Solitons and Physics of the Lysogenic to Lytic Transition in Enterobacteria Lambda Phage

TL;DR

This paper models the lysogenic to lytic transition in lambda phage using a soliton-based energy function, revealing how conformational changes in the protein backbone drive the switch.

Contribution

It introduces a novel soliton-based physical model of the lambda phage transition, linking protein backbone configurations to functional states.

Findings

Three loops are composites of two solitons each.

The repressive DNA binding turn is a single soliton.

Transition involves a saddle-node bifurcation with soliton-antisoliton annihilation.

Abstract

The lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding CI and CRO proteins. Here we address the Physics of this transition in terms of an energy function that portrays the backbone as a multi-soliton configuration. The precision of the individual solitons far exceeds the B-factor accuracy of the experimentally determined protein conformations giving us confidence to conclude that three of the four loops are each composites of two closely located solitons. The only exception is the repressive DNA binding turn, it is the sole single soliton configuration of the backbone. When we compare the solitons with the Protein Data Bank we find that the one preceding the DNA recognition helix is unique to the CI protein, prompting us to conclude that the lysogenic to lytic transition is due to a saddle-node bifurcation involving a soliton-antisoliton annihilation that removes the first loop.