This design project accompanies the Modeling and Manipulating Biomolecular Interactions section.
Bromodomains are protein domains that specifically recognize acetylated lysines. Given the prevalence of acetylated lysines in complexes involved in chromatin-remodeling, DNA damage and cell-cycle control, bromodomains play a key role in a variety of cellular processes. In this project, we will use computational tools to mutate an existing bromodomain such that it has a higher affinity for a novel acetylated peptide compared to its actual biological peptide substrate. The project will consist of four stages:
Note: Appendix A is a basic PyMOL primer. Appendix B is a basic PyRosetta primer.
|PROJECT HANDOUTS||SUPPORTING FILES|
|Protein Design Project - Parts 1 and 2 and Appendices A and B (PDF - 1.6MB)||2DVQ_project.pdb (PDB)|
|Protein Design Project - Part 3 and Appendices A and B (PDF - 2.2MB)||peptide_assignments.xls (XLS)|
|Protein Design Project - Part 4 and Appendices A and B (PDF - 2.2MB)|