(360bc) Understanding Protein Unfolding Under Different Stressors from Molecular Dynamics Simulations

Protein based therapeutics (biologics) have revolutionized the field of biopharmaceuticals and the industry is expected to grow steadily in the next decade. There are over 100 approved proteins for clinical use, including monoclonal antibodies, hormones, and fusion proteins. While proteins have a wide range of applicability and function, a major drawback is their instability, which makes them too fragile to be used alone as drugs. During storage or administration, proteins tend to unravel and lose their secondary structure due to adsorption to surfaces, interaction with other drug constituents, or changes in solution pH and temperature. Understanding how these conditions change protein structure can help with the formulation of a robust conjugate which can prevent proteins from misfolding. Quantification of weak links in the protein that are most susceptible to collapse when subjected to external stressors can help in the design of specific excipients that can prevent the degradation of these links, and aid in the rational design of conjugates that will stabilize and maintain protein structure.

To this end, we perform all-atom MD simulation to study the unfolding process of three proteins – egg-white lysozyme, insulin, and PKD Domain 1, under three different stressors – temperature, shear, and pH. Global secondary structure change during protein denaturation is characterized using backbone root-mean-square deviation (Cα-RMSD), hydrogen bond number, and hydrophobic solvent accessible surface area (SASA) and validated by using secondary structure plot and representative simulation trajectory snapshots. To further investigate specific links that breakdown first, root mean square fluctuation (RMSF), radial distribution function, and hydrogen bond formation, are systematically evaluated. Future work will focus on designing specific polymer conjugates that will prevent the onset of degradation of weak links to boost protein stability.