Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates (Q35841721)

10 August 2017

Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates (English)

1 reference

10 August 2017

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Xianghong Qi

1

1 reference

10 August 2017

John J Portman

series ordinal

2

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10 August 2017

language of work or name

English

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publication date

14 June 2007

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

10 August 2017

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10 August 2017

104

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10 August 2017

26

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10 August 2017

10841-10846

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End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Dynamics, energetics, and structure in protein folding

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Sub-microsecond protein folding

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Effects of denaturants on the dynamics of loop formation in polypeptides

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Statistical coil model of the unfolded state: resolving the reconciliation problem

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Downhill protein folding: evolution meets physics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Determination of barrier heights and prefactors from protein folding rate data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Three-body interactions improve the prediction of rate and mechanism in protein folding models

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

The protein folding 'speed limit'.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Critical nucleation size in the folding of small apparently two-state proteins

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Contact order revisited: influence of protein size on the folding rate

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

The topomer search model: A simple, quantitative theory of two-state protein folding kinetics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Measuring the rate of intramolecular contact formation in polypeptides

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Experiment and theory highlight role of native state topology in SH3 folding

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

A simple model for calculating the kinetics of protein folding from three-dimensional structures

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

A theoretical search for folding/unfolding nuclei in three-dimensional protein structures

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Folding funnels and energy landscapes of larger proteins within the capillarity approximation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Structural correlations in protein folding funnels

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

11 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling?

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Scaling of folding times with protein size

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Scanning malleable transition state ensembles: comparing theory and experiment for folding protein U1A.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Phi-value analysis of apo-azurin folding: comparison between experiment and theory

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Theoretical study of a landscape of protein folding-unfolding pathways. Folding rates at midtransition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Rapid collapse precedes the fast two-state folding of the cold shock protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

A limiting speed for protein folding at low solvent viscosity

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Simple physical models connect theory and experiment in protein folding kinetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Desolvation is a likely origin of robust enthalpic barriers to protein folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Effect of finite size on cooperativity and rates of protein folding.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Chevron behavior and isostable enthalpic barriers in protein folding: successes and limitations of simple Gō-like modeling.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891811

Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach

24 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Effects of Chain Stiffness on the Dynamics of Loop Formation in Polypeptides. Appendix: Testing a 1-Dimensional Diffusion Model for Peptide Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Outlining Folding Nuclei in Globular Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

Folding at the speed limit

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0609321104

A microscopic basis for the global appearance of energy landscapes

21 January 2018

1 reference

12 December 2020

Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble

1 reference

12 December 2020

New results for phase transitions from catastrophe theory

1 reference

12 December 2020

Evidence for barrier-limited protein folding kinetics on the microsecond time scale

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0609321104

1 reference

10 August 2017

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1 reference

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10 August 2017

PubMed publication ID

17569785

1 reference