More is different: 50 years of nuclear BCS

TL;DR

This paper explores the analogy between nuclear BCS theory and protein folding, highlighting how concepts like symmetry breaking and domain walls can model protein evolution and folding mechanisms, with implications for understanding molecular recognition.

Contribution

It introduces a novel application of nuclear physics concepts to model protein evolution and folding, emphasizing the role of emergent properties like domain walls and local elementary structures.

Findings

Protein folding involves symmetry-breaking phenomena similar to nuclear systems.

Local elementary structures (LES) stabilize early in the denatured state.

Peptides matching LES sequences can serve as probes to observe folding intermediates.

Abstract

Many of the concepts which are at the basis of the development associated with a quantitative treatment of the variety of phenomena associated with the spontaneous breaking of gauge symmetry in nuclei have been instrumental in connection with novel studies of soft matter, namely of protein evolution and protein folding. Although the route to these subjects and associated development does not necessarily imply the nuclear physics connection, such a connection has proven qualitatively and quantitatively inspiring. In particular to model protein evolution in terms of the alignment of quasispins displaying twenty different projections, one for each of the twenty amino acids occurring in nature, and the associated symmetry breaking in information (sequence) space. Emergent properties of the corresponding phase transition are domain walls which stabilize local elementary structures (LES), few groups of 10-20 aminoacids which become structured already in the denatured state provide the molecular recognition directing protein folding. In fact, their docking is closely related to the transition state of the process. While the two-step, yes or no, folding process, does not provide direct information concerning LES, one can force LES from virtual to become real, observable final state entities. Getting again inspiration from the nuclear case (virtual processes contributing to pair correlations can be forced to become real with the help of a probe which itself changes particle number by two), one would expect that to make real virtual LES, that is segments of the protein which already at an early stage of the folding process flicker in and out of their native conformation, one needs a probe which itself displays a similar behaviour. Peptides displaying a sequence identical to LES are such probes.