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Updated: May 1, 2026

Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation

Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation

Published on: October 4, 2024

Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.

Igor N Berezovsky^1,2

¹Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. igorb@a-star.edu.sg.

Methods in Molecular Biology (Clifton, N.J.)

|April 29, 2026

Summary

This summary is machine-generated.

The physics and evolution of globular proteins reveal that basic structural units like closed loops and elementary functional loops originated from early prebiotic peptides. This interplay shapes protein function and allosteric regulation, offering insights into life's origins.

Keywords:

Closed loops Dayhoff motifs Elementary functional loops Linear peptides Persistence length of the polymer Polymer physics Protein domains Protein dynamics and allosteric regulation of protein function Protein evolution Protein folds Protein function RNA duplexes

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Area of Science:

Biochemistry and Molecular Biology
Evolutionary Biology
Physical Chemistry

Background:

Globular proteins are fundamental to life, with their structure and function shaped by evolutionary and physical principles.
Early life likely involved simple peptides and RNA, with prebiotic evolution driving the emergence of complex molecular structures.
Understanding protein origins requires integrating physical constraints with evolutionary pressures.

Purpose of the Study:

To explore the interplay between physics and evolution in shaping globular protein structure and function.
To identify the roles of closed loops and elementary functional loops as basic units of protein architecture.
To elucidate the evolutionary trajectory from simple peptides to complex protein machinery.

Main Methods:

Theoretical analysis of protein folding and polymer physics.
Examination of evolutionary pathways from prebiotic peptides to modern proteins.
Discussion of allosteric regulation as an example of physics-driven evolution.

Main Results:

Protein chains' polymer nature dictates basic structural units like closed loops.
Early ring-like peptides evolved into functional domains, complexes, and molecular machines.
Allosteric regulation results from physics-driven conserved signaling patterns and evolution-driven sequence diversity.

Conclusions:

The physics of protein chains and nucleic acids played a crucial role in determining key structural units.
Evolutionary processes, guided by physical laws, led to the vast diversity of protein functions observed today.
Further research into the 3.5-billion-year history of protein evolution promises deeper insights into molecular life.