Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase (Q33896611)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19627112%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

title

Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase (English)

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3 February 2020

1 reference

1

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3 February 2020

Craig A McElroy

3

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3 February 2020

Mark P. Foster

5

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3 February 2020

author name string

Douglas W Byerly

2

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3 February 2020

Amber Simmons

4

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3 February 2020

language of work or name

English

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publication date

1 August 2009

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3 February 2020

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3 February 2020

volume

48

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3 February 2020

issue

32

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3 February 2020

page(s)

7595-7607

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Delineation of alternative conformational states in Escherichia coli peptide deformylase via thermodynamic studies for the binding of actinonin

3 February 2020

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Drug forecast - the peptide deformylase inhibitors as antibacterial agents

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5 July 2018

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5 July 2018

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Configurational entropy elucidates the role of salt-bridge networks in protein thermostability.

5 July 2018

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Heat capacity in proteins

5 July 2018

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Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs

5 July 2018

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5 July 2018

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Increased backbone mobility in beta-barrel enhances entropy gain driving binding of N-TIMP-1 to MMP-3.

5 July 2018

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5 July 2018

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Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species

5 July 2018

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Temperature dependence of the internal dynamics of a calmodulin-peptide complex

5 July 2018

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The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents

5 July 2018

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Mapping the surface of Escherichia coli peptide deformylase by NMR with organic solvents

5 July 2018

1 reference

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Crystal structure of type II peptide deformylase from Staphylococcus aureus

5 July 2018

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Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design

5 July 2018

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Characterization of an eukaryotic peptide deformylase from Plasmodium falciparum

5 July 2018

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Dipolar couplings in macromolecular structure determination

5 July 2018

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Nmr probes of molecular dynamics: overview and comparison with other techniques

5 July 2018

1 reference

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Peptide deformylase as an antibacterial drug target: target validation and resistance development

5 July 2018

1 reference

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Antibiotic Activity and Characterization of BB-3497, a Novel Peptide Deformylase Inhibitor

5 July 2018

1 reference

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Identification of a potent peptide deformylase inhibitor from a rationally designed combinatorial library

5 July 2018

1 reference

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Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms

5 July 2018

1 reference

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Peptide deformylase of eukaryotic protists: a target for new antiparasitic agents?

5 July 2018

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Structure-based thermodynamic analysis of the dissociation of protein phosphatase-1 catalytic subunit and microcystin-LR docked complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2881472

Characterization of cobalt(II)-substituted peptide deformylase: function of the metal ion and the catalytic residue Glu-133.

5 July 2018

1 reference

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Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition

5 July 2018

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Substrate recognition and selectivity of peptide deformylase. Similarities and differences with metzincins and thermolysin

5 July 2018

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Structural basis for the design of antibiotics targeting peptide deformylase

5 July 2018

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Determination of substrate specificity for peptide deformylase through the screening of a combinatorial peptide library

5 July 2018

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Iron center, substrate recognition and mechanism of peptide deformylase

5 July 2018

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Solution structure of nickel-peptide deformylase

5 July 2018

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5 July 2018

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Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra

5 July 2018

1 reference

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Structure of peptide deformylase and identification of the substrate binding site

5 July 2018

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Purification, characterization, and inhibition of peptide deformylase from Escherichia coli.

5 July 2018

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Crystal structure of the Escherichia coli peptide deformylase

5 July 2018

1 reference

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Contributions to protein entropy and heat capacity from bond vector motions measured by NMR spin relaxation.

5 July 2018

1 reference

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Structure-function relationships within the peptide deformylase family. Evidence for a conserved architecture of the active site involving three conserved motifs and a metal ion.

5 July 2018

1 reference

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Insights into the local residual entropy of proteins provided by NMR relaxation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2881472

Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2881472

Evaluation of linked protonation effects in protein binding reactions using isothermal titration calorimetry

5 July 2018

1 reference

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A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase

5 July 2018

1 reference

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5 July 2018

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The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase

5 July 2018

1 reference

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5 July 2018

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Coupling of local folding to site-specific binding of proteins to DNA

5 July 2018

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Cobalt as probe and label of proteins

5 July 2018

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Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation

5 July 2018

1 reference

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Enzymatic properties of Escherichia coli peptide deformylase

5 July 2018

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Protein dynamics and distance determination by NOE measurements.

5 July 2018

1 reference

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Rapid measurement of binding constants and heats of binding using a new titration calorimeter

5 July 2018

1 reference

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Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease

5 July 2018

1 reference

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Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible.

5 July 2018

1 reference

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Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions

5 July 2018

1 reference

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Discovery and refinement of a new structural class of potent peptide deformylase inhibitors.

5 July 2018

1 reference

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Prediction of charge-induced molecular alignment: residual dipolar couplings at pH 3 and alignment in surfactant liquid crystalline phases

29 October 2018

1 reference

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Temperature Dependence of the Backbone Dynamics of Ribonuclease A in the Ground State and Bound to the Inhibitor 5‘-Phosphothymidine (3‘-5‘)Pyrophosphate Adenosine 3‘-Phosphate

29 October 2018

1 reference

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Co-crystallization of Staphylococcus aureus peptide deformylase (PDF) with potent inhibitors

29 October 2018

1 reference

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Impact of mobility on structure-based drug design for the MMPs

29 October 2018

1 reference

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Distinctive features of the two classes of eukaryotic peptide deformylases

29 October 2018

1 reference

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Deformylase as a novel antibacterial target.

29 October 2018

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A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings.

29 October 2018

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Synthesis and antibacterial activity of peptide deformylase inhibitors

29 October 2018

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15N NMR relaxation studies of free and inhibitor-bound 4-oxalocrotonate tautomerase: backbone dynamics and entropy changes of an enzyme upon inhibitor binding

29 October 2018

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12 December 2020

Studies concerning the antibiotic actinonin. Part I. The constitution of actinonin. A natural hydroxamic acid with antibiotic activity

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12 December 2020

The C-terminal domain of peptide deformylase is disordered and dispensable for activity

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12 December 2020

Design and Synthesis of Substrate Analogue Inhibitors of Peptide Deformylase†

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12 December 2020

The use of model selection in the model-free analysis of protein dynamics

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12 December 2020

Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide

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12 December 2020

Role of salt bridge formation in antigen-antibody interaction. Entropic contribution to the complex between hen egg white lysozyme and its monoclonal antibody HyHEL10

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12 December 2020

Correlation between binding and dynamics at SH2 domain interfaces

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12 December 2020

NMR relaxation studies of the role of conformational entropy in protein stability and ligand binding

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12 December 2020

Identifiers

DOI

10.1021/BI900600B

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19627112%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19627112%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

1 reference