Simulation, experiment, and evolution: understanding nucleation in protein S6 folding (Q34375343)

1 August 2017

Simulation, experiment, and evolution: understanding nucleation in protein S6 folding (English)

1 reference

1 August 2017

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Eugene I. Shakhnovich

series ordinal

3

object named as

Eugene I Shakhnovich

1 reference

1 August 2017

Isaac A Hubner

1

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PubMed ID

15150413

1 August 2017

Mikael Oliveberg

series ordinal

2

1 reference

PubMed ID

15150413

1 August 2017

language of work or name

English

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publication date

18 May 2004

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

1 August 2017

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1 August 2017

101

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1 August 2017

22

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1 August 2017

8354-8359

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Side-chain dynamics and protein folding.

1 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Determination of a transition state at atomic resolution from protein engineering data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Molecular dynamics simulations of protein folding from the transition state

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Characterisation of the transition states for protein folding: towards a new level of mechanistic detail in protein engineering analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

From snapshot to movie: phi analysis of protein folding transition states taken one step further

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Salt-induced detour through compact regions of the protein folding landscape

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Go-ing for the prediction of protein folding mechanisms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

The FSSP database: fold classification based on structure-structure alignment of proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Application of physical organic chemistry to engineered mutants of proteins: Hammond postulate behavior in the transition state of protein folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Crystal structure of the ribosomal protein S6 from Thermus thermophilus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Theoretical Studies of Protein Folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

Commitment and nucleation in the protein G transition state.

6 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0401672101

Conformational plasticity in folding of the split beta-alpha-beta protein S6: evidence for burst-phase disruption of the native state

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0401672101

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0401672101

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0401672101

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.0401672101

Evolutionary conservation of the folding nucleus.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0401672101

A Correlation of Reaction Rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0401672101

Parallel protein-unfolding pathways revealed and mapped

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0401672101

Complete change of the protein folding transition state upon circular permutation.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

27 October 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0401672101

Conserved residues and the mechanism of protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0401672101

Interpreting the folding kinetics of helical proteins

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=420398

High-energy channeling in protein folding

9 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15150413

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15150413

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0401672101

1 reference

1 August 2017

0 references

1 reference

1 reference

1 August 2017

1 reference

PubMed ID

15150413