Phi-value analysis by molecular dynamics simulations of reversible folding (Q33756182)

29 July 2017

Phi-value analysis by molecular dynamics simulations of reversible folding (English)

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29 July 2017

3

Amedeo Caflisch

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29 July 2017

Giovanni Settanni

1

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29 July 2017

Francesco Rao

series ordinal

2

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29 July 2017

language of work or name

English

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publication date

11 January 2005

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

29 July 2017

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29 July 2017

102

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29 July 2017

3

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29 July 2017

628-633

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describes a project that uses

29 July 2017

molecular dynamics simulation

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Relationship of Leffler (Bronsted) alpha values and protein folding Phi values to position of transition-state structures on reaction coordinates

inferred from title

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

Phi-value analysis and the nature of protein-folding transition states

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

The folding transition state of the cold shock protein is strongly polarized

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

Transition states for protein folding have native topologies despite high structural variability

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

Origin of unusual phi-values in protein folding: evidence against specific nucleation sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

The present view of the mechanism 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=545520

Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: similarities and differences in the folding of homologous 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=545520

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

The ensemble folding kinetics of protein G from an all-atom Monte Carlo 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=545520

Molecular dynamics simulations of protein folding from the transition state

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

Evaluation of a fast implicit solvent model for molecular dynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

Computer-based redesign of a protein folding pathway

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

Folding simulations of a three-stranded antiparallel beta -sheet peptide

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

Fast kinetics and mechanisms 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=545520

De novo design of a monomeric three-stranded antiparallel beta-sheet

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

Is protein folding hierarchic? II. Folding intermediates and transition states

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545520

Dynamical theory of activated processes in globular 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=545520

The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway 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=545520

Thermodynamics and kinetics of non-native interactions in protein folding: a single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state

21 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0406754102

Commitment and nucleation in the protein G transition state.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0406754102

Structure of the transition state for folding of a protein derived from experiment and simulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0406754102

On the transition coordinate for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0406754102

Parallel protein-unfolding pathways revealed and mapped

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0406754102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0406754102

21 January 2018

Protein-folding dynamics

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0406754102

Native topology or specific interactions: what is more important for protein folding?

21 January 2018

1 reference

12 December 2020

Weak temperature dependence of the free energy surface and folding pathways of structured peptides

1 reference

12 December 2020

Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model

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12 December 2020

The protein folding network

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12 December 2020

Identifiers

DOI

10.1073/PNAS.0406754102

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29 July 2017

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29 July 2017

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