scholarly journals Transient, Sparsely Populated Compact States of Apo and Calcium-Loaded Calmodulin Probed by Paramagnetic Relaxation Enhancement: Interplay of Conformational Selection and Induced Fit

2011 ◽  
Vol 133 (46) ◽  
pp. 18966-18974 ◽  
Author(s):  
Nicholas J. Anthis ◽  
Michaeleen Doucleff ◽  
G. Marius Clore
Keyword(s):  
Paramagnetic Relaxation ◽  
Paramagnetic Relaxation Enhancement ◽  
Induced Fit ◽  
Conformational Selection

Association/dissociation Mechanisms of Intrinsically Disordered Region of Protein Beyond Conformational Selection and Induced Fit

2019 ◽  
Author(s):  
Duy Phuoc Tran ◽  
Akio Kitao
Keyword(s):  
Free Energy ◽  
Transcriptional Activation ◽  
Binding Free Energy ◽  
Energy Structure ◽  
Induced Fit ◽  
Hydrogen Bond Formation ◽  
Conformational Selection ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Region ◽  
Dissociation Mechanisms

<p>We investigate association and dissociation mechanisms of a typical intrinsically disordered region (IDR), transcriptional activation subdomain of tumor repressor protein p53 (TAD-p53) with murine double-minute clone 2 protein (MDM2). Using the combination of cycles of association and dissociation parallel cascade molecular dynamics, multiple standard MD, and Markov state model, we are successful in obtaining the lowest free energy structure of MDM2/TAD-p53 complex as the structure very close to that in crystal without prior knowledge. This method also reproduces the experimentally measured standard binding free energy, and association and dissociation rate constants solely with the accumulated MD simulation cost of 11.675 μs, in spite of the fact that actual dissociation occurs in the order of a second. Although there exist a few complex intermediates with similar free energies, TAD-p53 first binds MDM2 as the second lowest free energy intermediate dominantly (> 90% in flux), taking a form similar to one of the intermediate structures in its monomeric state. The mechanism of this step has a feature of conformational selection. In the second step, dehydration of the interface, formation of π-π stackings of the side-chains, and main-chain relaxation/hydrogen bond formation to complete α-helix take place, showing features of induced fit. In addition, dehydration (dewetting) is a key process for the final relaxation around the complex interface. These results demonstrate a more fine-grained view of the IDR association/dissociation beyond classical views of protein conformational change upon binding.</p>

scholarly journals Structure-Free Validation of Residual Dipolar Coupling and Paramagnetic Relaxation Enhancement Measurements of Disordered Proteins

Biochemistry ◽  
2015 ◽  
Vol 54 (46) ◽  
pp. 6876-6886 ◽  
Author(s):  
Francisco N. Newby ◽  
Alfonso De Simone ◽  
Maho Yagi-Utsumi ◽  
Xavier Salvatella ◽  
Christopher M. Dobson ◽  
...  
Keyword(s):  
Dipolar Coupling ◽  
Residual Dipolar Coupling ◽  
Paramagnetic Relaxation ◽  
Paramagnetic Relaxation Enhancement ◽  
Disordered Proteins

From Selection to Instruction and Back — Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts

2021 ◽  
Author(s):  
Jovica D Badjic ◽  
Radoslav Z Pavlović ◽  
Remy F Lalisse ◽  
Alexandar L Hansen ◽  
Christopher A Waudby ◽  
...  
Keyword(s):  
Induced Fit ◽  
Conformational Selection

Conformational Selection versus Induced Fit in Kinases: The Case of PI3K-γ

2011 ◽  
Vol 51 (3) ◽  
pp. 642-646 ◽  
Author(s):  
Marco D'Abramo ◽  
Obdulia Rabal ◽  
Julen Oyarzabal ◽  
Francesco Luigi Gervasio
Keyword(s):  
Induced Fit ◽  
Conformational Selection

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

A Computational Study of Competing Conformational Selection and Induced Fit in an Abiotic System

2021 ◽  
Author(s):  
Jovica D. Badjic ◽  
Christopher M Hadad ◽  
Remy F Lalisse ◽  
Radoslav Z Pavlović
Keyword(s):  
Computational Study ◽  
Elastic Band ◽  
Induced Fit ◽  
Conformational Selection

Host-guest complexations can be described by two competing mechanisms, conformational selection (CS) and induced fit (IF). In this work, we used a combination of nudged elastic band (NEB), adaptive steered...

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