Repository logo

Infoscience

  • English
  • French
Log In
Logo EPFL, École polytechnique fédérale de Lausanne

Infoscience

  • English
  • French
Log In
  1. Home
  2. Academic and Research Output
  3. Journal articles
  4. Mechanics of Allostery: Contrasting the Induced Fit and Population Shift Scenarios
 
research article

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

Ravasio, Riccardo  
•
Flatt, Solange Marie  
•
Yan, Le
Show more
November 19, 2019
Biophysical Journal

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 k*(a) similar to 1/N for cooperative binding, where N is the number of residues. We find that the population shift scenario is more robust to mutations affecting stiffness because binding becomes more and more cooperative with stiffness up to the same characteristic value k*(a), beyond which cooperativity saturates instead of decaying. We numerically confirm these findings in a nonlinear mechanical model. Dynamical considerations suggest that a stiffness of order k*(a) 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 fair anticorrelation between the stiffness of the allosteric response and protein size in our data set.

  • Details
  • Metrics
Type
research article
DOI
10.1016/j.bpj.2019.10.002
Web of Science ID

WOS:000497815800017

Author(s)
Ravasio, Riccardo  
Flatt, Solange Marie  
Yan, Le
Zamuner, Stefano  
Brito, Carolina
Wyart, Matthieu  
Date Issued

2019-11-19

Publisher

CELL PRESS

Published in
Biophysical Journal
Volume

117

Issue

10

Start page

1954

End page

1962

Subjects

Biophysics

•

dynamics

•

cooperativity

•

architecture

•

transitions

•

proteins

•

motions

•

models

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
PCSL  
LBS  
Available on Infoscience
December 5, 2019
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/163574
Logo EPFL, École polytechnique fédérale de Lausanne
  • Contact
  • infoscience@epfl.ch

  • Follow us on Facebook
  • Follow us on Instagram
  • Follow us on LinkedIn
  • Follow us on X
  • Follow us on Youtube
AccessibilityLegal noticePrivacy policyCookie settingsEnd User AgreementGet helpFeedback

Infoscience is a service managed and provided by the Library and IT Services of EPFL. © EPFL, tous droits réservés