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Research Projects

Methods for studying static and dynamic protein interactions


Protein arrangement in the nuclear pore complex (Rout et al, unpublished)

Knowledge of the makeup, structure and dynamics of protein assemblies is a key to the understanding of many cellular processes. Thus, a central focus of our laboratory, which also hosts the NIH NCRR-funded Resource for the Mass Spectrometric Analysis of Biological Macromolecules, has been the development of biochemical tools (especially mass spectrometry-based tools) for studying protein interactions and the application of these tools for the elucidation and functional definition of cellular protein assemblies. Although currently available tools are already revolutionizing aspects of biological research, further improvements are highly desirable. Thus, we are actively engaged in research on the following list of activities (where the references are to prior related work from our group).

  1. isolating in vivo interactions with improved fidelity (Strambio-de-Castillia et al., 2005, Tackett et al., 2005, Cristea et al., 2005, Cristea et al., 2006)
  2. identifying low affinity specifically-associating components (Archambault et al., 2004)
  3. better discerning bona fide interactors from non-specific interactors (Strambio-de-Castillia et al., 2005, Tackett et al., 2005, Cristea et al., 2005)
  4. identifying protein components of complexes with improved sensitivity (Cristea et al., 2005, Krutchinsky et al., 2001)
  5. exhaustive mapping of the modifications on interactors (Chang et al., 2004)
  6. identifying low stoichiometry components (Tackett et al., 2005, Archambault et al., 2004)
  7. accurately determining the stoichiometry of components of complexes (Rout et al. 2000)
  8. mapping which proteins within a complex interact directly in vivo (Coman et al., 2004, Leslie et al., 2004, Qin & Chait, 1997)
  9. mapping the detailed contact sites between interactors in vivo (Coman et al., 2004, Trester-Zedlitz et al., 2003)
  10. following the dynamics of protein interactions (Tackett et al., 2005)