Calculation of mutational free energy changes in transition states for protein folding (Q30164603)

18 September 2017

Calculation of mutational free energy changes in transition states for protein folding (English)

1 reference

18 September 2017

0 references

2

Emanuele Paci

1 reference

PMCID

1303238

18 September 2017

Kresten Lindorff-Larsen

object named as

Kresten Lindorff-Larsen

series ordinal

1

0 references

Michele Vendruscolo

series ordinal

5

object named as

Michele Vendruscolo

1 reference

18 September 2017

4

Christopher M Dobson

1 reference

18 September 2017

Luis Serrano

3

1 reference

PMCID

1303238

18 September 2017

language of work or name

English

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publication date

1 August 2003

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18 September 2017

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18 September 2017

85

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18 September 2017

2

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18 September 2017

1207-1214

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Protein folding: bringing theory and experiment closer together

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Is there a unifying mechanism for 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=1303238

Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

A simple physical model for binding energy hot spots in protein-protein complexes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Non-native interactions, effective contact order, and protein folding: a mutational investigation with the energetically frustrated hydrophobic 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=1303238

Protein folding kinetics beyond the phi value: using multiple amino acid substitutions to investigate the structure of the SH3 domain 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=1303238

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Molecular dynamics simulations of the protein unfolding/folding reaction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Molecular dynamics simulations of protein folding from 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=1303238

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Protein folding and unfolding at atomic resolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Hydrophobic core packing in the SH3 domain 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=1303238

ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Mapping the folding pathway of an immunoglobulin domain: structural detail from Phi value analysis and movement 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=1303238

Protein folding theory: from lattice to all-atom models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

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=1303238

Understanding protein folding via free-energy surfaces from theory and experiment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

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=1303238

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=1303238

3 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Experiment and theory highlight role of native state topology in SH3 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=1303238

Mutational analysis of acylphosphatase suggests the importance of topology and contact order 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=1303238

Hierarchy of structure loss in MD simulations of src SH3 domain unfolding.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

"New view" of protein folding reconciled with the old through multiple unfolding simulations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

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=1303238

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=1303238

WHAT IF: a molecular modeling and drug design program

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of 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=1303238

Protein engineering study of protein L by simulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Im7 folding mechanism: misfolding on a path to the native state

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of u

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303238

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=1303238

On the transition coordinate for protein folding

26 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974556-1

The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974556-1

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974556-1

Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974556-1

10.1016/S0006-3495(03)74556-1

7 January 2021

Identifiers

DOI

1 reference

18 September 2017

1 reference

18 September 2017

1 reference

PMCID

1303238