Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation (Q21092524)

3

Daniel D

Robinson

1 reference

15 August 2022

Ana J Narváez

4

Ana J

Narváez

1 reference

15 August 2022

Bryn Hardwick

5

Bryn

Hardwick

1 reference

15 August 2022

Meredith Roberts-Thomson

6

Meredith

Roberts-Thomson

1 reference

15 August 2022

Ashok R Venkitaraman

7

Ashok R

Venkitaraman

1 reference

15 August 2022

Guy H Grant

8

Guy H

Grant

1 reference

15 August 2022

Mike C Payne

9

Mike C

PLOS Computational Biology

Payne

1 reference

15 August 2022

language of work or name

English

0 references

publication date

2010

0 references

published in

0 references

volume

6

0 references

issue

8

0 references

page(s)

e1000880

0 references

copyright license

Creative Commons Attribution 4.0 International

start time

12 August 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

molecular dynamics simulation

1 reference

based on heuristic

inferred from title

cites work

RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

M-phase kinases induce phospho-dependent ubiquitination of somatic Wee1 by SCFbeta-TrCP

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

The crystal structure of the human polo-like kinase-1 polo box domain and its phospho-peptide complex

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Polo-like kinase (Plk)1 depletion induces apoptosis in cancer cells

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Structural and functional analyses of minimal phosphopeptides targeting the polo-box domain of polo-like kinase 1

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Molecular and structural basis of polo-like kinase 1 substrate recognition: Implications in centrosomal localization

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

The molecular basis for phosphodependent substrate targeting and regulation of Plks by the Polo-box domain

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

The role of water in sequence-independent ligand binding by an oligopeptide transporter protein

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Substrate specificity and affinity of a protein modulated by bound water molecules

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

All-atom empirical potential for molecular modeling and dynamics studies of proteins

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Assembly of Cell Regulatory Systems Through Protein Interaction Domains

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Polo-like kinases and the orchestration of cell division

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Exploring Potential Binding Modes of Small Drug-like Molecules to the Polo-Box Domain of Human Polo-like Kinase 1.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Prediction of the water content in protein binding sites

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Computations of standard binding free energies with molecular dynamics simulations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Deficiency in chromosome congression by the inhibition of Plk1 polo box domain-dependent recognition

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Dynamics of conserved waters in human Hsp90: implications for drug design

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Polo on the Rise-from Mitotic Entry to Cytokinesis with Plk1.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Role of the active-site solvent in the thermodynamics of factor Xa ligand binding

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Water as an active constituent in cell biology

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

BI 2536, a potent and selective inhibitor of polo-like kinase 1, inhibits tumor growth in vivo.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Water at biomolecular binding interfaces

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Water mediation in protein folding and molecular recognition

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Normal cells, but not cancer cells, survive severe Plk1 depletion

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Regulation of cell cycle checkpoints by polo-like kinases

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Structure and function of Polo-like kinases

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Molecular dynamics simulations of biomolecules

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Polo-like kinase 1 phosphorylates cyclin B1 and targets it to the nucleus during prophase

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

A fluorescence polarization based Src-SH2 binding assay

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

In vitro biological activity of a novel small-molecule inhibitor of polo-like kinase 1.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Inhibitors of Polo-like kinase reveal roles in spindle-pole maintenance

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

ON01910, a non-ATP-competitive small molecule inhibitor of Plk1, is a potent anticancer agent.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

A structural basis for 14-3-3sigma functional specificity.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Protocol for MM/PBSA molecular dynamics simulations of proteins

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

High-energy water sites determine peptide binding affinity and specificity of PDZ domains

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Different Plk1 functions show distinct dependencies on Polo-Box domain-mediated targeting

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2920843

Targeting polo-like kinase 1 for cancer therapy.

30 May 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

Purification and molecular cloning of Plx1, a Cdc25-regulatory kinase from Xenopus egg extracts

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

Comparative estimation of vibrational entropy changes in proteins through normal modes analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

Temperature and size dependence for Monte Carlo simulations of TIP4P water

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

The identification and characterization of the marine natural product scytonemin as a novel antiproliferative pharmacophore

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

Wortmannin, a widely used phosphoinositide 3-kinase inhibitor, also potently inhibits mammalian polo-like kinase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

Inhibition of polo-like kinase 1 by blocking polo-box domain-dependent protein-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

Calorimetric examination of high-affinity Src SH2 domain-tyrosyl phosphopeptide binding: dissection of the phosphopeptide sequence specificity and coupling energetics

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20711360

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000880

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1000880

0 references

DBLP publication ID

journals/ploscb/HugginsMRNHRVGP10

1 reference