Jerrica returns to the program for the second time this summer. She is now an upcoming senior at Central State University in Wilberforce, Ohio. This time she is working in the Stan Lab under the guidance of Yashan Fonseka in using computational methods of studying the mystifying process of protein folding.
Here is how Jerrica explains her research:
We are interested in the Halotag (pdbid: 4kaf) due to its simple structure and mechanical weakness and how it interacts with the ClpYΔI hexamer nanomachine
Using a CHARMM package, we study the folding assistance or degradation processes used to check the folding pathways. To probe the unfolding and translocation mechanisms of the substrate using ClpYΔI, we perform Langevin dynamics coupled with targeted molecular dynamics (TMD) using the effective energy function (EEF1) implicit solvation model. EEF1 implicit solvation model uses an atomistic representation for the protein while generally representing solvent as continuous field in a vacuum. Using TMD we can simulate the allosteric motion within ClpYΔI. ClpYΔI undergoes a conformational change from open(pdbid 1do2) to close(pdbid 1do0) while exerting a force on the substrate at the central pore region of ClpYΔI. We have two main interests: in one setup we simulate the invivo arrangement while another mimics the experimental setup of single-molecule experiments. Our current data indicates that the unfolding and translocation of the substrate in restrained and unstrained geometric setups will result in different unfolding mechanisms.
In this video Jerrica explains why she became interested in chemistry.