scholarly journals Interplay between conformational selection and induced fit in multidomain protein–ligand binding probed by paramagnetic relaxation enhancement

2014 ◽  
Vol 186 ◽  
pp. 3-12 ◽  
Author(s):  
G. Marius Clore
Keyword(s):  
Ligand Binding ◽  
Paramagnetic Relaxation ◽  
Paramagnetic Relaxation Enhancement ◽  
Induced Fit ◽  
Multidomain Protein ◽  
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

Mechanistic insights into peptide and ligand binding of the ATAD2-bromodomain via atomistic simulations disclosing a role of induced fit and conformational selection

2018 ◽  
Vol 20 (36) ◽  
pp. 23222-23232 ◽  
Author(s):  
Yang Zhou ◽  
Muzammal Hussain ◽  
Guanglin Kuang ◽  
Jiancun Zhang ◽  
Yaoquan Tu
Keyword(s):  
Ligand Binding ◽  
Peptide Binding ◽  
Atomistic Simulations ◽  
Induced Fit ◽  
Conformational Selection

Atomistic simulations of the ATAD2-bromodomain disclose a role of induced fit and conformational selection upon ligand and peptide binding.

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
Sign in / Sign up

Export Citation Format

Share Document