The role of co-solutes in complexation of globular proteins with synthetic polyelectrolytes in aqueous solutionsSimončič, Matjaž (Avtor) Lukšič, Miha (Mentor) globular proteinspolyelectrolytescomplexationco-solutesaqueous solutionsIn the present work, the influence of various co-solutes on the aggregation between globular proteins as well as on the complexation of globular proteins with synthetic polyelectrolytes (PEs) was investigated. Conclusions were drawn using an assortment of experimental techniques, molecular dynamics (MD) simulations, and other theoretical approaches. The modulating role of three types of co-solutes was studied: salts (NaCl, NaBr, NaI, NaNO3), polyethylene glycol (PEG) with different molecular weights, and two sugar analogs (sucrose, sucralose). The effect of co-solutes was investigated with respect to the colloidal stability of protein- and protein-PE-containing aqueous solutions as well as on the conformational stability of the protein in such solutions. It was found that protein aggregation and protein-PE complexation can be explained in light of the balance between attractive and repulsive electrostatic interactions (forces) depending on the pH of the solution with respect to the isoionic point of the protein (pI). The strength of the interactions and their modulation depend strongly on the heterogeneous charge distribution of the protein surface and the protein-PE system studied, however, some general conclusions can be drawn. The modulating role of salts was most pronounced considering protein-protein and protein-PE interactions, with the effect depending on the pH of the solution with respect to the pI as well as on the concentration of salt ions. Moreover, it was shown that the modulating effect of a salt depends on the chemical identity of the salt anion, as more chaotropic anions screen electrostatic forces more effectively. In addition, complexation of proteins with PEs for protein-PE pairs studied can be accompanied by conformational changes of the protein related to the extent of complex formation, which can in some cases be regulated by the presence of salt ions. Although the effect of neutral (non-ionic) co-solutes, such as PEG or sugars on protein aggregation and protein-PE complexation was less pronounced, we nevertheless showed that under certain conditions macromolecular association can be modulated. In particular, chemical modification of sucrose was demonstrated to change its water-structuring capability around proteins, which altered the stabilizing property of the sugar with respect to protein aggregation and protein-PE complexation. Protein surface anisotropy and the localization of protein binding sites (charge patches) were shown to be important in evaluating protein-PE complexation. A theoretical approach combining a machine-learning (ML) algorithm and target molecular docking for more efficient protein-ligand docking was developed and tested on a series of protein complexes with peptides as well as with small organic molecules. We demonstrated the advantages of implementing ML in classical docking protocols, which is particularly convenient when no experimental data on protein-ligand complexes are available, such as for protein complexes with synthetic PEs.20232023-03-31 16:00:02Doktorsko delo/naloga145053sl