Exploring Protein Dynamics in the Complex Cellular Milieu: Computational Folding and Hydrodynamics of Novel Bioengineered Protein Probes
By: Michelle Chong
Departments: Biology, Chemistry & Biochemistry
Faculty Advisor: Dr. Raymond Esquerra
The cellular interior is an intricate and dense milieu containing proteins, DNA, lipids, and organic molecules. Our research aims to enhance our comprehension of how proteins move within this complex environment. To achieve this goal, our laboratory has created protein probes that can monitor rotational diffusion in situ. The rotational diffusion of our protein probe depends on its size and folded shape. Fortunately, recent advancements in AI-driven structure prediction, such as AlphaFold2 and trRosetta, have made it possible to computationally fold our novel proteins with high accuracy. To develop a model that correlates the rotational diffusion time of our protein with protein hydrodynamics, we are using computational folding of our novel bioengineered protein probe and combining this structure with protein hydrodynamics. We analyze the protein structure generated by AlphaFold2 using ChimeraX to measure protein inertia. Additionally, we compute the viscosity of an ellipsoidal shaped object using Perrin's equation, which is derived from Fick's law.