TCF4 Simulation Video
MD Simulation of TCF4 bound to CREB-binding protein video
by Ryan Godwin, Ph.D. student, Department of Physics, Wake Forest University
Sam Cho, Ph.D, Assistant Professor, WFU
Class name: PHY 320/620: Physics of Biological Macromolecules, Fall Semester 2012
View video here:
TCF4 and CREB-binding Protein MD Simulation from Sam Cho on Vimeo.
Final Project: MD Simulation of TCF4 bound to CREB-binding protein
Project description: Our class performed molecular dynamics (MD) simulations of TCF4 bound to CREB-binding protein on Wake Forest University’s DEAC Supercomputing facilities. Molecular dynamics simulations are like a computational microscope that describes the physical movements of atoms and molecules over a period of time. The forces between each of the atoms and molecules at a given time determine where they will move next by numerically solving Newton’s equations of motion, over and over again until the simulation ends. The result is a series of “snapshots” that can be stitched together into a “movie” like the one seen above.
In previous years, we chose some obscure biomolecular system to perform our simulations. This year, to give the students a more meaningful experience, they performed simulations of TCF4 bound to CREB-binding protein, whose structure was recently solved using a technique called nuclear magnetic resonance by an international team consisting from Queen’s University (Kingston, ON), University of Toronto (Toronto, ON), and Centre National de la Recherche Scientifique (Grenoble, France). This was an ideal biological system to study because it was just the right size for the students to perform scientifically meaningful simulations in a short period of time.
On the last day of class, Theresa and Paúl Pauca shared their story of their son Victor so that the students can know that their simulations had a biological relevance. This talk was designed to encourage socially relevant learning and disability awareness at the University level.
Student comments about the class:
“I especially enjoyed seeing how our project was useful to good people.”
“I enjoyed the simulations and applying what we learned in the semester to understand the real-world applications of the theory.”
