Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins.

Yann Chalopin,Julien Sparfel

doi:10.3389/fmolb.2021.736376

Abstract

Proteins are among the most complex molecular structures, which have evolved to develop broad functions, such as energy conversion and transport, information storage and processing, communication, and regulation of chemical reactions. However, the mechanisms by which these dynamical entities coordinate themselves to perform biological tasks remain hotly debated. Here, a physical theory is presented to explain how functional dynamical behavior possibly emerge in complex/macro molecules, thanks to the effect that we term bilocalization of thermal vibrations. More specifically, our approach allows us to understand how structural irregularities lead to a partitioning of the energy of the vibrations into two distinct sets of molecular domains, corresponding to slow and fast motions. This shape-encoded spectral allocation, associated to the genetic sequence, provides a close access to a wide reservoir of dynamical patterns, and eventually allows the emergence of biological functions by natural selection. To illustrate our approach, the SPIKE protein structure of SARS-COV2 is considered.

Highlights

In his seminal book “What is Life,” Erwin Schrödinger exposed his physical vision of modern molecular biology by priorly emphasizing the intrinsically aperiodic character of living microscopic systems
If it is well known that a protein is a dynamical object with multiscale behaviors, there are no tools that surpass the traditional normal mode analysis to highlight the domains characterizing the motions at a given frequency/time period
We have developed a theory to link the topological structure of a molecule and its function by studying the motions imposed by its complex form

Summary

Introduction

In his seminal book “What is Life,” Erwin Schrödinger exposed his physical vision of modern molecular biology by priorly emphasizing the intrinsically aperiodic character of living microscopic systems (notably the nucleic acids). His vision arose from the observation that such biological structures failed the physical theories of the time, which were centered, for the most part, on the principle of the periodicity of crystal structures. Thermal expansion or even thermal conductivity are quantities predicted with substantial precision (Ashcroft and David Mermin, 1976), thanks to the well known physical concept of first Brillouin zone

Methods

Discussion

Conclusion