Browsing by Author "Saven, Jeffery G."
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Item Computational Design of Single-Peptide Nanocages with Nanoparticle Templating(Molecules, 2022-02-12) Villegas, José A.; Sinha, Nairiti J.; Teramoto, Naozumi; Von Bargen, Christopher D.; Pochan, Darrin J.; Saven, Jeffery G.Protein complexes perform a diversity of functions in natural biological systems. While computational protein design has enabled the development of symmetric protein complexes with spherical shapes and hollow interiors, the individual subunits often comprise large proteins. Peptides have also been applied to self-assembly, and it is of interest to explore such short sequences as building blocks of large, designed complexes. Coiled-coil peptides are promising subunits as they have a symmetric structure that can undergo further assembly. Here, an α-helical 29-residue peptide that forms a tetrameric coiled coil was computationally designed to assemble into a spherical cage that is approximately 9 nm in diameter and presents an interior cavity. The assembly comprises 48 copies of the designed peptide sequence. The design strategy allowed breaking the side chain conformational symmetry within the peptide dimer that formed the building block (asymmetric unit) of the cage. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) techniques showed that one of the seven designed peptide candidates assembled into individual nanocages of the size and shape. The stability of assembled nanocages was found to be sensitive to the assembly pathway and final solution conditions (pH and ionic strength). The nanocages templated the growth of size-specific Au nanoparticles. The computational design serves to illustrate the possibility of designing target assemblies with pre-determined specific dimensions using short, modular coiled-coil forming peptide sequences.Item Genetic Fusion of Thermoresponsive Polypeptides with UCST-type Behavior Mediates 1D Assembly of Coiled-Coil Bundlemers(Angewandte Chemie International Edition, 2023-05-09) Patkar, Sai S.; Tang, Yao; Bisram, Arriana M.; Zhang, Tianren; Saven, Jeffery G.; Pochan, Darrin J.; Kiick, Kristi L.Graphical Abstract: Available at: https://doi.org/10.1002/anie.202301331 Computationally designed coiled coil-forming peptides were functionalized with thermoresponsive resilin-like polypeptides (RLPs) of various lengths and produced via biosynthetic methods in bacterial expression hosts. Interactions between RLPs upon cooling below their upper critical solution temperature (UCST) resulted in nanofibrillar assembly. Abstract Thermoresponsive resilin-like polypeptides (RLPs) of various lengths were genetically fused to two different computationally designed coiled coil-forming peptides with distinct thermal stability, to develop new strategies to assemble coiled coil peptides via temperature-triggered phase separation of the RLP units. Their successful production in bacterial expression hosts was verified via gel electrophoresis, mass spectrometry, and amino acid analysis. Circular dichroism (CD) spectroscopy, ultraviolet-visible (UV/Vis) turbidimetry, and dynamic light scattering (DLS) measurements confirmed the stability of the coiled coils and showed that the thermosensitive phase behavior of the RLPs was preserved in the genetically fused hybrid polypeptides. Cryogenic-transmission electron microscopy and coarse-grained modeling revealed that functionalizing the coiled coils with thermoresponsive RLPs leads to their thermally triggered noncovalent assembly into nanofibrillar assemblies.Item Intramolecular structure and dynamics in computationally designed peptide-based polymers displaying tunable chain stiffness(Physical Review Materials, 2021-09-07) Sinha, Nairiti J.; Shi, Yi; Kloxin, Christopher J.; Saven, Jeffery G.; Faraone, Antonio; Jensen, Grethe V.; Pochan, Darrin JPolymers assembled using computationally designed coiled coil bundlemers display tunable stiffness via control of interbundlemer covalent connectivity as confirmed using small-angle neutron scattering. Neutron spin echo spectroscopy reveals that rigid rod polymers show a decay rate Γ∼Q2 (Q is the scattering vector) expected of straight cylinders. Semirigid polymers assembled using bundlemers linked via 4-armed organic linker show flexible segmental dynamics at mid-Q and Γ∼Q2 behavior at high Q. The results give insight into linker flexibility-dependent interbundlemer dynamics in the hybrid polymers.