Axis-dependent anisotropy in protein unfolding from integrated nonequilibrium single-molecule experiments, analysis, and simulation (Q36696329)

15 August 2017

Axis-dependent anisotropy in protein unfolding from integrated nonequilibrium single-molecule experiments, analysis, and simulation (English)

1 reference

15 August 2017

Rene A Nome

1 reference

15 August 2017

Jason Ming Zhao

series ordinal

1 reference

15 August 2017

Wouter D Hoff

series ordinal

1 reference

15 August 2017

Norbert F Scherer

series ordinal

1 reference

15 August 2017

language of work or name

English

0 references

publication date

19 December 2007

1 reference

Proceedings of the National Academy of Sciences of the United States of America

15 August 2017

1 reference

inferred from page(s)

published in

1 reference

15 August 2017

104

1 reference

15 August 2017

1 reference

15 August 2017

20799-20804

1 reference

Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability.

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Anisotropic deformation response of single protein molecules.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Single-molecule detection of structural changes during Per-Arnt-Sim (PAS) domain activation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Atom-by-atom analysis of global downhill protein folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Protein structure by mechanical triangulation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Free energy surfaces from single-molecule force spectroscopy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Predicting the signaling state of photoactive yellow protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Protein unfolding in the cell

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Pulling geometry defines the mechanical resistance of a beta-sheet protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Kinetics from nonequilibrium single-molecule pulling experiments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Photoactive Yellow Protein: A Prototypic PAS Domain Sensory Protein and Development of a Common Signaling Mechanism

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Experimental identification of downhill protein folding.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Understanding protein folding with energy landscape theory. Part I: Basic concepts

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Folding and signaling share the same pathway in a photoreceptor

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Free energy reconstruction from nonequilibrium single-molecule pulling experiments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Probing the nature of the blue-shifted intermediate of photoactive yellow protein in solution by NMR: hydrogen-deuterium exchange data and pH studies

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Submicrosecond real-time fluorescence sampling: application to protein folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

PAS domains: internal sensors of oxygen, redox potential, and light

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Solution structure and backbone dynamics of the photoactive yellow protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila: picosecond transient absorption spectroscopy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Photoactive yellow protein: a structural prototype for the three-dimensional fold of the PAS domain superfamily.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Contact order, transition state placement and the refolding rates of single domain proteins.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Theory of protein folding: the energy landscape perspective

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

The eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Simple model of protein folding kinetics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Properties of a water-soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Models for the Specific Adhesion of Cells to Cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Evidence for trans-cis isomerization of the p-coumaric acid chromophore as the photochemical basis of the photocycle of photoactive yellow protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Measurement and global analysis of the absorbance changes in the photocycle of the photoactive yellow protein from Ectothiorhodospira halophila

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Protein folding intermediates: native-state hydrogen exchange

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Cooperativity principles in protein folding.

28 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Reciprocal Relations in Irreversible Processes. I

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

The mechanical stability of ubiquitin is linkage dependent

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Force-clamp spectroscopy monitors the folding trajectory of a single protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Single-molecule unfolding force distributions reveal a funnel-shaped energy landscape

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Nonequilibrium Equality for Free Energy Differences

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Complete chemical structure of photoactive yellow protein: novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Formation of a new buried charge drives a large-amplitude protein quake in photoreceptor activation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

The solution structure of a transient photoreceptor intermediate: Delta25 photoactive yellow protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Lack of negative charge in the E46Q mutant of photoactive yellow protein prevents partial unfolding of the blue-shifted intermediate

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Global conformational changes upon receptor stimulation in photoactive yellow protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Light induces destabilization of photoactive yellow protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Decreased resistance to bacterial infection and granulocyte defects in IAP-deficient mice.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Intrinsic rates and activation free energies from single-molecule pulling experiments

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2410074

Denatured states of ribonuclease A have compact dimensions and residual secondary structure

5 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Polysaccharide elasticity governed by chair–boat transitions of the glucopyranose ring

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701281105

Thiol ester-linked p-coumaric acid as a new photoactive prosthetic group in a protein with rhodopsin-like photochemistry

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18093935

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0701281105

1 reference

15 August 2017

0 references

1 reference

15 August 2017

PubMed publication ID

18093935

1 reference