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
- B.S., Chemical Engineering, Rutgers University, 2016
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:
- What mechanisms do these enzymes use to regulate ATP hydrolysis?
- How do subunits of the motor "talk" with one another in order to accomplish their task?
- What mechanisms of these motors are conserved throughout biology?
- 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.
- Pajak, J; Dill, E; Reyes-Aldrete, E; White, MA; Kelch, BA; Jardine, PJ; Arya, G; Morais, MC, Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor., Nucleic Acids Research, vol 49 no. 11 (2021), pp. 6474-6488 [10.1093/nar/gkab372] [abs].
- Woodson, M; Pajak, J; Mahler, BP; Zhao, W; Zhang, W; Arya, G; White, MA; Jardine, PJ; Morais, MC, A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA., Science Advances, vol 7 no. 19 (2021) [10.1126/sciadv.abc1955] [abs].
- Pajak, J; Atz, R; Hilbert, BJ; Morais, MC; Kelch, BA; Jardine, PJ; Arya, G, Viral packaging ATPases utilize a glutamate switch to couple ATPase activity and DNA translocation., Proceedings of the National Academy of Sciences of the United States of America, vol 118 no. 17 (2021) [10.1073/pnas.2024928118] [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].