Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model. (Q35963359)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

30 December 2019

title

Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

30 December 2019

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

30 December 2019

author name string

Zhonglin Luo

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

30 December 2019

Jiandong Ding

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

30 December 2019

language of work or name

English

0 references

publication date

18 May 2007

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

30 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

30 December 2019

volume

93

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

30 December 2019

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

30 December 2019

page(s)

2152-2161

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

Force field influences in beta-hairpin folding simulations

30 December 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Structural comparison of the two alternative transition states for folding of TI I27.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Folding, misfolding, and amyloid protofibril formation of WW domain FBP28.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

P versus Q: structural reaction coordinates capture protein folding on smooth landscapes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

The "first in-last out" hypothesis on protein folding revisited

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Quantifying kinetic paths of protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Characterization of the conformational space of a triple-stranded beta-sheet forming peptide with molecular dynamics simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

The folding pathway of ubiquitin from all-atom molecular dynamics simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Critical nucleation size in the folding of small apparently two-state proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Coarse-grained sequences for protein folding and design

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Direct molecular dynamics observation of protein folding transition state ensemble

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Determination of a transition state at atomic resolution from protein engineering data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

The dual role of a loop with low loop contact distance in folding and domain swapping

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

How the folding rate constant of simple, single-domain proteins depends on the number of native contacts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

NMR solution structure of the isolated Apo Pin1 WW domain: comparison to the x-ray crystal structures of Pin1

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Folding rate prediction using total contact distance

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Using flexible loop mimetics to extend -value analysis to secondary structure interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Ultrafast folding of WW domains without structured aromatic clusters in the denatured state

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Functions of WW domains in the nucleus

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

NeW wrinkles for an old domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

A surprising simplicity to protein folding.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Structural analysis of WW domains and design of a WW prototype

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Stability of the beta-sheet of the WW domain: A molecular dynamics simulation study

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Contact order, transition state placement and the refolding rates of single domain proteins.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Structural and functional analysis of the mitotic rotamase Pin1 suggests substrate recognition is phosphorylation dependent

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

VMD: visual molecular dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Testing simplified proteins models of the hPin1 WW domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Phi-analysis at the experimental limits: mechanism of beta-hairpin formation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Topological frustration and the folding of interleukin-1 beta

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Transition state contact orders correlate with protein folding rates.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Hammond behavior versus ground state effects in protein folding: evidence for narrow free energy barriers and residual structure in unfolded states

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Role of hydrophilic and hydrophobic contacts in folding of the second beta-hairpin fragment of protein G: molecular dynamics simulation studies of an all-atom model

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Incorporating beta-turns and a turn mimetic out of context in loop 1 of the WW domain affords cooperatively folded beta-sheets

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1959547

Exploring the energy landscape of a beta hairpin in explicit solvent

24 September 2018

1 reference

12 December 2020

Converging on proline: the mechanism of WW domain peptide recognition

1 reference

12 December 2020

Class-specific correlations between protein folding rate, structure-derived, and sequence-derived descriptors

1 reference

12 December 2020

Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions

1 reference

12 December 2020

The folding mechanism of a beta-sheet: the WW domain

1 reference

12 December 2020

Optimized Monte Carlo data analysis

1 reference

12 December 2020

10.1529/BIOPHYSJ.106.102095

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

30 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17513360%20AND%20SRC:MED&resulttype=core&format=json

30 December 2019

PubMed publication ID

17513360

1 reference