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 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 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.

A Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding

2020 ◽  
Author(s):  
Edward Miller ◽  
Robert Murphy ◽  
Daniel Sindhikara ◽  
Ken Borrelli ◽  
Matthew Grisewood ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Structure Prediction ◽  
Heavy Atom ◽  
Accurate Solution ◽  
Binding Modes ◽  
Induced Fit Docking ◽  
Induced Fit ◽  
Test Set ◽  
Cross Docking ◽  
Public Data

We present a reliable and accurate solution to the induced fit docking problem for protein-ligand binding by combining ligand-based pharmacophore docking (Phase), rigid receptor docking (Glide), and protein structure prediction (Prime) with explicit solvent molecular dynamics simulations. We provide an in-depth description of our novel methodology and present results for 41 targets consisting of 415 cross-docking cases divided amongst a training and test set. For both the training and test-set, we compute binding modes with a ligand-heavy atom RMSD to within 2.5 Å or better in over 90% of cross-docking cases compared to less than 70% of cross-docking cases using our previously published induced-fit docking algorithm and less than 41% using rigid receptor docking. Applications of the predicted ligand-receptor structure in free energy perturbation calculations is demonstrated for both public data and in active drug discovery projects, both retrospectively and prospectively.

scholarly journals MloK1 Ligand Binding Simulations Indicate an Induced-Fit Mechanism

2012 ◽  
Vol 102 (3) ◽  
pp. 410a
Author(s):  
Béla Voß ◽  
Sebastian Peuker ◽  
U. Benjamin Kaupp ◽  
Helmut Grubmüller
Keyword(s):  
Ligand Binding ◽  
Induced Fit
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