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Binding Pockets in Proteins Induced by Mechanical Stress.

Matteo Tiberti¹, Bob-Dan Lechner¹, Arianna Fornili^1,2

¹School of Biological and Chemical Sciences , Queen Mary University of London , London E1 4NS , United Kingdom.

Journal of Chemical Theory and Computation

|December 12, 2018

Summary

Researchers discovered a new "mechano-pocket" that forms in cardiac muscle proteins when mechanical force is applied. This finding, revealed by simulations, suggests a new druggable target and a general mechanism for pocket formation under stress.

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Area of Science:

Biophysics
Structural Biology
Cardiovascular Research

Background:

Immunoglobulin-like (Ig-like) domains are crucial structural components in many proteins, including those in cardiac muscle.
Understanding protein dynamics and structural changes under mechanical stress is vital for deciphering cellular function and disease mechanisms.

Purpose of the Study:

To report the novel observation of a pocket forming in response to mechanical force applied to an Ig-like domain from cardiac muscle.
To investigate the mechanism of this force-induced pocket formation using computational simulations.
To explore the potential druggability and broader implications of this phenomenon.

Main Methods:

Molecular dynamics (MD) simulations were employed to model and analyze the behavior of an Ig-like domain under applied mechanical force.
Force-probe simulations were used to observe and characterize the structural changes, specifically pocket formation, at the atomic level.

Main Results:

The study presents the first observation of a pocket opening in an Ig-like domain upon application of mechanical force.
This previously uncharacterized mechanism, termed "mechano-pocket" formation, was revealed through detailed MD simulations.
Preliminary analysis indicates that these mechano-pockets are potentially druggable targets.

Conclusions:

Mechanical force can induce the formation of novel pockets in Ig-like domains of cardiac proteins.
The identified "mechano-pocket" represents a potentially druggable site, opening new avenues for therapeutic intervention.
This mechanism may be generalizable to other domains within the same protein fold family, suggesting a widespread phenomenon in response to mechanical stress.