Universality and diversity of folding mechanics for three-helix bundle proteins (Q36458838)

14 August 2017

Universality and diversity of folding mechanics for three-helix bundle proteins (English)

1 reference

14 August 2017

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Eugene I. Shakhnovich

series ordinal

3

object named as

Eugene I Shakhnovich

1 reference

14 August 2017

Jae Shick Yang

1

1 reference

14 August 2017

Stefan Wallin

series ordinal

2

1 reference

14 August 2017

language of work or name

English

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publication date

14 January 2008

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

14 August 2017

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14 August 2017

105

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14 August 2017

3

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14 August 2017

895-900

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A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Conformational entropy of alanine versus glycine in protein denatured states

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

The mechanical unfolding of ubiquitin through all-atom Monte Carlo simulation with a Go-type potential.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Distinguishing between cooperative and unimodal downhill protein folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Understanding ensemble protein folding at atomic detail

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Flexibly varying folding mechanism of a nearly symmetrical protein: B domain of protein A.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Kinetic definition of protein folding transition state ensembles and reaction coordinates

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

High-resolution protein folding with a transferable potential

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Latest folding game results: protein A barely frustrates computationalists

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Testing protein-folding simulations by experiment: B domain of protein A.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Probing the folding and unfolding dynamics of secondary and tertiary structures in a three-helix bundle protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Unifying features in protein-folding mechanisms

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Experimental tests of villin subdomain folding simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Meeting halfway on the bridge between protein folding theory and experiment

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

The complete folding pathway of a protein from nanoseconds to microseconds

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Large-scale context in protein folding: villin headpiece

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

An atomically detailed study of the folding pathways of protein A with the stochastic difference equation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

A structure-based method for derivation of all-atom potentials for protein folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

SCOP: a structural classification of proteins database

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Matching theory and experiment in protein folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Clustering of low-energy conformations near the native structures of small proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Protein folding: matching theory and experiment

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Exploring the folding free energy surface of a three-helix bundle protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Absence of a stable intermediate on the folding pathway of protein A.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Direct observation of fast protein folding: the initial collapse of apomyoglobin

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242684

Transition state ensemble for the folding of B domain of protein A: a comparison of distributed molecular dynamics simulations with experiments

28 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707284105

All-atom generalized-ensemble simulations of small proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707284105

Phi-analysis of the folding of the B domain of protein A using multiple optical probes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707284105

Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707284105

Preorganized secondary structure as an important determinant of fast protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707284105

A discussion of the solution for the best rotation to relate two sets of vectors

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707284105

On the transition coordinate for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707284105

Folding of a small helical protein using hydrogen bonds and hydrophobicity forces

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707284105

Folding of small proteins using a single continuous potential

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707284105

The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707284105

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707284105

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=2242684

First-principles calculation of the folding free energy of a three-helix bundle protein

4 December 2018

1 reference

12 December 2020

All-atom ab initio folding of a diverse set of proteins

1 reference

12 December 2020

The protein folding network

1 reference

12 December 2020

Ab initio folding of helix bundle proteins using molecular dynamics simulations

1 reference

12 December 2020

Free-Energy Landscape of the Villin Headpiece in an All-Atom Force Field

1 reference

12 December 2020

Characterization of the folding kinetics of a three-helix bundle protein via a minimalist Langevin model

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0707284105

1 reference

14 August 2017

0 references

1 reference

1 reference

14 August 2017

PubMed publication ID

18195374

1 reference