Solubility and Aggregation of Selected Proteins Interpreted on the Basis of Hydrophobicity Distribution.

Magdalena Ptak-Kaczor,Leszek Konieczny,Katarzyna Stapor,Irena Roterman,Mateusz Banach,Piotr Fabian

doi:10.3390/ijms22095002

Abstract

Protein solubility is based on the compatibility of the specific protein surface with the polar aquatic environment. The exposure of polar residues to the protein surface promotes the protein’s solubility in the polar environment. The aquatic environment also influences the folding process by favoring the centralization of hydrophobic residues with the simultaneous exposure to polar residues. The degree of compatibility of the residue distribution, with the model of the concentration of hydrophobic residues in the center of the molecule, with the simultaneous exposure of polar residues is determined by the sequence of amino acids in the chain. The fuzzy oil drop model enables the quantification of the degree of compatibility of the hydrophobicity distribution observed in the protein to a form fully consistent with the Gaussian 3D function, which expresses an idealized distribution that meets the preferences of the polar water environment. The varied degrees of compatibility of the distribution observed with the idealized one allow the prediction of preferences to interactions with molecules of different polarity, including water molecules in particular. This paper analyzes a set of proteins with different levels of hydrophobicity distribution in the context of the solubility of a given protein and the possibility of complex formation.

Highlights

There are two environments of biological activity for proteins: an aquatic environment, and a membrane environment
The proteins discussed here were selected taking into account the criteria of gradually developed structures: from a monomer with high solubility; through a chain with a domain structure, complexes with various forms of their stabilization, and domain-swapping; and further through complex quaternary structures with ligands present; to a multi-chain complex anchored in a membrane that acts as a channel for the transport of molecules
Type III antifreeze proteins are proteins whose biological activity is related to their solubility

Summary

Introduction

There are two environments of biological activity for proteins: an aquatic environment, and a membrane environment. The possibility of protein solubility is critical to protein activity. The aggregation of proteins can be treated as partial non-solubility, which is sometimes necessary in order to ensure biological activity, as well as loss of activity, as is observed in the misfolded proteins [7,8,9,10,11,12,13,14,15,16,17,18]—of which the amyloids are spectacular examples [19]. The intensively applied machine learning technique (applied in PROSO, for example) enables the prediction of protein solubility in heterologous expression in Escherica coli [20,21]

Results

Discussion

Conclusion