Population shift vs induced fit: The case of bovine seminal ribonuclease swapping dimer

Biopolymers ◽  
2004 ◽  
Vol 73 (6) ◽  
pp. 689-695 ◽  
Author(s):  
Antonello Merlino ◽  
Luigi Vitagliano ◽  
Filomena Sica ◽  
Adriana Zagari ◽  
Lelio Mazzarella
Keyword(s):  
Induced Fit ◽  
Bovine Seminal Ribonuclease ◽  
Population Shift

scholarly journals Mechanics of allostery: contrasting the induced fit and population shift scenarios

2019 ◽  
Author(s):  
Riccardo Ravasio ◽  
Solange Flatt ◽  
Le Yan ◽  
Stefano Zamuner ◽  
Carolina Brito ◽  
...  
Keyword(s):  
Proper Function ◽  
Cooperative Binding ◽  
Induced Fit ◽  
Data Set ◽  
Elastic Mode ◽  
Allosteric Proteins ◽  
Protein Size ◽  
Distant Location ◽  
Population Shift ◽  
Optimal Stiffness

In allosteric proteins, binding a ligand can affect function at a distant location, for example by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed number of stable configurations, explain such cooperative binding from a thermodynamic viewpoint. Yet, understanding what mechanical principles constrain these models remains a challenge. Here we provide an empirical study on 34 proteins supporting the idea that allosteric conformational change generally occurs along a soft elastic mode presenting extended regions of high shear. We argue, based on a detailed analysis of how the energy profile along such a mode depends on binding, that in the induced fit scenario there is an optimal stiffness for cooperative binding, where N is the number of residues involved in the allosteric response. We find that the population shift scenario is more robust to mutation affecting stiffness, as binding becomes more and more cooperative with stiffness up to the same characteristic value , beyond which cooperativity saturates instead of decaying. We confirm numerically these findings in a non-linear mechanical model. Dynamical considerations suggest that a stiffness of order is favorable in that scenario as well, supporting that for proper function proteins must evolve a functional elastic mode that is softer as their size increases. In consistency with this view, we find a significant anticorrelation between the stiffness of the allosteric response and protein size in our data set.

scholarly journals Mechanics of Allostery: Contrasting the Induced Fit and Population Shift Scenarios

2019 ◽  
Vol 117 (10) ◽  
pp. 1954-1962 ◽  
Author(s):  
Riccardo Ravasio ◽  
Solange Marie Flatt ◽  
Le Yan ◽  
Stefano Zamuner ◽  
Carolina Brito ◽  
...  
Keyword(s):  
Induced Fit ◽  
Population Shift

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>

'Induced Fit-Lock and Key' Model in Enzymic Reactions*

2011 ◽  
Vol 38 (5) ◽  
pp. 418-426 ◽  
Author(s):  
Zi-Jian ZHANG ◽  
Rong PAN ◽  
Yuan ZHOU ◽  
Rong-Qiao HE
Keyword(s):  
Induced Fit

Reverse Induced Fit-Driven MAS-Downstream Transduction: Looking for Metabotropic Agonists

2017 ◽  
Vol 24 (39) ◽  
Author(s):  
Larissa Pernomian ◽  
Mayara S. Gomes ◽  
Carlos H. Tomich de Paula da Silva ◽  
Joaquin M.C. Rosa
Keyword(s):  
Induced Fit
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