Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations (Q41933651)

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5 February 2020

title

Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations (English)

1 reference

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5 February 2020

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2

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5 February 2020

Peter Hore

3

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5 February 2020

K Hun Mok

4

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5 February 2020

author name string

Z Gattin

1

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5 February 2020

W F van Gunsteren

5

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5 February 2020

language of work or name

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1 October 2009

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5 February 2020

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5 February 2020

volume

18

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5 February 2020

issue

10

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5 February 2020

page(s)

2090-2099

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Molecular simulation as an aid to experimentalists.

5 February 2020

cites work

1 reference

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Critical assessment of methods of protein structure prediction-Round VII

5 June 2018

1 reference

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet

5 June 2018

1 reference

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A microscopic view of miniprotein folding: enhanced folding efficiency through formation of an intermediate

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

The GROMOS software for biomolecular simulation: GROMOS05.

5 June 2018

1 reference

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Conformational change in unsolvated Trp-cage protein probed by fluorescence

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Random-coil behavior and the dimensions of chemically unfolded proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

5 June 2018

1 reference

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Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Trp-cage: Folding free energy landscape in explicit water

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Designing a 20-residue protein

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Critical assessment of methods of protein structure prediction (CASP): round IV.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Exendin-4 and glucagon-like-peptide-1: NMR structural comparisons in the solution and micelle-associated states

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

UV-resonance raman thermal unfolding study of Trp-cage shows that it is not a simple two-state miniprotein

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

A limiting speed for protein folding at low solvent viscosity

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Possible locally driven folding pathways of TC5b, a 20-residue protein

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2786973

The effect of motional averaging on the calculation of NMR-derived structural properties

18 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19693803

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State Financial support from the Schweizerischer Nationalfonds (Project no. 21-50929.97) is gratefully acknowledged

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19693803

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19693803

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PRO.223

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19693803%20AND%20SRC:MED&resulttype=core&format=json

5 February 2020

1 reference

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5 February 2020

PubMed publication ID

19693803

1 reference