Direct molecular dynamics observation of protein folding transition state ensemble (Q30164998)

18 September 2017

Direct molecular dynamics observation of protein folding transition state ensemble (English)

1 reference

molecular dynamics simulation

18 September 2017

0 references

0 references

4

H Eugene Stanley

1 reference

18 September 2017

2

Nikolay V Dokholyan

1 reference

18 September 2017

3

Sergey V Buldyrev

1 reference

18 September 2017

1

Feng Ding

1 reference

PMCID

1302427

18 September 2017

Eugene I. Shakhnovich

series ordinal

5

object named as

Eugene I Shakhnovich

1 reference

PMCID

1302427

18 September 2017

language of work or name

English

0 references

publication date

1 December 2002

1 reference

18 September 2017

8

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

1 reference

18 September 2017

83

1 reference

18 September 2017

6

1 reference

18 September 2017

3525-3532

1 reference

Multiple protein folding nuclei and the transition state ensemble in two-state proteins

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Three key residues form a critical contact network in a protein folding transition state

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Circularization changes the folding transition state of the src SH3 domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

The identification of conserved interactions within the SH3 domain by alignment of sequences and structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

The SH3-fold family: experimental evidence and prediction of variations in the folding pathways

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Long-range order in the src SH3 folding transition state

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Identifying the protein folding nucleus using molecular dynamics.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Discrete molecular dynamics studies of the folding of a protein-like model.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Obligatory steps in protein folding and the conformational diversity of the transition state

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

A protein engineering analysis of the transition state for protein folding: simulation in the lattice model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Folding thermodynamics of a model three-helix-bundle protein.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Folding dynamics of the src SH3 domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Folding dynamics and mechanism of beta-hairpin formation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Nucleation mechanisms in protein folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

3 June 2018

How does a protein fold?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Mapping the transition state and pathway of protein folding by protein engineering

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Transient folding intermediates characterized by protein engineering

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Transition states and the meaning of Phi-values in protein folding kinetics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Interpreting the folding kinetics of helical proteins

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

How do small single-domain proteins fold?

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Specific nucleus as the transition state for protein folding: evidence from the lattice model.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Noninteracting local‐structure model of folding and unfolding transition in globular proteins. I. Formulation

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302427

Is protein unfolding the reverse of protein folding? A lattice simulation analysis

26 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975352-6

On the transition coordinate for protein folding

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975352-6

Can protein unfolding simulate protein folding?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975352-6

7 January 2021

Finding the right fold

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975352-6

10.1016/S0006-3495(02)75352-6

7 January 2021

Identifiers

DOI

1 reference

18 September 2017

1 reference

18 September 2017

1 reference

PMCID

1302427