De Novo-Designed α-Helical Barrels as Receptors for Small Molecules

Abstract

We describe de novo-designed α-helical barrels (αHBs) that bind and discriminate between lipophilic biologically active molecules. αHBs have five or more α-helices arranged around central hydrophobic channels the diameters of which scale with oligomer state. We show that pentameric, hexameric, and heptameric αHBs bind the environmentally sensitive dye 1,6-diphenylhexatriene (DPH) in the micromolar range and fluoresce. Displacement of the dye is used to report the binding of nonfluorescent molecules: palmitic acid and retinol bind to all three αHBs with submicromolar inhibitor constants; farnesol binds the hexamer and heptamer; but β-carotene binds only the heptamer. A co-crystal structure of the hexamer with farnesol reveals oriented binding in the center of the hydrophobic channel. Charged side chains engineered into the lumen of the heptamer facilitate binding of polar ligands: a glutamate variant binds a cationic variant of DPH, and introducing lysine allows binding of the biosynthetically important farnesol diphosphate.

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

“…These same principles are also true within synthetic biology, 126 where researchers seek to use molecular design in order to develop targeted drug therapies, augment photosynthesis, 127 construct protein architectures which can operate as purpose-built catalysts, 128,129 or develop new supramolecular structures which can bind small molecules. 130 For this reason, we are looking to extend Narupa's flexible API beyond atomistic modelling to also communicate with coarse-grained modelling engines.…”

Navigating the structural landscape ofde novoα–helical bundles

“…60 These barrels are a growing class of both natural and designed proteins that are robust and have potential in protein engineering and synthetic biology. 55,[62][63][64]76,77 Nonetheless, CC-Hex was discovered serendipitously: it was a variant of a de novo designed parallel coiled-coil tetramer, CC-Tet. 59 Herein, we have described a series of point and en bloc changes to the CC-Hex sequence.…”

“…62 These a-helical barrels are more-robust to mutation and serve as platforms for rational design to introduce new functions. 63, 64 Herein, we return to the mutants of CC-Hex and explore structural plasticity in the coiled-coil structural landscape. This must be navigated to deliver robust de novo designs.…”

Towards functional de novo designed proteins

“…( Figure 1 Legend Continued) heptameric coiled coil, CC-Hept (PDB: 4PNA). Functions have then been incorporated into these scaffolds; for example, a model of farnesyl diphosphate (green) bound in a heptameric coiled coil [31 ]. Computational design often uses databases of protein fragments to assign thousands of potential amino-acid sequences to the design target.…”