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1. The Need for Speed: Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity

   https://doi.org/10.1128/JVI.01647-18  

   Barahona, Claudia J.; Basantes, L. Emilia; Tompkins, Kassidy J.; Heitman, Desirae M.; Chukwu, Barbara I.; Sanchez, Juan; Sanchez, Jonathan L.; Ghadirian, Niloofar; Park, Chad K.; Horton, N. C.; et al (March 2019, Journal of Virology)

   ABSTRACT Here, we investigate an unusual antiviral mechanism developed in the bacterium Streptomyces griseus . SgrAI is a type II restriction endonuclease that forms run-on oligomer filaments when activated and possesses both accelerated DNA cleavage activity and expanded DNA sequence specificity. Mutations disrupting the run-on oligomer filament eliminate the robust antiphage activity of wild-type SgrAI, and the observation that even relatively modest disruptions completely abolish this anti-viral activity shows that the greater speed imparted by the run-on oligomer filament mechanism is critical to its biological function. Simulations of DNA cleavage by SgrAI uncover the origins of the kinetic advantage of this newly described mechanism of enzyme regulation over more conventional mechanisms, as well as the origin of the sequestering effect responsible for the protection of the host genome against damaging DNA cleavage activity of activated SgrAI. IMPORTANCE This work is motivated by an interest in understanding the characteristics and advantages of a relatively newly discovered enzyme mechanism involving filament formation. SgrAI is an enzyme responsible for protecting against viral infections in its host bacterium and was one of the first such enzymes shown to utilize such a mechanism. In this work, filament formation by SgrAI is disrupted, and the effects on the speed of the purified enzyme as well as its function in cells are measured. It was found that even small disruptions, which weaken but do not destroy filament formation, eliminate the ability of SgrAI to protect cells from viral infection, its normal biological function. Simulations of enzyme activity were also performed and show how filament formation can greatly speed up an enzyme’s activation compared to that of other known mechanisms, as well as to better localize its action to molecules of interest, such as invading phage DNA. 

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2. The run-on oligomer filament enzyme mechanism of SgrAI: Part 2. Kinetic modeling of the full DNA cleavage pathway

   https://doi.org/10.1074/jbc.RA118.003682  

   Park, Chad K.; Sanchez, Jonathan L.; Barahona, Claudia; Basantes, L. Emilia; Sanchez, Juan; Hernandez, Christian; Horton, N. C. (September 2018, Journal of Biological Chemistry)
3. Probing the Run-On Oligomer of Activated SgrAI Bound to DNA

   https://doi.org/10.1371/journal.pone.0124783  

   Shah, Santosh; Sanchez, Jonathan; Stewart, Andrew; Piperakis, Michael M.; Cosstick, Richard; Nichols, Claire; Park, Chad K.; Ma, Xin; Wysocki, Vicki; Bitinaite, Jurate; et al (April 2015, PLOS ONE)
4. Shapes of a filament on the surface of a bubble

   https://doi.org/10.1098/rspa.2021.0353  

   Prasath, S. Ganga; Marthelot, Joel; Govindarajan, Rama; Menon, Narayanan (September 2021, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences)

   The shape assumed by a slender elastic structure is a function both of the geometry of the space in which it exists and the forces it experiences. We explore, by experiments and theoretical analysis, the morphological phase space of a filament confined to the surface of a spherical bubble. The morphology is controlled by varying bending stiffness and weight of the filament, and its length relative to the bubble radius. When the dominant considerations are the geometry of confinement and elastic energy, the filament lies along a geodesic and when gravitational energy becomes significant, a bifurcation occurs, with a part of the filament occupying a longitude and the rest along a curve approximated by a latitude. Far beyond the transition, when the filament is much longer than the diameter, it coils around the selected latitudinal region. A simple model with filament shape as a composite of two arcs captures the transition well. For better quantitative agreement with the subcritical nature of bifurcation, we study the morphology by numerical energy minimization. Our analysis of the filament’s morphological space spanned by one geometric parameter, and one parameter that compares elastic energy with body forces, may provide guidance for packing slender structures on complex surfaces. 

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5. Effect of Core Oligomer Length on the Phase Behavior and Assembly of π-Conjugated Peptides

   https://doi.org/10.1021/acsami.0c02095  

   Jira, Edward R.; Shmilovich, Kirill; Kale, Tejaswini S.; Ferguson, Andrew; Tovar, John D.; Schroeder, Charles M. (May 2020, ACS Applied Materials & Interfaces)