Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations (Q37001294)

17 August 2017

Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations (English)

1 reference

17 August 2017

Zhonglin Luo

1

1 reference

17 August 2017

Jiandong Ding

series ordinal

2

1 reference

17 August 2017

Yaoqi Zhou

series ordinal

3

1 reference

17 August 2017

language of work or name

English

0 references

publication date

1 June 2008

1 reference

Journal of Chemical Physics

17 August 2017

1 reference

17 August 2017

128

1 reference

17 August 2017

22

1 reference

17 August 2017

225103

1 reference

Influence of hPin1 WW N-terminal domain boundaries on function, protein stability, and folding

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Force field influences in beta-hairpin folding simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Model systems for beta-hairpins and beta-sheets

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Structure-function-folding relationship in a WW domain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Folding and aggregation kinetics of a beta-hairpin

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Natural-like function in artificial WW domains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Mapping the transition state of the WW domain beta-sheet.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Mechanisms and kinetics of beta-hairpin formation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Understanding beta-hairpin formation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

A statistical mechanical model for beta-hairpin kinetics.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Folding dynamics and mechanism of beta-hairpin formation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

VMD: visual molecular dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Folding transition-state and denatured-state ensembles of FSD-1 from folding and unfolding simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

Testing simplified proteins models of the hPin1 WW domain

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

An analysis of side chain interactions and pair correlations within antiparallel beta-sheets: the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2596927

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

27 June 2018

1 reference

Folding of the GB1 hairpin peptide from discrete path sampling.

21 January 2018

1 reference

Complex folding pathways in a simple beta-hairpin

21 January 2018

1 reference

Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide

21 January 2018

1 reference

Engineering a beta-sheet protein toward the folding speed limit.

21 January 2018

1 reference

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

21 January 2018

1 reference

The role of the turn in beta-hairpin formation during WW domain folding

21 January 2018

1 reference

Peptide binding induces large scale changes in inter-domain mobility in human Pin1.

21 January 2018

1 reference

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

Molecular dynamics simulations at constant pressure and/or temperature

21 January 2018

1 reference

Probing Local Structural Events in β-Hairpin Unfolding with Transient Nonlinear Infrared Spectroscopy

21 January 2018

1 reference

Sampling the complex energy landscape of a simple β-hairpin

21 January 2018

1 reference

Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in β-hairpins

21 January 2018

1 reference

Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation

21 January 2018

1 reference

12 December 2020

Native topology or specific interactions: what is more important for protein folding?

1 reference

12 December 2020

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

1 reference

12 December 2020

Evidence of turn and salt bridge contributions to beta-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G

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 mechanism of beta-hairpin formation

1 reference

12 December 2020

Guidelines for protein design: the energetics of beta sheet side chain interactions

1 reference

12 December 2020

Sequence-specific dynamics modulate recognition specificity in WW domains

1 reference

12 December 2020

Minimal model systems for beta sheet secondary structure in proteins

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.2936832

1 reference

17 August 2017

1 reference

17 August 2017

PubMed publication ID

18554060

1 reference