James Fraser

@fraserlab.com

3652 Followers 509 Following

Professor and Chair @UCSF/@UCSF_BTS - dynamic structural biology and open science - (he/him) - fraserlab.com

Proposed model of the Orf9b-Tom70 equilibrium Orf9b transcripts are translated to produce monomeric Orf9b proteins that can bind to Tom70 leading to a suppression of IFN. Monomeric Orf9b can also undergo a conformational change and bind to a second copy of Orf9b to form the homodimer. The Orf9b homodimer is in equilibrium between free Orf9b monomers and Orf9b monomers bound to Tom70. Upon lipid binding, the homodimer is tightly stabilized and slowly releases monomeric Orf9b.
A. I. Mathematical model overlay to FP competition kinetic assay using the lipid-bound Orf9b homodimer as the competitor. II. Mathematical model overlay to FP competition kinetic assay using the apo-Orf9b homodimer as the competitor.
ODE for Tom70/Orf9b interactions: 1. d[Orf9b-FITC]/dt = -k1[Orf9b-FITC][Tom70]+k2[Orf9b-FITC:Tom70] 2. d[Orf9b β-monomer]/dt = 2(-k3[Orf9b β-monomer]^2+k4[Orf9b dimer])-kα[Orf9b β- monomer]^2+kβ[Orf9b α-monomer] 3. d[Orf9b dimer]/dt = k3[Orf9b β-monomer]^2-k4[Orf9b dimer] 4. d[Tom70]/dt = -k1[Orf9b-FITC][Tom70]-k5[Orf9b α-monomer][T]+k6[Orf9b α- monomer:Tom70]+k2[PT] 5. d[Orf9b α-monomer:Tom70]/dt = k5[Orf9b α-monomer][Tom70]-k6[Orf9b α- monomer:Tom70] 6. d[Orf9b α-monomer]/dt = -k5[Orf9b α monomer][Tom70]-kβ[Orf9b α-monomer]+k6[Orf9b α-monomer:Tom70]+kα[Orf9b β-monomer]^2
From left to right: A large protein complex with several helices (colored in blue and purple) representing Orf9b bound to Tom70. Orf9b detaching from Tom70 and undergoing a β-sheet to α-helix transition, shown in purple. The α-helical form of Orf9b transitioning to a β-sheet-rich homodimer. The final step showing the dissociation of the homodimer into individual monomers. Arrows indicate equilibrium transitions between states, with labels highlighting key conformational changes: "β-sheet to α-helix" and "Dissociation".
The image contains a message from "Exeter Pre-editing" regarding an update about the indexing of the Version of Record for eLife content. The main points are: eLife content will be widely indexed, including by PubMed and OpenAlex. However, starting June 2025, eLife content will not receive an impact factor. A link is provided for more details: https://elifesciences.org/inside-elife/ae620829. The recipient is asked to confirm awareness of the change and whether they are happy to continue. The response box shows "Yes! Death to Impact Factor!" with the "Mark as resolved" checkbox selected.
A cookie to preprint pipeline V2
A structural illustration of the VatD trimer (left) showing its ribbon model with chains in gray, pink, and cyan. Acetyl-CoA (orange sticks) is bound in its pocket. Zoomed-in views (right) depict molecular interactions: the central panel shows Acetyl-CoA interacting with catalytic residues H82 and T88, while the rightmost panel highlights the binding of the antibiotic VM1 in the peptidyl transferase center (PTC) and nascent peptide exit tunnel (NPET), with key contacts involving Guanosine 2505 and a critical hydroxyl group (OH).
An annotated molecular surface representation of the VatD trimer highlighting three fragment binding sites: the Active site (pink), the Acetyl-CoA (Ac-CoA) site (blue), and Accessory sites (yellow). Fragment-bound molecules are visualized as stick models at their respective binding locations, showing the spatial arrangement of the trimer interface.
A sign saying that if you want a cookie you have to leave a preprint print out.
A diagram comparing the crystal structures of ABLE-fragment complexes to the design structure of the KABLE1-6NBT complex. Left panel: The carboxylate-imidazole interaction in the crystal structures of ABLE bound to fragments is depicted. His49 is highlighted as a key residue, interacting with carboxylate-containing fragments. Right panel: The design structure of KABLE1-6NBT is shown, where His49 is replaced with Asp49 to facilitate a strong 6NBT-carboxylate interaction. Additional key residues, Gln75 and Tyr75, are labeled and illustrated forming a hydrogen-bond network with 6NBT. The transition highlights the rational design process of converting ABLE's binding site into a functional active site for catalyzing the Kemp elimination reaction.
A stepwise illustration of the transformation of the protein ABLE into FABLE through fragment screening and sequence design. Left (ABLE-Apixaban): The initial protein, ABLE, is shown bound to the drug apixaban, with the binding pocket highlighted and apixaban's structure displayed. Second (ABLE-7-hydroxycoumarin): After fragment screening, ABLE binds the fragment 7-hydroxycoumarin, with its chemical structure shown above the pocket, demonstrating the potential to adapt to new ligands. Third (ABLE-Cou485): Sequence design modifies the binding pocket to accommodate Cou485, a larger fluorophore. The structure of Cou485 is shown above the panel. Right (FABLE-Cou485): The final designed protein, FABLE, specifically binds Cou485. The optimized binding pocket is highlighted, showing a tight fit for the fluorophore. This progression illustrates the use of fragment screening and rational design to transform a generalist binder into a specialist for a turn-on fluorophore.
A diagram showcasing fragment screening and binding site characterization in a helical protein scaffold. Left panel: A single fragment bound in the B site of the protein is displayed, emphasizing the structural arrangement of the binding pocket. Center: A funnel graphic depicts the fragment screening workflow: 320 fragments screened, 242 processed (high-quality diffraction datasets collected), 43 hits identified, resulting in a hit rate of 18%. Right panel: A superimposed visualization of multiple fragments binding within the protein's B site, demonstrating the diversity of fragment binding poses. The fragments are color-coded, with the binding pocket highlighted.
A diagram illustrating the evolution of protein functionality through sequence and chemical space. ABLE (bottom left): Depicted as a helical bundle binding the drug apixaban, labeled as a "specialist" in binding apixaban. Its binding site is shown as a filled cavity with the drug's structure. ABLE as a generalist (center): After fragment screening, ABLE evolves to weakly bind various small molecule fragments, shown in a diverse array within the cavity. This transition highlights the exploration of chemical space. FABLE (top right): Derived from fragment-inspired design, FABLE binds turn-on fluorophores. The binding site is reconfigured to fit fluorophores like Cou485, with their chemical structures displayed. KABLE (bottom right): Another fragment-inspired evolution turns ABLE into KABLE, a Kemp eliminase. The structure of the substrate (5-nitrobenzisoxazole) is shown, with the binding site adapted for catalysis. The axes represent "Sequence Space" (vertical) and "Chemical Space" (horizontal), emphasizing how the protein evolves through these dimensions to achieve specialized functions. This schematic encapsulates the journey of ABLE from a specific binder to a generalist and then into two specialized proteins with distinct functionalities.
Picture of James Fraser and Dan Tawfik
Selfie at the beam line
figure from science
image from biorxiv covered by figure legend!
A screenshot of the fraserlab website