(481a) Turning a Protein’s Achilles’ Heel into a Stronghold: Using Protein Denaturation Pathways to Rationally Design Polymer Conjugates from Molecular Dynamics Simulations

The therapeutic potential of proteins has revolutionized the field of biopharmaceuticals as they can treat a wide range of diseases, from diabetes to cancer. However, proteins are fragile, and many of them are too ephemeral to be used in therapeutics without external stabilizing agents. During storage and administration, they unravel and lose their secondary structure due to several different factors, including fluctuations in temperature, solution pH, shearing forces, and other external stressors.

If we can capture the ‘weak links’ in a protein that breakdown when subjected to a stressor, we can rationally engineer materials that can stabilize a protein and prevent it from unravelling. To do so, we employ all-atom molecular dynamics simulations, and subject three proteins of different sizes – lysozyme, bovine serum albumin (BSA), and BrCas12b – to denaturation via temperature, pH and shear stress. By accessing the global structural change and local residue level details, we capture the unfolding process and identify residues that degrade first. The recent development of random heteropolymers (RHPs) containing four distinct methacrylate-based monomers provides a promising new avenue of soft materials that possess the ability to shield proteins when mixed even without chemical conjugation, contributing to improved activity and stability of proteins outside their native environment. We generate simulated polymer sequences via the Composition Drift program. The stability of the protein in the mixture was evaluated using a high-temperature unfolding protocol. We find that the RHPs stabilize proteins more effectively than Polyethylene Glycol (PEG). By leveraging knowledge of a protein’s weak point, we further tailor RHP design, opening a new avenue for customized protein stabilization strategies.