(Q31036350)

5 September 2017

Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning (English)

1 reference

5 September 2017

Z Nevin Gerek

1

1 reference

PMCID

3188487

5 September 2017

S Banu Ozkan

series ordinal

2

1 reference

5 September 2017

6 October 2011

1 reference

PLOS Computational Biology

5 September 2017

1 reference

5 September 2017

7

1 reference

5 September 2017

10

1 reference

5 September 2017

e1002154

1 reference

Creative Commons Attribution 4.0 International

5 September 2017

start time

6 October 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Biophysical characterization of the complex between human papillomavirus E6 protein and synapse-associated protein 97.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Interaction energy based protein structure networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Crystallographic and Nuclear Magnetic Resonance Evaluation of the Impact of Peptide Binding to the Second PDZ Domain of Protein Tyrosine Phosphatase 1E

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Manipulation of conformational change in proteins by single-residue perturbations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

A flexible docking scheme to explore the binding selectivity of PDZ domains

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Hidden dynamic allostery in a PDZ domain.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

The origin of allosteric functional modulation: multiple pre-existing pathways

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Protein elastic network models and the ranges of cooperativity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Sending signals dynamically

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Probing the flexibility of large conformational changes in protein structures through local perturbations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Surface sites for engineering allosteric control in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Allosteric regulation and catalysis emerge via a common route.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Allostery: absence of a change in shape does not imply that allostery is not at play

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Reassessing a sparse energetic network within a single protein domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Flexible ligand docking to multiple receptor conformations: a practical alternative

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Deriving protein dynamical properties from weighted protein contact number.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

An allosteric intramolecular PDZ-PDZ interaction modulates PTP-BL PDZ2 binding specificity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Interdomain interactions in the tumor suppressor discs large regulate binding to the synaptic protein GukHolder

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Dynamically driven protein allostery.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

The changing landscape of protein allostery

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Evolutionary information for specifying a protein fold

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Quantifying allosteric effects in proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Functional dynamics of PDZ binding domains: a normal-mode analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Is allostery an intrinsic property of all dynamic proteins?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Ligand-dependent dynamics and intramolecular signaling in a PDZ domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

The role of dynamics in allosteric regulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

PDZ Domain Proteins: Plug and Play!

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Signaling complex organization by PDZ domain proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Evolutionarily conserved networks of residues mediate allosteric communication in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

PDZ domains: structural modules for protein complex assembly

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Anisotropy of fluctuation dynamics of proteins with an elastic network model

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Evolutionarily conserved pathways of energetic connectivity in protein families

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits*

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Biochemistry. An ensemble view of allostery.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002154

Local motions in a benchmark of allosteric proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002154

Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002154

Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002154

Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002154

Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002154

RosettaLigand docking with full ligand and receptor flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002154

Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002154

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002154

Harmonicity in slow protein dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002154

Normal modes and essential dynamics.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188487

Evaluation of energetic and dynamic coupling networks in a PDZ domain protein

25 November 2018

1 reference

12 December 2020

Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior

1 reference

12 December 2020

On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: illustrations using lattice model

1 reference

12 December 2020

Allostery without conformational change. A plausible model

1 reference

12 December 2020

Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved

1 reference

12 December 2020

Allostery in a coarse-grained model of protein dynamics

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1002154

Identifiers

DOI

1 reference

5 September 2017

journals/ploscb/GerekO11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

5 September 2017

1 reference

PMCID

3188487