The origins of asymmetry in the folding transition states of protein L and protein G. (Q38270380)

1 September 2017

The origins of asymmetry in the folding transition states of protein L and protein G. (English)

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1 September 2017

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John Karanicolas

1

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PMCID

2373711

1 September 2017

Charles L Brooks

series ordinal

2

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PMCID

2373711

1 September 2017

language of work or name

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1 October 2002

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1 September 2017

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1 September 2017

11

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1 September 2017

10

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1 September 2017

2351-2361

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Viewing protein folding from many perspectives

1 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Computer-based redesign of a protein folding pathway

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Mechanisms of protein folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Barriers in protein folding reactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Experiment and theory highlight role of native state topology in SH3 folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

The fundamentals of protein folding: bringing together theory and experiment

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Folding funnels and frustration in off-lattice minimalist protein landscapes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Molecular picture of folding of a small alpha/beta protein

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

The environmental dependency of protein folding best explains prion and amyloid diseases

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Conformational analysis of peptides corresponding to all the secondary structure elements of protein L B1 domain: secondary structure propensities are not conserved in proteins with the same fold

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional heteronuclear NMR spectroscopy.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

The complexity and accuracy of discrete state models of protein structure

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Fast folding of a prototypic polypeptide: the immunoglobulin binding domain of streptococcal protein G.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

The Protein Data Bank: a computer-based archival file for macromolecular structures

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Structure-derived potentials and protein simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Identifying the protein folding nucleus using molecular dynamics.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Kinetic analysis of folding and unfolding the 56 amino acid IgG-binding domain of streptococcal protein G.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Critical role of beta-hairpin formation in protein G folding.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

The single helix in protein L is largely disrupted at the rate-limiting step in folding.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

How do small single-domain proteins fold?

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373711

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

31 August 2018

1 reference

https://api.crossref.org/works/10.1110%2FPS.0205402

A breakdown of symmetry in the folding transition state of protein L

21 January 2018

1 reference

https://api.crossref.org/works/10.1110%2FPS.0205402

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1110%2FPS.0205402

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1110%2FPS.0205402

Kinetics of Folding of the IgG Binding Domain of Peptostreptoccocal Protein L

21 January 2018

1 reference

https://api.crossref.org/works/10.1110%2FPS.0205402

Structural Transitions in the Protein L Denatured State Ensemble

21 January 2018

1 reference

https://api.crossref.org/works/10.1110%2FPS.0205402

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1110%2FPS.0205402

Characterization of the free energy spectrum of peptostreptococcal protein L

21 January 2018

1 reference

https://api.crossref.org/works/10.1110%2FPS.0205402

NMR characterization of residual structure in the denatured state of protein L

21 January 2018

1 reference

https://api.crossref.org/works/10.1110%2FPS.0205402

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1110%2FPS.0205402

Interpreting the folding kinetics of helical proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1110%2FPS.0205402

Proton nuclear magnetic resonance sequential assignments and secondary structure of an immunoglobulin light chain-binding domain of protein L

21 January 2018

1 reference

12 December 2020

Calculations on folding of segment B1 of streptococcal protein G

1 reference

12 December 2020

Structure and dynamics of an acid-denatured protein G mutant

1 reference

12 December 2020

Folding dynamics of the B1 domain of protein G explored by ultrarapid mixing

1 reference

12 December 2020

Optimized Monte Carlo data analysis

1 reference

12 December 2020

Identifiers

DOI

10.1110/PS.0205402

1 reference

1 September 2017

1 reference

1 September 2017

1 reference

PMCID

2373711