Julio Fernandez, PhD

Our primary research interest is the stability and folding dynamics of modular proteins as investigated by an atomic force microscope (AFM). With the AFM we measure the force needed to unfold single protein domains. Using these data we investigate the presence of folding intermediates, misfolding events, the speed of refolding, and the rate of spontaneous unfolding for many different types of protein modules or wild-type modular proteins such as titin, fibronectin, ubiquitin, and spectrin. Additionally, we have used this method to establish a micro-mechanical basis for bulk muscle elasticity.

The large modular protein titin is thought to be responsible for the passive elasticity of muscle. To investigate the molecular basis of this elasticity, we dissected the individual mechanical elements of titin and studied their extensibility. We used protein engineering technologies extensively to construct polyproteins that give distinctive mechanical fingerprints when stretched by single molecule atomic force microscopy techniques. For sections which did not undergo a characteristic catastrophic failure, we used well-characterized Ig domains to create a force fingerprint, ensuring that each recording was of only a single molecule. In the end, we were able to add up all of the components of elasticity investigated through this piecewise method and reproduce macroscopic extensibility of cardiac titin in situ.

The extra-cellular matrix (ECM) determines the elasticity and tensile strength of tissues and finely regulates cell adhesion and cell migration, and thus seems a natural target for force spectroscopy. We are beginning to investigate the major protein component of the ECM, fibronectin, and a polysaccharide component of ECM, heparin.

Ubiquitin is a highly conserved globular protein that is responsible for tagging other proteins for entry into a variety of reaction pathways including proteasome mediated degradation. Tagging occurs when a number of ubiquitin modules are ligated to lysine residues on the marked protein, but the specific manner that these ubiquitin modules are ligated together can vary. We are testing the mechanical properties of ubiquitin polymers with subunits that attach to one another differently.