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Van Horn, Wade D.

Publications and source records attributed to Van Horn, Wade D..

Competition between inside-out unfolding and pathogenic aggregation in an amyloid-forming β-propeller

Studies of folded-to-misfolded transitions using model protein systems reveal a range of unfolding needed for exposure of amyloid-prone regions for subsequent fibrillization. Here, we probe the relationship between unfolding and aggregation for glaucoma-associated myocilin. Mutations within the olfactomedin domain of myocilin (OLF) cause a gain-of-function, namely cytotoxic intracellular aggregation, which hastens disease progression. Aggregation by wild-type OLF (OLF WT ) competes with its chemical unfolding, but only below the threshold where OLF loses tertiary structure. Representative moderate (OLF D380A ) and severe (OLF I499F ) disease variants aggregate differently, with rates comparable to OLF WT in initial stages of unfolding, and variants adopt distinct partially folded structures seen along the OLF WT urea-unfolding pathway. Whether initiated with mutation or chemical perturbation, unfolding propagates outward to the propeller surface. In sum, for this large protein prone to amyloid formation, the requirement for a conformational change to promote amyloid fibrillization leads to direct competition between unfolding and aggregation.

59 BASIC BIOLOGICAL SCIENCES↗

CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Cryoelectron microscopy requires molecular modeling for refinement of structures. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins. Here, we introduce CryoFold, a pipeline of molecular dynamics simulations that determines ensembles of protein structures by integrating density data of varying sparsity at 3–5 Å resolution with sequence information and coarse-grained topological knowledge of the protein folds. We present six examples, folding proteins between 72 and 2,000 residues, including large membrane and multi-domain systems, and results from two Electron Microscopy Data Bank (EMDB) competitions. Driven by data from a single state, CryoFold discovers ensembles of common low-energy models together with rare low-probability structures that capture the equilibrium distribution of proteins constrained by the density maps. Many of these conformations are experimentally validated and functionally relevant. We arrive at a set of best practices for data-guided protein folding that are controlled using a Python graphical user interface (GUI).

59 BASIC BIOLOGICAL SCIENCES↗