Joshua Pajak



My research focuses on uncovering the mechanisms by which bacteriophages package their genome during replication. I use physics-based computational methods rooted in statistical mechanics and stochastic processes to simulate the viral DNA packaging proteins under a variety of conditions. As my research continues, I draw inspiration from related ATPases such as helicases, translocases, and proteases to find conserved mechanisms involved in ATP hydrolysis and motor function.

Appointments and Affiliations

  • Student

Contact Information


  • B.S., Chemical Engineering, Rutgers University, 2016

Research Interests

My current research interests focus on uncovering the molecular basis of force generation, translocation, and coordination of of viral DNA packaging ATPase enzymes. Specifically, I am working on detailing:

  1. What mechanisms do these enzymes use to regulate ATP hydrolysis?
  2. How do subunits of the motor "talk" with one another in order to accomplish their task?
  3. What mechanisms of these motors are conserved throughout biology?
  4. How do these enzymes grip - and just as importantly, ungrip - DNA during translocation?

Along with collaborators, I have recently proposed that viral DNA packaging ATPases utilize a helical-to-planar ratchet model of DNA translocation.

Representative Publications

  • Pajak, J; Arya, G; Smith, DE, Biophysics of DNA Packaging (2021), pp. 160-166 [10.1016/b978-0-12-809633-8.20966-7] [abs].
  • delToro, D; Ortiz, D; Ordyan, M; Pajak, J; Sippy, J; Catala, A; Oh, C-S; Vu, A; Arya, G; Smith, DE; Catalano, CE; Feiss, M, Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif., Journal of Molecular Biology, vol 431 no. 22 (2019), pp. 4455-4474 [10.1016/j.jmb.2019.08.012] [abs].
  • Ortiz, D; delToro, D; Ordyan, M; Pajak, J; Sippy, J; Catala, A; Oh, C-S; Vu, A; Arya, G; Feiss, M; Smith, DE; Catalano, CE, Evidence that a catalytic glutamate and an 'Arginine Toggle' act in concert to mediate ATP hydrolysis and mechanochemical coupling in a viral DNA packaging motor., Nucleic Acids Research, vol 47 no. 3 (2019), pp. 1404-1415 [10.1093/nar/gky1217] [abs].
  • Pajak, J; Atz, R; Hilbert, BJ; Morais, MC; Kelch, BA; Jardine, P; Arya, G, Viral Packaging ATPases Utilize a Glutamate Switch to Couple ATPase Activity and DNA Translocation [10.1101/2020.12.01.406595] [abs].