Rational Design of Solution Additives for the Prevention of Protein Aggregation

• Published in: Biophysical journal 2004-09, Vol.87 (3), p.1631-1639
• Main Authors: Baynes, Brian M., Trout, Bernhardt L.
• Format: Article
• Language: English
• Subjects: Additives; Biophysical Phenomena; Biophysical Theory and Modeling; Biophysics; Carbonic Anhydrases - chemistry; Drug Design; Entropy; Interferon-gamma - chemistry; Kinetics; Models, Chemical; Models, Statistical; Models, Theoretical; Oxidative Stress; Oxygen - chemistry; Protein Binding; Protein Conformation; Protein Denaturation; Protein Folding; Proteins; Reaction kinetics
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1529/biophysj.104.042473

We have developed a statistical-mechanical model of the effect of solution additives on protein association reactions. This model incorporates solvent radial distribution functions obtained from all-atom molecular dynamics simulations of particular proteins into simple models of protein interactions. In this way, the effects of additives can be computed along the entire association/dissociation reaction coordinate. We used the model to test our hypothesis that a class of large solution additives, which we term “neutral crowders,” can slow protein association and dissociation by being preferentially excluded from protein-protein encounter complexes, in a manner analogous to osmotic stress. The magnitude of this proposed “gap effect” was probed for two simple model systems: the association of two spheres and the association of two planes. Our results suggest that for a protein of 20 Å radius, an 8 Å additive can increase the free energy barrier for association and dissociation by as much as 3–6 kcal/mol. Because the proposed gap effect is present only for reactions involving multiple molecules, it can be exploited to develop novel additives that affect protein association reactions although having little or no effect on unimolecular reactions such as protein folding. This idea has many potential applications in areas such as the stabilization of proteins against aggregation during folding and in pharmaceutical formulations.