1 reference

12 December 2020

Force-Induced Change in Protein Unfolding Mechanism: Discrete or Continuous Switch?

1 reference

12 December 2020

Topography of the free-energy landscape probed via mechanical unfolding of proteins

1 reference

12 December 2020

Molecular catch bonds and the anti-Hammond effect in polymer mechanochemistry

1 reference

12 December 2020

Identifiers

DOI

10.1002/PRO.2727

1 reference

9 August 2017

1 reference

9 August 2017

1 reference

PubMed ID

26088347