Two-dimensional structure in a generic model of triangular proteins and protein trimers

TL;DR

This study models two-dimensional structures of triangular proteins and trimers using hard-disk simulations with attractive interactions, revealing diverse phases and structural motifs relevant to protein crystal formation.

Contribution

It introduces a generic model for 2D triangular proteins and trimers with specific binding, exploring their phase behavior and structural motifs through simulations.

Findings

Identification of fluid phases with tetramers, pentamers, and hexamers.

Discovery of a high-density solid phase based on hexamer motifs.

Observation of a transition between ordered and disordered solid phases.

Abstract

Motivated by the diversity and complexity of two-dimensional crystals formed by triangular proteins and protein trimers, we have investigated the structures and phase behavior of hard-disk trimers. In order to mimic specific binding interactions, each trimer possesses on `attractive' disk which can interact with similar disks on other trimers via an attractive square-well potential. At low density and low temperature, the fluid phase mainly consists of tetramers, pentamers, or hexamers. Hexamers provide the structural motif for a high-density, low-temperature periodic solid phase, but we also identify a metastable periodic structure based on a tetramer motif. At high density there is a transition between orientationally ordered and disordered solid phases. The connections between simulated structures and those of 2D protein crystals -- as seen in electron microscopy -- are briefly discussed.