Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein. (Q36501036)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20408169%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

title

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein (English)

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31 January 2020

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2

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31 January 2020

3

Angel E Garcia

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31 January 2020

author name string

Ryan Day

series ordinal

1

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31 January 2020

language of work or name

English

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publication date

1 June 2010

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31 January 2020

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31 January 2020

volume

78

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31 January 2020

issue

8

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31 January 2020

page(s)

1889-1899

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Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field.

31 January 2020

cites work

1 reference

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Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

30 September 2017

1 reference

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Computing the stability diagram of the Trp-cage miniprotein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

The Trp-cage: optimizing the stability of a globular miniprotein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Cooperation between a salt bridge and the hydrophobic core triggers fold stabilization in a Trp-cage miniprotein.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Replica exchange with solute tempering: efficiency in large scale systems

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

A pre-existing hydrophobic collapse in the unfolded state of 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=3534748

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Stereoelectronic tuning of the structure and stability of the trp cage miniprotein.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Comparison of multiple Amber force fields and development of improved protein backbone parameters

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Trp-cage: Folding free energy landscape in explicit water

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

The Trp cage: folding kinetics and unfolded state topology via molecular dynamics 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=3534748

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

All-Atom Structure Prediction and Folding Simulations of a Stable 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=3534748

Pressure-temperature phase diagrams of biomolecules

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Designing a 20-residue 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=3534748

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Folding funnels and frustration in off-lattice minimalist protein landscapes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of 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=3534748

Energetics of protein structure.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics 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=3534748

Preserving the Boltzmann ensemble in replica-exchange molecular dynamics

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Rate constant and reaction coordinate of Trp-cage folding in explicit water

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Computational study of the Trp-cage miniprotein based on the ECEPP/3 force field.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

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

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

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

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

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

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Exploring the temperature-pressure phase diagram of staphylococcal nuclease.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534748

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin

21 September 2018

1 reference

12 December 2020

Molecular dynamics simulations of pressure effects on hydrophobic interactions

1 reference

12 December 2020

Unfolding thermodynamics of Trp-cage, a 20 residue miniprotein, studied by differential scanning calorimetry and circular dichroism spectroscopy

1 reference

12 December 2020

Temperature- and pressure-induced unfolding and refolding of ubiquitin: a static and kinetic Fourier transform infrared spectroscopy study

1 reference

12 December 2020

A direct comparison of protein structure in the gas and solution phase: the Trp-cage

1 reference

12 December 2020

Ultrafast folding of a computationally designed Trp-cage mutant: Trp2-cage

1 reference

12 December 2020

Thermodynamics of protein denaturation. Effect of pressure on the denaturation on ribonuclease A

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.22702

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20408169%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

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31 January 2020

PubMed publication ID

20408169

1 reference