Entanglement in Biology-Pierced Lassos and Deep Knots

University Of California-San Diego, La Jolla CA

Investigators

Abstract

Unexpectedly, proteins can tie themselves into knots in their native folds. Since protein folding from an unstructured molecular chain into the native-state is already complex, the existence of knotted chains immediately raises the questions: how does the chain cross itself to form a knot and how does the knot affect function? The PIs discovered a class of proteins, with leptin as the founding member. This growing class now includes well over 350 protein families, spanning a huge range of fold types and including all secondary structure elements. The goal of the current project is to use a multifaceted approach to investigate how the fundamental mechanisms of knotting/unknotting/threading are initiated and relate to overall protein folding, and how the knotted functional and folding landscapes are related. One of the PIs has been involved in K-12 outreach by performing scientific experiments at local grammar schools which are greater than 50% minority students, by also helping to train children in middle school for the Science Olympiad, hosting High School students as research interns for the summer and by hosting people interested in a career in teaching in primary and secondary schools as research assistants in her laboratory. This effort will allow the PI to convey a true excitement for science to the K-12 population and she is currently in the planning stages of intensifying her K-12 outreach efforts by coordinating visits to local bilingual schools accompanied by successful minority, male and female students from UCSD that will provide role models for the local students. The simplest backbone, deep-knotted proteins are the 31 trefoil knots such as in the trefoil methyltransferase (MT) families. The PIs showed that an extended time in the denatured state is required for unknotting in these proteins. The PIs will investigate whether specific regions identified as barriers to untying in the MTs also contribute to functional regulation and ligand gating in the native states because of long-range coupling of topologically frustrated regions. The preliminary data are consistent with this hypothesis. Further exploration building upon these foundational studies will allow the PIs to investigate the interplay between the strained topology inherent in a knotted conformation and communication between functional sites. These studies will allow the PIs to describe, for the first time, the physical-chemical variables necessary to overcome the topological barrier for initiating threading as well as the role of the PL on the functional dynamics of a protein This project is being jointly supported by the Physics of Living Systems program in the Division of Physics and the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences.