Allosteric Communication Pathways and Thermal Rectification in PDZ-2 Protein: A Computational Study

TL;DR

This computational study reveals that heat diffuses asymmetrically in PDZ-2 proteins via hydrogen bonds, acting as thermal rectifiers, which may influence allosteric signaling and heat management in biological and material systems.

Contribution

The paper demonstrates that hydrogen bonds in PDZ-2 proteins can act as thermal rectifiers, revealing a new property of asymmetric heat diffusion in protein structures.

Findings

Heat flows preferentially through two allosteric pathways.

Normal length hydrogen bonds (~2.85 Å) act as thermal rectifiers.

Short hydrogen bonds (~2.60 Å) lead to symmetrical heat diffusion.

Abstract

Allosteric communication in proteins is a central and yet unsolved problem of structural biochemistry. Previous findings, from computational biology (Ota and Agard, 2005), have proposed that heat diffuses in a protein through cognate protein allosteric pathways. This work studied heat diffusion in the well-known PDZ-2 protein, and confirmed that this protein has two cognate allosteric pathways and that heat flows preferentially through these. Also, a new property was also observed for protein structures - heat diffuses asymmetrically through the structures. The underling structure of this asymmetrical heat flow was a normal length hydrogen bond (~2.85 {\AA}) that acted as a thermal rectifier. In contrast, thermal rectification was compromised in short hydrogen bonds (~2.60 {\AA}), giving rise to symmetrical thermal diffusion. Asymmetrical heat diffusion was due, on a higher scale, to the local, structural organization of residues that, in turn, was also mediated by hydrogen bonds. This asymmetrical/symmetrical energy flow may be relevant for allosteric signal communication directionality in proteins and for the control of heat flow in materials science.