Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins

TL;DR

This study uses Wang-Landau sampling to classify folding and transition behaviors of hydrophobic-polar lattice proteins on surfaces, revealing generic hierarchies linked to surface strength and sequence properties.

Contribution

It introduces a universal classification scheme for folding hierarchies of HP proteins interacting with surfaces, applicable across different sequences and surface types.

Findings

Identification of generic folding and transition categories

Connection between transition types and surface attraction strength

Validation across multiple benchmark sequences

Abstract

The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are considered with different types of surfaces, each of which attract either all monomers, only hydrophobic (H) monomers, or only polar (P) monomers, respectively. The diversity of folding behavior in dependence of surface strength is discussed. Analyzing the combined patterns of various structural observables, such as, e.g., the derivatives of the numbers of surface contacts, together with the specific heat, we are able to identify generic categories of folding and transition hierarchies. We also infer a connection between these transition categories and the relative surface strengths, i.e., the ratio of the surface attractive strength to the interchain attraction among H monomers. The validity of our proposed classification scheme is reinforced by the analysis of additional benchmark sequences. We thus believe that the folding hierarchies and identification scheme are generic for HP proteins interacting with attractive surfaces, regardless of chain length, sequence, or surface attraction.