Piotr E. Marszalek
Center For Biologically Inspired Materials and Material Systems
Department of Mechanical Engineering and Materials Science
Monday, April 25, 2011
The nanomechanics of proteins, nucleic acids and polysaccharides
Compared to other single-molecule techniques, AFM is uniquely capable of determining molecules’ high energy conformations that cannot be examined by other techniques such as X-ray crystallography or NMR due to its ability to apply large stretching forces. In my talk, I will present our AFM studies of fundamental relationships between structural and mechanical properties of polysaccharides, proteins, and DNA. AFM stretching measurements on polysaccharides reveal that their elasticity is governed by force-induced conformational transitions within sugar rings, such as chair-boat transitions. High resolution AFM stretching measurements of repeat proteins captured their unusually strong folding forces, and when combined with molecular dynamics simulations allowed us to fully reconstruct their vectorial folding pathways. We show that when fully stretched and then relaxed, a large ankyrin repeat protein NI6C starts folding by the formation of local secondary structures, followed by the nucleation of three N-terminal repeats that is then followed by the vectorial and sequential folding of the remaining repeats. We hypothesize that the AFM controlled vectorial folding of polypeptides captures their co-translational folding behavior in vivo. Our DNA research is aimed at exploiting AFM for development of new single-molecule assays for detecting and examining DNA damage and damage repair. This research, in addition to its basic science aspects may lay a foundation for the future use of AFM in the nanoscale DNA diagnostics.