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

scientific article published on November 2, 2010

Crystallographic and Nuclear Magnetic Resonance Evaluation of the Impact of Peptide Binding to the Second PDZ Domain of Protein Tyrosine Phosphatase 1E is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1021/BI101131F
P953full work available at URLhttps://europepmc.org/articles/pmc3001272?pdf=render
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20839809/?tool=EBI
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20839809/pdf/?tool=EBI
https://europepmc.org/articles/PMC3001272
https://europepmc.org/articles/PMC3001272?pdf=render
https://doi.org/10.1021/bi101131f
https://pubs.acs.org/doi/pdf/10.1021/bi101131f
P3181OpenCitations bibliographic resource ID2088087
P932PMC publication ID3001272
P698PubMed publication ID20839809
P5875ResearchGate publication ID46271605

P50authorJun ZhangQ57017646
Hengming KeQ61519113
George N PhillipsQ95337388
P2093author name stringHuanchen Wang
Andrew L. Lee
Aram Chang
Paul J. Sapienza
Sarah R. Hengel
P2860cites workIdentification and characterization of RA-GEF-2, a Rap guanine nucleotide exchange factor that serves as a downstream target of M-RasQ24291612
Energetics of peptide recognition by the second PDZ domain of human protein tyrosine phosphatase 1EQ24293758
Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactionsQ24300821
Ligand-dependent dynamics and intramolecular signaling in a PDZ domainQ24303478
PHENIX: a comprehensive Python-based system for macromolecular structure solutionQ24654617
Evidence for PDZ domains in bacteria, yeast, and plantsQ24673542
Processing of X-ray diffraction data collected in oscillation modeQ26778468
Mechanical network in titin immunoglobulin from force distribution analysisQ27335952
Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptorQ27621669
Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BLQ27638244
Crystal structure of DegP (HtrA) reveals a new protease-chaperone machineQ27638626
Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineeringQ27643278
Dynamic scaffolding in a G protein-coupled signaling systemQ27648729
Allosteric activation of DegS, a stress sensor PDZ proteaseQ27648951
Determination of Multicomponent Protein Structures in Solution Using Global Orientation and Shape RestraintsQ27657269
The structure of the harmonin/sans complex reveals an unexpected interaction mode of the two Usher syndrome proteinsQ27659663
Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZQ27732927
Inference of macromolecular assemblies from crystalline stateQ27860457
Coot: model-building tools for molecular graphicsQ27860505
NMRPipe: a multidimensional spectral processing system based on UNIX pipesQ27860859
NMR View: A computer program for the visualization and analysis of NMR dataQ27860951
Measurement of J and dipolar couplings from simplified two-dimensional NMR spectraQ27860984
Refinement of macromolecular structures by the maximum-likelihood methodQ27861011
The CCP4 suite: programs for protein crystallographyQ27861090
The Adenomatous Polyposis Coli-protein (APC) interacts with the protein tyrosine phosphatase PTP-BL via an alternatively spliced PDZ domainQ28144272
Solution NMR of proteins within polyacrylamide gels: diffusional properties and residual alignment by mechanical stress or embedding of oriented purple membranesQ28201061
PDZ domains and the organization of supramolecular complexesQ28209906
PDZ domains: folding and bindingQ28235804
Ezrin induces long-range interdomain allostery in the scaffolding protein NHERF1Q28251491
An allosteric intramolecular PDZ-PDZ interaction modulates PTP-BL PDZ2 binding specificityQ28255843
Therapeutic use of PDZ protein-protein interaction antagonismQ28284263
Probing the flexibility of large conformational changes in protein structures through local perturbationsQ28475173
Measurement of Proton, Nitrogen, and Carbonyl Chemical Shielding Anisotropies in a Protein Dissolved in a Dilute Liquid Crystalline PhaseQ29391678
Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nucleaseQ29547582
Evolutionarily conserved pathways of energetic connectivity in protein familiesQ29615037
PDZ domain proteins of synapsesQ29616399
Interdomain interactions in the tumor suppressor discs large regulate binding to the synaptic protein GukHolderQ30159642
Multiple-site exchange in proteins studied with a suite of six NMR relaxation dispersion experiments: an application to the folding of a Fyn SH3 domain mutantQ30160081
Dynamic activation of protein function: a view emerging from NMR spectroscopy.Q30329163
Weak alignment offers new NMR opportunities to study protein structure and dynamics.Q30332340
A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing.Q30362842
Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility.Q30384111
Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteinsQ30485355
Dynamic allostery in the methionine repressor revealed by force distribution analysisQ30914370
Protein dynamics investigated by inherent structure analysisQ33927207
Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysisQ33935989
PDZ domains: More than just a glueQ34131353
Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromoleculesQ34313182
Functional dynamics of PDZ binding domains: a normal-mode analysisQ34410311
PDZ domains-glue and guide.Q35169335
A PDZ domain recapitulates a unifying mechanism for protein foldingQ35575881
Making protein interactions druggable: targeting PDZ domainsQ35968398
New tools provide new insights in NMR studies of protein dynamicsQ36449003
Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case studyQ36943279
Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysisQ37019487
Characterization of enzyme motions by solution NMR relaxation dispersion.Q37087357
Allostery: absence of a change in shape does not imply that allostery is not at playQ37114191
Hidden dynamic allostery in a PDZ domain.Q37416575
Frameworks for understanding long-range intra-protein communicationQ37438472
Sending signals dynamicallyQ37440289
PDZ domain binding selectivity is optimized across the mouse proteomeQ40191457
A flexible docking scheme to explore the binding selectivity of PDZ domainsQ40496890
Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transitionQ40578290
Acid cleavage/deprotection in Fmoc/tBu solid-phase peptide synthesisQ40614847
Toward flexibility-activity relationships by NMR spectroscopy: dynamics of Pin1 ligandsQ42272075
Dynamic dysfunction in dihydrofolate reductase results from antifolate drug binding: modulation of dynamics within a structural stateQ43115788
Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain proteinQ43552352
Direct Observation of Protein−Ligand Interaction KineticsQ44592422
Tracing kinetic intermediates during ligand bindingQ44986323
Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusionQ46824329
REDCAT: a residual dipolar coupling analysis toolQ47892565
Interesting structural and dynamical behaviors exhibited by the AF-6 PDZ domain upon Bcr peptide binding.Q55046212
Validation of Protein Structure from Anisotropic Carbonyl Chemical Shifts in a Dilute Liquid Crystalline PhaseQ57080155
Concentration measurements by PULCON using X-filtered or 2D NMR spectraQ57825681
Measuring Protein Concentrations by NMR SpectroscopyQ57825691
Scaffold proteins as dynamic switchesQ58035261
Probing Chemical Shifts of Invisible States of Proteins with Relaxation Dispersion NMR Spectroscopy: How Well Can We Do?Q59102877
A Flexible Docking Procedure for the Exploration of Peptide Binding Selectivity to Known Structures and Homology Models of PDZ DomainsQ60429769
Allostery without conformational change. A plausible modelQ70806307
A TROSY CPMG sequence for characterizing chemical exchange in large proteinsQ73289769
Probing the Kinetic Landscape of Transient Peptide−Protein Interactions by Use of Peptide 15N NMR Relaxation Dispersion Spectroscopy: Binding of an Antithrombin Peptide to Human ProthrombinQ79129188
Evaluation of energetic and dynamic coupling networks in a PDZ domain proteinQ79164244
Crystal structure of the second PDZ domain of SAP97 in complex with a GluR-A C-terminal peptideQ79309457
Pump-probe molecular dynamics as a tool for studying protein motion and long range couplingQ80168581
Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behaviorQ84194113
P433issue43
P407language of work or nameEnglishQ1860
P304page(s)9280-91
P577publication date2010-11-02
P1433published inBiochemistryQ764876
P1476titleCrystallographic and Nuclear Magnetic Resonance Evaluation of the Impact of Peptide Binding to the Second PDZ Domain of Protein Tyrosine Phosphatase 1E
P478volume49

Reverse relations

cites work (P2860)
Q64027972A non-equilibrium approach to allosteric communication
Q31108126Accurate prediction of the dynamical changes within the second PDZ domain of PTP1e
Q42543066Allosteric activation of the Par-6 PDZ via a partial unfolding transition
Q31036350Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning
Q37899566Dynamic allostery: linkers are not merely flexible
Q55445745Energy transport pathway in proteins: Insights from non-equilibrium molecular dynamics with elastic network model.
Q36812412Fas-associated phosphatase 1 (Fap1) influences βcatenin activity in myeloid progenitor cells expressing the Bcr-abl oncogene
Q48059314Hidden electrostatic basis of dynamic allostery in a PDZ domain.
Q47195432Implications of short time scale dynamics on long time processes.
Q27678876Kinetic response of a photoperturbed allosteric protein
Q38016834Ligand binding by PDZ domains.
Q27677356Ligand-Induced Dynamic Changes in Extended PDZ Domains from NHERF1
Q30431541MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues.
Q51553044Mechanisms for allosteric activation of protease DegS by ligand binding and oligomerization as revealed from molecular dynamics simulations.
Q90288644Neural networks for protein structure and function prediction and dynamic analysis
Q35578839Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges
Q47427287Peptide binding to the PDZ3 domain by conformational selection
Q59135283Protein tyrosine phosphatase L1 inhibits high-grade serous ovarian carcinoma progression by targeting IκBα
Q62761879REDAN: relative entropy-based dynamical allosteric network model
Q28551601Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery
Q38559525Some (dis)assembly required: partial unfolding in the Par-6 allosteric switch
Q54287344The mechanism of binding of the second PDZ domain from the Protein Tyrosine Phosphatase-BL to the Adenomatous Polyposis Coli tumor suppressor.
Q42175762The role of Fas-associated phosphatase 1 in leukemia stem cell persistence during tyrosine kinase inhibitor treatment of chronic myeloid leukemia
Q37408300The spatial structure of cell signaling systems
Q30427743The underappreciated role of allostery in the cellular network.
Q41195544Understanding the effect of alternative splicing in the folding and function of the second PDZ from protein tyrosine phosphatase-BL.

Search more.