Julio Fernandez, PhD

Departments And Divisions

  • Department of Biological Sciences (Columbia University)
  • Professor of Biological Sciences (Columbia University)

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.

Lab Locations

  • Northwest Corner Building

    550 West 120th Street
    Room 808, Mail Code: 4814
    New York, NY 10027
    Phone:
    (212) 854-9141
    Email:
    jf2120@columbia.edu

Contact Info

Research Interests

  • Biophysics/Ion Channels
  • Cellular/Molecular/Developmental Neuroscience

Publications

  • Li H, Linke WA, Oberhauser AF, Carrion-Vazquez M, Kerkvliet JG, Lu H, Marszalek PE, Fernandez JM. (2002) Reverse engineering of the giant muscle protein titin. Nature. 418(6901):998-1002.
  • Marszalek PE, Li H, Fernandez JM. (2001) Fingerprinting polysaccharides with single molecule atomic force spectroscopy. Nature Biotech. 19: 258-262.
  • Fernandez JM, Chu S, Oberhauser AF. (2001) RNA structure - Pulling on hair(pins) Science 292 (5517): 653-654.
  • Fisher TE, Carrion-Vazquez M, Oberhauser AF, Li H, Marszalek PE, Fernandez JM. (2000). Single molecule force spectroscopy of modular proteins in the nervous system. Neuron 27(3):435-446.