A framework for protein and membrane interactions

TL;DR

The paper introduces the BioBeta Framework, a formal model for representing and analyzing protein and membrane interactions in living cells, enabling multi-level biological modeling and comparison.

Contribution

It presents a novel formalism that unifies protein and membrane interaction modeling with a clear semantics, linking it to bigraphical reactive systems for enhanced analysis.

Findings

BioBeta formalism encodes protein and membrane interactions.

It provides a formal basis for higher-level membrane activities.

BioBeta's expressivity is demonstrated through comparison with kappa-calculus.

Abstract

We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction levels; in particular, higher-level (e.g. membrane) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. A BioBeta specification provides a protein signature together a set of protein reactions, in the spirit of the kappa-calculus. Moreover, the specification describes when a protein configuration triggers one of the only two membrane interaction allowed, that is "pinch" and "fuse". In this paper we define the syntax and semantics of BioBeta, analyse its properties, give it an interpretation as biobigraphical reactive systems, and discuss its expressivity by comparing with kappa-calculus and modelling significant examples. Notably, BioBeta has been designed after a bigraphical metamodel for the same purposes. Hence, each instance of the calculus corresponds to a bigraphical reactive system, and vice versa (almost). Therefore, we can inherith the rich theory of bigraphs, such as the automatic construction of labelled transition systems and behavioural congruences.