About

Justin Kollman is a Professor in the Department of Biochemistry at the University of Washington. His research focuses on examining the structures of the complex macromolecular machinery involved in cellular organization, with particular emphasis on bacterial cytoskeletal systems and organelles. His structural approach centers on cryo-electron microscopy, which he combines with X-ray crystallography. This integrative methodology enables him to generate mechanistic insights across a broad range of size and resolution scales.

Research topics

• Biophysics
• Chemistry
• Biochemistry
• Biology
• Crystallography
• Cell biology
• Nanotechnology
• Materials science

Selected publications

• Nucleation limited assembly and polarized growth of a <i>de novo</i> -designed allosterically modulatable protein filament

  bioRxiv (Cold Spring Harbor Laboratory) · 2024

  • Biophysics
  • Chemistry
  • Cell biology

  The design of inducibly assembling protein nanomaterials is an outstanding challenge. Here, we describe the computational design of a protein filament formed from a monomeric subunit that binds a peptide ligand. The cryoEM structure of the micron-scale fibers is very close to the computational design model. The ligand acts as a tunable allosteric modulator: while not part of the fiber subunit-subunit interfaces, the assembly of the filament is dependent on ligand addition, with longer peptides having more extensive interaction surfaces with the monomer, promoting more rapid growth. Seeded growth and capping experiments reveal that the filaments grow primarily from one end. We show that designed nucleators that present 12 copies of the peptide ligand promote fiber assembly at concentrations where otherwise assembly occurs very slowly, likely by generating critical local concentrations of monomer in the assembly competent conformation. Following filament assembly, the peptide ligand can be exchanged with free peptide in solution fused to any functional protein of interest, opening the door to a wide variety of tunable engineered materials.

  DOI

• De novo design of pH-responsive self-assembling helical protein filaments

  Nature Nanotechnology · 2024 · 60 citations

  • Nanotechnology
  • Biophysics
  • Materials science

  Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures that are environmentally responsive remains a challenge. Here we describe the de novo design of pH-responsive protein filaments built from subunits containing six or nine buried histidine residues that assemble into micrometre-scale, well-ordered fibres at neutral pH. The cryogenic electron microscopy structure of an optimized design is nearly identical to the computational design model for both the subunit internal geometry and the subunit packing into the fibre. Electron, fluorescent and atomic force microscopy characterization reveal a sharp and reversible transition from assembled to disassembled fibres over 0.3 pH units, and rapid fibre disassembly in less than 1 s following a drop in pH. The midpoint of the transition can be tuned by modulating buried histidine-containing hydrogen bond networks. Computational protein design thus provides a route to creating unbound nanomaterials that rapidly respond to small pH changes.

  DOI

• The Giardia ventrolateral flange is a lamellar membrane protrusion that supports attachment

  PLoS Pathogens · 2022 · 13 citations

  • Cell biology
  • Biology
  • Materials science

  Attachment to the intestinal epithelium is critical to the lifestyle of the ubiquitous parasite Giardia lamblia. The ventrolateral flange is a sheet-like membrane protrusion at the interface between parasites and attached surfaces. This structure has been implicated in attachment, but its role has been poorly defined. Here, we identified a novel actin associated protein with putative WH2-like actin binding domains we named Flangin. Flangin complexes with Giardia actin (GlActin) and is enriched in the ventrolateral flange making it a valuable marker for studying the flanges' role in Giardia biology. Live imaging revealed that the flange grows to around 1 μm in width after cytokinesis, then remains uniform in size during interphase, grows in mitosis, and is resorbed during cytokinesis. A flangin truncation mutant stabilizes the flange and blocks cytokinesis, indicating that flange disassembly is necessary for rapid myosin-independent cytokinesis in Giardia. Rho family GTPases are important regulators of membrane protrusions and GlRac, the sole Rho family GTPase in Giardia, was localized to the flange. Knockdown of Flangin, GlActin, and GlRac result in flange formation defects. This indicates a conserved role for GlRac and GlActin in forming membrane protrusions, despite the absence of canonical actin binding proteins that link Rho GTPase signaling to lamellipodia formation. Flangin-depleted parasites had reduced surface contact and when challenged with fluid shear force in flow chambers they had a reduced ability to remain attached, confirming a role for the flange in attachment. This secondary attachment mechanism complements the microtubule based adhesive ventral disc, a feature that may be particularly important during mitosis when the parental ventral disc disassembles in preparation for cytokinesis. This work supports the emerging view that Giardia's unconventional actin cytoskeleton has an important role in supporting parasite attachment.

  PublisherOA PDFDOI

• BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1

  Nature Structural & Molecular Biology · 2021 · 87 citations

  • Cell biology
  • Biology
  • Chemistry
  PublisherOA PDFDOI

• Computational design of transmembrane pores

  Nature · 2020 · 171 citations

  • Biophysics
  • Chemistry
  • Nanotechnology
  DOI

• Lysogenic host–virus interactions in SAR11 marine bacteria

  Nature Microbiology · 2020 · 47 citations

  • Biology
  • Microbiology
  • Ecology
  PublisherOA PDFDOI

Frequent coauthors

• Jason Lee

  3 shared

• Joseph L. Watson

  University of Washington

  2 shared

• Chris Habrian

  Stanford University

  2 shared

• Eric M. Lynch

  2 shared

• William Sheffler

  2 shared

• Brian L Hua

  Centers for Disease Control and Prevention

  2 shared

• Hao Shen

  University of Washington

  2 shared

• Emmanuel Derivery

  MRC Laboratory of Molecular Biology

  2 shared

Similar researchers at University of Washington

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