(Q35993395)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

title

Structural distributions from single-molecule measurements as a tool for molecular mechanics (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

4

1 reference

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3 February 2020

author name string

Jeffrey A Hanson

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

Jason Brokaw

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

Carl C Hayden

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

Haw Yang

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

publication date

22 June 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

volume

396

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

page(s)

61-71

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

All-atom empirical potential for molecular modeling and dynamics studies of proteins

3 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

The radial distribution function of worm-like chains.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Many local motions cooperate to produce the adenylate kinase conformational transition

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Entropic mechanism of large fluctuation in allosteric transition

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Dynamic active-site protection by the M. tuberculosis protein tyrosine phosphatase PtpB lid domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Mechanically-induced chemical changes in polymeric materials

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Small- and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Quantitative evaluation of cross correlation between two finite-length time series with applications to single-molecule FRET.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

A general statistical test for correlations in a finite-length time series

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

A practical guide to single-molecule FRET

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Effect of flexibility and cis residues in single-molecule FRET studies of polyproline

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Illuminating the mechanistic roles of enzyme conformational dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Probing polyproline structure and dynamics by photoinduced electron transfer provides evidence for deviations from a regular polyproline type II helix.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

A 10-A spectroscopic ruler applied to short polyprolines

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Simultaneous time- and wavelength-resolved fluorescence microscopy of single molecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Thermal fluctuations of grafted microtubules provide evidence of a length-dependent persistence length

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Single-molecule fluorescence studies of protein folding and conformational dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Specificity and versatility of SH3 and other proline-recognition domains: structural basis and implications for cellular signal transduction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Recognition of proline-rich motifs by protein-protein-interaction domains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Information bounds and optimal analysis of dynamic single molecule measurements

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Ten years of tension: single-molecule DNA mechanics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Is polyproline II a major backbone conformation in unfolded proteins?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Polyproline II structure in a sequence of seven alanine residues.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Magnetic tweezers: micromanipulation and force measurement at the molecular level

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Polyproline II helical structure in protein unfolded states: lysine peptides revisited

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Distance estimates from paramagnetic enhancements of nuclear relaxation in linear and flexible model peptides

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

A survey of left-handed polyproline II helices

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Estimating the persistence length of a worm-like chain molecule from force-extension measurements

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Entropic elasticity of lambda-phage DNA

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Energy transfer: a spectroscopic ruler

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Conformational energy and configurational statistics of poly-L-proline

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Fluorescence resonance energy transfer and nucleic acids

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Measuring distances within unfolded biopolymers using fluorescence resonance energy transfer: The effect of polymer chain dynamics on the observed fluorescence resonance energy transfer efficiency

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Single molecule conformational dynamics of adenylate kinase: energy landscape, structural correlations, and transition state ensembles

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Conformational properties of poly-L-proline in concentrated salt solutions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Mechanical reconfiguration of stereoisomers

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Size, shape, and flexibility of proteins and DNA.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Kinetics and statistical distributions of single-molecule conformational dynamics

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Method to derive restoring forces of strained molecules from kinetic measurements.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Size, shape, and flexibility of RNA structures

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Detection of intensity change points in time-resolved single-molecule measurements

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Accurate single-pair Förster resonant energy transfer through combination of pulsed interleaved excitation, time correlated single-photon counting, and fluorescence correlation spectroscopy.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Quantitative single-molecule conformational distributions: a case study with poly-(L-proline).

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Optical torque wrench: angular trapping, rotation, and torque detection of quartz microparticles.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Generalized born model with a simple smoothing function.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Tracer studies on f-actin fluctuations.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Conformational properties of poly-L-proline form II in dilute solution.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361908

Calculation of the Characteristic Ratio of Randomly Coiled Poly(L-proline)

23 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22661822

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Kinetic mechanism for conformational transitions between poly-L-prolines I and II: a study utilizing the cis-trans specificity of a proline-specific protease

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22661822

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.CHEMPHYS.2011.06.014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

PubMed publication ID

22661822

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22661822%20AND%20SRC:MED&resulttype=core&format=json