Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot (Q30528367)

13 August 2017

Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot (English)

1 reference

13 August 2017

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Wenfei Li

1

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author name string

Tsuyoshi Terakawa

series ordinal

2

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13 August 2017

Wei Wang

series ordinal

3

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13 August 2017

Shoji Takada

series ordinal

4

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13 August 2017

language of work or name

English

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publication date

2 July 2012

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13 August 2017

6

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

inferred from page(s)

published in

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13 August 2017

109

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13 August 2017

44

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13 August 2017

17789-17794

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Coarse-grained molecular simulations of large biomolecules

13 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Single-molecule fluorescence experiments determine protein folding transition path times

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

How fast-folding proteins fold

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

The complex folding network of single calmodulin molecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Structure and folding of a designed knotted protein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Slipknotting upon native-like loop formation in a trefoil knot protein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

A Stevedore's protein knot

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Dodging the crisis of folding proteins with knots

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

From the first protein structures to our current knowledge of protein folding: delights and scepticisms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

The folding mechanics of a knotted protein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Two-state folding observed in individual protein molecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

The fast protein folding problem

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Fast kinetics and mechanisms in protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Theory of protein folding: the energy landscape perspective

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Submillisecond protein folding kinetics studied by ultrarapid mixing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

VMD: visual molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Funnels, pathways, and the energy landscape of protein folding: a synthesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

Mapping the transition state and pathway of protein folding by protein engineering

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3497823

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

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1201807109

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.1201807109

Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1201807109

Topological frustration and the folding of interleukin-1 beta

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1201807109

The natively helical chain segment 169-188 of Escherichia coli adenylate kinase is formed in the latest phase of the refolding transition

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1201807109

Desolvation is a likely origin of robust enthalpic barriers to protein folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1201807109

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1201807109

Knots in Globule and Coil Phases of a Model Polyethylene

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1201807109

Submillisecond kinetics of protein folding

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22753508

12 December 2020

inferred from PubMed ID database lookup

Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22753508

12 December 2020

inferred from PubMed ID database lookup

Atomistic analysis of pseudoknotted RNA unfolding

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22753508

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1073/PNAS.1201807109

1 reference

13 August 2017

0 references

1 reference

13 August 2017

1 reference