Simulating Unfolding in Kinetically Stable Proteins
Co-Investigator: Chris Bystroff
Associate Professor, Department of Biology, Rensselaer Polytechnic Institute
Co-Investigator: Mohammed J. Zaki
Associate Professor, Department of Computer Science, Rensselaer Polytechnic Institute
Co-Investigator: Wilfredo Colón
Associate Professor, Department of Chemistry and Biological Chemistry, Rensselaer Polytechnic Institute
The kinetic stability of a protein is the inverse of its unfolding rate. Proteins unfold at rates ranging from reciprocal seconds to reciprocal decades. A new 2D gel electrophoretic method has been devised to separate proteins based on their kinetic stability. Using this method, we have identified all kinetically stable proteins in E. coli and yeast and found them to have certain interesting structural characteristics: kinetically stable proteins are almost always multimers, never all alpha helical, and often have N-terminal or C-terminal extensions that wrap around the exterior or cross from one domain to the other, like a rope or latch. Unfolding kinetically stable proteins requires an ordered series of unfolding steps before the core of the protein is accessed and exposed to solvent, like the steps in untying a knot or unlocking a box. We developed a computational model to simulate the topologically allowed pathways for protein unfolding. Each internal contact can be broken once along the pathway, only when a pivot or a hinge motion is topologically possible. By assigning energetic costs and entropic driving forces to each pivot or hinge motion and applying a finite element algorithm, we can calculate the transient concentrations of each conformational state in the pathway and simulate the kinetics of protein unfolding. Our computational model exhibits two-state behavior with respect to temperature and ‘denaturants’ and qualitatively reproduces the dependence of the unfolding rate on the presence of ‘latch’ motifs, dimerization, and other topological features.