Protein folded states are kinetic hubs (Q33934376)

30 July 2017

Protein folded states are kinetic hubs (English)

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Correction for Bowman et al., Protein folded states are kinetic hubs

30 July 2017

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corrigendum / erratum

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2

Vijay S Pande

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30 July 2017

Gregory R Bowman

1

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PubMed ID

20534497

30 July 2017

language of work or name

English

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publication date

1 June 2010

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30 July 2017

6

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

inferred from page(s)

published in

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30 July 2017

107

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30 July 2017

24

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30 July 2017

10890-10895

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Enhanced modeling via network theory: Adaptive sampling of Markov state models

30 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Unfolded-state dynamics and structure of protein L characterized by simulation and experiment

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Rapid equilibrium sampling initiated from nonequilibrium data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Progress and challenges in the automated construction of Markov state models for full protein systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

The roles of entropy and kinetics in structure prediction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Intrinsic disorder in proteins associated with neurodegenerative diseases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Ruggedness in the folding landscape of protein L.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Using generalized ensemble simulations and Markov state models to identify conformational states

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

The unfolded state of the C-terminal domain of the ribosomal protein L9 contains both native and non-native structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

What have we learned from the studies of two-state folders, and what are the unanswered questions about two-state protein folding?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

The protein folding problem

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Transition networks for modeling the kinetics of conformational change in macromolecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Protein folding by zipping and assembly

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Sub-microsecond protein folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Single-molecule Forster resonance energy transfer study of protein dynamics under denaturing conditions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Protein folding pathways from replica exchange simulations and a kinetic network model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Protein folding in high-dimensional spaces: hypergutters and the role of nonnative interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Multiple parallel-pathway folding of proline-free Staphylococcal nuclease

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

On the simulation of protein folding by short time scale molecular dynamics and distributed computing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Emergence of Scaling in Random Networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Global optimization of clusters, crystals, and biomolecules.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Observation of strange kinetics in protein folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Collective dynamics of 'small-world' networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

From Levinthal to pathways to funnels

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Funnels, pathways, and the energy landscape of protein folding: a synthesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Nucleation, rapid folding, and globular intrachain regions in proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Intermediates in the folding reactions of small proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

The folding of hen lysozyme involves partially structured intermediates and multiple pathways

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Protein folding funnels: a kinetic approach to the sequence-structure relationship

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890711

Coarse master equations for peptide folding dynamics.

5 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003962107

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003962107

Destabilization of the Escherichia coli RNase H kinetic intermediate: switching between a two-state and three-state folding mechanism.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003962107

Preorganized secondary structure as an important determinant of fast protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003962107

Tuning lambda6-85 towards downhill folding at its melting temperature.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003962107

A one-dimensional free energy surface does not account for two-probe folding kinetics of protein alpha(3)D.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003962107

The ultimate speed limit to protein folding is conformational searching

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003962107

Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003962107

Low barrier kinetics: dependence on observables and free energy surface

21 January 2018

1 reference

12 December 2020

Order of steps in the cytochrome C folding pathway: evidence for a sequential stabilization mechanism

1 reference

12 December 2020

Rapid Cooperative Two-state Folding of a Miniature α–β Protein and Design of a Thermostable Variant

1 reference

12 December 2020

The protein folding network

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1003962107

1 reference

release_6fumsij245bbbgabarfhx22pma

30 July 2017

0 references

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/6fumsij245bbbgabarfhx22pma

24 November 2022

mapped directly with Wikidata item

PMCID

2890711

1 reference

30 July 2017

1 reference

PubMed ID

20534497