(Q30410943)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

title

Geofold: topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

Mohammed J. Zaki

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

author name string

Vibin Ramakrishnan

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

Sai Praveen Srinivasan

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

Saeed M Salem

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

Wilfredo Colón

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

Christopher Bystroff

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

language of work or name

English

0 references

publication date

21 December 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

volume

80

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

issue

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

page(s)

920-934

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

Constraining local structure can speed up folding by promoting structural polarization of the folding pathway

19 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Identifying the subproteome of kinetically stable proteins via diagonal 2D SDS/PAGE.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Routes are trees: the parsing perspective on 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=3277656

FOLD-RATE: prediction of protein folding rates from amino acid sequence

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

How well can simulation predict protein folding kinetics and thermodynamics?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Protein folding: the stepwise assembly of foldon units

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Folding lambda-repressor at its speed limit

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Protein degradation and protection against misfolded or damaged 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=3277656

Equilibrium denaturation studies of the Escherichia coli factor for inversion stimulation: implications for in vivo function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Protein unfolding: rigidity lost

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

An information theory model of hydrophobic interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

HMMSTR: a hidden Markov model for local sequence-structure correlations in 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=3277656

Molecular simulation study of cooperativity in hydrophobic association

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

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=3277656

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Contact order, transition state placement and the refolding rates of single domain 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=3277656

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step 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=3277656

From Levinthal to pathways to funnels

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Side-chain conformational entropy 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=3277656

Empirical scale of side-chain conformational entropy 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=3277656

Engineered disulfide bonds as probes of the folding pathway of barnase: increasing the stability of proteins against the rate of denaturation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

A reexamination of the folding mechanism of dihydrofolate reductase from Escherichia coli: verification and refinement of a four-channel model.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Early intermediates in the folding of dihydrofolate reductase from Escherichia coli detected by hydrogen exchange and NMR

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

A new computational model for protein folding based on atomic solvation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Disulfide mutants of barnase. I: Changes in stability and structure assessed by biophysical methods and X-ray crystallography

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Folding of dihydrofolate reductase from Escherichia coli.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

An engineered disulfide bond in dihydrofolate reductase.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Stabilization of phage T4 lysozyme by engineered disulfide bonds

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

Transient folding intermediates characterized 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=3277656

Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in 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=3277656

Transient intermediates in the folding of dihydrofolate reductase as detected by far-ultraviolet circular dichroism 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=3277656

Methods for molecular dynamics simulations of protein folding/unfolding in solution

20 June 2018

1 reference

The building block folding model and the kinetics of protein folding

21 January 2018

1 reference

TASSER: an automated method for the prediction of protein tertiary structures in CASP6.

21 January 2018

1 reference

KineticDB: a database of protein folding kinetics.

21 January 2018

1 reference

The location of an engineered inter-subunit disulfide bond in factor for inversion stimulation (FIS) affects the denaturation pathway and cooperativity

21 January 2018

1 reference

Testing the relationship between foldability and the early folding events of dihydrofolate reductase from Escherichia coli

21 January 2018

1 reference

Folding mechanism of FIS, the intertwined, dimeric factor for inversion stimulation

21 January 2018

1 reference

Integrated prediction of protein folding and unfolding rates from only size and structural class

21 January 2018

1 reference

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

Outlining Folding Nuclei in Globular Proteins

21 January 2018

1 reference

Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277656

MASKER: improved solvent-excluded molecular surface area estimations using Boolean masks

26 November 2018

1 reference

12 December 2020

Predicting protein folding pathways

1 reference

12 December 2020

Disulfide mutants of barnase. II: Changes in structure and local stability identified by hydrogen exchange

1 reference

12 December 2020

Reversible temperature and pressure denaturation of a protein fragment: a replica exchange molecular dynamics simulation study

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.23249

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22189917 AND SRC:MED&resulttype=core&format=json

19 January 2020

PubMed publication ID

22189917

1 reference