Coordinate-dependent diffusion in protein folding (Q33667020)

28 July 2017

Coordinate-dependent diffusion in protein folding (English)

1 reference

28 July 2017

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Robert B Best

1

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Gerhard Hummer

object named as

Gerhard Hummer

series ordinal

2

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language of work or name

English

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publication date

28 December 2009

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

28 July 2017

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28 July 2017

107

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28 July 2017

3

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28 July 2017

1088-1093

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CHARMM: the biomolecular simulation program

28 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Chemical, physical, and theoretical kinetics of an ultrafast folding protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Measuring internal friction of an ultrafast-folding protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Diffusive reaction dynamics on invariant free energy profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Universality and diversity of folding mechanics for three-helix bundle proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Loop formation in unfolded polypeptide chains on the picoseconds to microseconds time scale

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Recent successes of the energy landscape theory of protein folding and function

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Atom-by-atom analysis of global downhill protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Effects of denaturants on the dynamics of loop formation in polypeptides

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

P versus Q: structural reaction coordinates capture protein folding on smooth landscapes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Reaction coordinates and rates from transition paths

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

The effects of nonnative interactions on protein folding rates: theory and simulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

The protein folding 'speed limit'.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Simulations of the role of water in the protein-folding mechanism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Kinetics from nonequilibrium single-molecule pulling experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Native-like mean structure in the unfolded ensemble of small proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

The origins of asymmetry in the folding transition states of protein L and protein G.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Measuring the rate of intramolecular contact formation in polypeptides

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

The speed limit for protein folding measured by triplet-triplet energy transfer.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Observation of strange kinetics in protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Limited internal friction in the rate-limiting step of a two-state protein folding reaction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Folding funnels and frustration in off-lattice minimalist protein landscapes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Solution structure of the albumin-binding GA module: a versatile bacterial protein domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

From Levinthal to pathways to funnels

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Kinetics and thermodynamics of folding in model proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

The role of solvent viscosity in the dynamics of protein conformational changes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

The ultimate speed limit to protein folding is conformational searching

21 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

A limiting speed for protein folding at low solvent viscosity

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

Effective stochastic dynamics on a protein folding energy landscape

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

Critical role of beta-hairpin formation in protein G folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

From transition paths to transition states and rate coefficients.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

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.0910390107

Speeding protein folding beyond the G(o) model: how a little frustration sometimes helps

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

Monte Carlo simulations of biomolecules: The MC module in CHARMM.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

Measurement of submicrosecond intramolecular contact formation in peptides at the single-molecule level

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824289

Diffusive Model of Protein Folding Dynamics with Kramers Turnover in Rate

30 October 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

Protein Folding Kinetics Under Force from Molecular Simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

Folding at the speed limit

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910390107

Folding time predictions from all-atom replica exchange simulations

21 January 2018

1 reference

12 December 2020

Upper limit of the time scale for diffusion and chain collapse in chymotrypsin inhibitor 2

1 reference

12 December 2020

Diffusional barrier crossing in a two-state protein folding reaction

1 reference

12 December 2020

Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin

1 reference

12 December 2020

Exact solution of the Muñoz-Eaton model for protein folding

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0910390107

1 reference

28 July 2017

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1 reference

28 July 2017

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PubMed ID

20080558