scholarly journals Trapping Conformational States Along Ligand-Binding Dynamics of Peptide Deformylase: The Impact of Induced Fit on Enzyme Catalysis

PLoS Biology ◽  
2011 ◽  
Vol 9 (5) ◽  
pp. e1001066 ◽  
Author(s):  
Sonia Fieulaine ◽  
Adrien Boularot ◽  
Isabelle Artaud ◽  
Michel Desmadril ◽  
Frédéric Dardel ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Enzyme Catalysis ◽  
Peptide Deformylase ◽  
Conformational States ◽  
Induced Fit ◽  
The Impact

scholarly journals A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

2011 ◽  
Vol 7 (5) ◽  
pp. e1002054 ◽  
Author(s):  
Daniel-Adriano Silva ◽  
Gregory R. Bowman ◽  
Alejandro Sosa-Peinado ◽  
Xuhui Huang
Keyword(s):  
Ligand Binding ◽  
Induced Fit ◽  
Conformational Selection

scholarly journals A Structural Snapshot of CYP2B4 in Complex with Paroxetine Provides Insights into Ligand Binding and Clusters of Conformational States

2013 ◽  
Vol 346 (1) ◽  
pp. 113-120 ◽  
Author(s):  
Manish B. Shah ◽  
Irina Kufareva ◽  
Jaime Pascual ◽  
Qinghai Zhang ◽  
C. David Stout ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Conformational States

scholarly journals Novel Conformational States of Peptide Deformylase from Pathogenic BacteriumLeptospira interrogans

2005 ◽  
Vol 280 (51) ◽  
pp. 42391-42396 ◽  
Author(s):  
Zhaocai Zhou ◽  
Xiaomin Song ◽  
Weimin Gong
Keyword(s):  
Peptide Deformylase ◽  
Conformational States

scholarly journals Impact of deep eutectic solvents (DESs) and individual DES components on alcohol dehydrogenase catalysis: Connecting experimental data and molecular dynamics simulations

2021 ◽  
Author(s):  
Jan Philipp Bittner ◽  
Ningning Zhang ◽  
Lei Huang ◽  
Pablo Dominguez de Maria ◽  
Sven Jakobtorweihen ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Alcohol Dehydrogenase ◽  
Molecular Dynamics Simulations ◽  
Enzyme Catalysis ◽  
Deep Eutectic Solvents ◽  
Knowledge Based ◽  
Dynamics Simulations ◽  
The Impact ◽  
Knowledge Based Design

For a knowledge-based design of enzyme catalysis in deep eutectic solvents (DESs), the influence of the DESs properties (e.g., water activity, viscosity), and the impact of DESs and their individual...

scholarly journals Structural and biophysical characterization of the tandem substrate-binding domains of the ABC importer GlnPQ

Open Biology ◽  
2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Evelyn Ploetz ◽  
Gea K. Schuurman-Wolters ◽  
Niels Zijlstra ◽  
Amarins W. Jager ◽  
Douglas A. Griffith ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Single Molecule ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Transmembrane Domain ◽  
Substrate Binding ◽  
Titration Calorimetry ◽  
Uptake System ◽  
Conformational States ◽  
Binding Domains

The ATP-binding cassette transporter GlnPQ is an essential uptake system that transports glutamine, glutamic acid and asparagine in Gram-positive bacteria. It features two extra-cytoplasmic substrate-binding domains (SBDs) that are linked in tandem to the transmembrane domain of the transporter. The two SBDs differ in their ligand specificities, binding affinities and their distance to the transmembrane domain. Here, we elucidate the effects of the tandem arrangement of the domains on the biochemical, biophysical and structural properties of the protein. For this, we determined the crystal structure of the ligand-free tandem SBD1-2 protein from Lactococcus lactis in the absence of the transporter and compared the tandem to the isolated SBDs. We also used isothermal titration calorimetry to determine the ligand-binding affinity of the SBDs and single-molecule Förster resonance energy transfer (smFRET) to relate ligand binding to conformational changes in each of the domains of the tandem. We show that substrate binding and conformational changes are not notably affected by the presence of the adjoining domain in the wild-type protein, and changes only occur when the linker between the domains is shortened. In a proof-of-concept experiment, we combine smFRET with protein-induced fluorescence enhancement (PIFE–FRET) and show that a decrease in SBD linker length is observed as a linear increase in donor-brightness for SBD2 while we can still monitor the conformational states (open/closed) of SBD1. These results demonstrate the feasibility of PIFE–FRET to monitor protein–protein interactions and conformational states simultaneously.

scholarly journals Complementary oligonucleotides regulate induced fit ligand binding in duplexed aptamers

2017 ◽  
Vol 8 (3) ◽  
pp. 2251-2256 ◽  
Author(s):  
Jeffrey D. Munzar ◽  
Andy Ng ◽  
Mario Corrado ◽  
David Juncker
Keyword(s):  
Ligand Binding ◽  
Induced Fit ◽  
Complementary Oligonucleotide

Hybridizing a complementary oligonucleotide to an ATP aptamer is shown to functionally regulate a newly revealed induced fit ligand-binding pathway.

scholarly journals Resolving Three-State Ligand-Binding Mechanisms by Isothermal Titration Calorimetry: A Simulation Study

2017 ◽  
Author(s):  
Evgenii L. Kovrigin
Keyword(s):  
Ligand Binding ◽  
Isothermal Titration Calorimetry ◽  
Simulation Study ◽  
Titration Calorimetry ◽  
Induced Fit ◽  
State Process ◽  
Binding Mechanisms

ABSTRACTIn this paper, I theoretically analyzed ITC profiles for three-state equilibria involving ligand binding coupled to isomerization or dimerization transitions. Simulations demonstrate that the mechanisms where the free or ligand-bound protein undergoes dimerization (such that the ligand cannot bind to or dissociate from the dimer) produce very distinctive titration profiles. In contrast, profiles of the pre-existing equilibrium or induced-fit models cannot be distinguished from a simple two-state process, requiring data from additional techniques to positively identify these mechanisms.

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