Biology subjects

Sutherland, G. A.

Publications and source records attributed to Sutherland, G. A..

2 recordsLinked to original sources

bioRxiv2026

Cryo-EM structures of Cereibacter sphaeroides ferrochelatase reveal an oligomeric state that occludes the substrate-binding site

Protoporphyrin IX (PPIX) is the last shared intermediate of heme and (bacterio)chlorophyll ((B)Chl) biosynthesis. Insertion of iron into PPIX by the PPIX ferrochelatase (FeCh) PpfC produces heme, whereas magnesium insertion by magnesium chelatase (MgCh) initiates (B)Chl synthesis. Chlorophototrophic organisms must regulate this biosynthetic node to ensure the correct flux of PPIX to each of these crucial tetrapyrrole products, presenting a particularly acute problem for the facultative bacterium Cereibacter (previously Rhodobacter) sphaeroides, which can switch between chemotrophic (respiratory) and phototrophic (photosynthetic) growth modes. To elucidate the structural basis for the catalytic and regulatory functions of C. sphaeroides FeCh (PpfCCs), we used cryogenic electron microscopy to determine its structure, to our knowledge the first such information for a Gram-negative or phototrophic organism. We determined the 2.6 [A] structure of an active site mutant of PpfCCs, which forms a dimer with a monomer-to-monomer interface that coordinates two hemes. We also determined a 2.5 [A] structure of the wild-type enzyme, in which two dimers interact in a homotetrameric arrangement that occludes PPIX binding at the active site of each monomer. We propose that the PpfCCs dimer likely docks onto the inner membrane in a manner analogous to the human enzyme, whereas the tetramer represents a transiently inactive state whereby the hydrophobic lips and active site are both occluded. These novel oligomerization states of FeCh may have evolved to influence the flux of tetrapyrroles through the heme/BChl branchpoint in purple bacteria.

biochemistry↗

bioRxiv2023

Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom

Although AlphaFold2 (AF2) and RoseTTAFold (RF) have transformed structural biology by enabling high-accuracy protein structure modeling, they are unable to model covalent modifications or interactions with small molecules and other non-protein molecules that can play key roles in biological function. Here, we describe RoseTTAFold All-Atom (RFAA), a deep network capable of modeling full biological assemblies containing proteins, nucleic acids, small molecules, metals, and covalent modifications given the sequences of the polymers and the atomic bonded geometry of the small molecules and covalent modifications. Following training on structures of full biological assemblies in the Protein Data Bank (PDB), RFAA has comparable protein structure prediction accuracy to AF2, excellent performance in CAMEO for flexible backbone small molecule docking, and reasonable prediction accuracy for protein covalent modifications and assemblies of proteins with multiple nucleic acid chains and small molecules which, to our knowledge, no existing method can model simultaneously. By fine-tuning on diffusive denoising tasks, we develop RFdiffusion All-Atom (RFdiffusionAA), which generates binding pockets by directly building protein structures around small molecules and other non-protein molecules. Starting from random distributions of amino acid residues surrounding target small molecules, we design and experimentally validate proteins that bind the cardiac disease therapeutic digoxigenin, the enzymatic cofactor heme, and optically active bilin molecules with potential for expanding the range of wavelengths captured by photosynthesis. We anticipate that RFAA and RFdiffusionAA will be widely useful for modeling and designing complex biomolecular systems.

biochemistry↗