Design of Coiled-Coil Protein Nanostructures for Therapeutics and Drug Delivery

Annual Review of Chemical and Biomolecular Engineering, Journal Year: 2024, Volume and Issue: 15(1), P. 25 - 50

Published: April 10, 2024

Coiled-coil protein motifs have become widely employed in the design of biomaterials. Some these designs been studied for use drug delivery due to unique ability coiled-coils impart stability, oligomerization, and supramolecular assembly. To leverage properties improve delivery, release, targeting, a variety nano- mesoscale architectures adopted. therapeutics developed by using coiled-coil alone, designing higher-order assemblies such as fibers hydrogels, combining proteins with other biocompatible structures lipids polymers. We review recent development criteria used generate functional varying sizes morphologies.

Language: Английский

---

Crystal Structure of de Novo Designed Coiled-Coil Protein Origami Triangle

Journal of the American Chemical Society, Journal Year: 2023, Volume and Issue: 145(31), P. 16995 - 17000

Published: July 24, 2023

Coiled-coil protein origami (CCPO) uses modular coiled-coil building blocks and topological principles to design polyhedral structures distinct from those of natural globular proteins. While the CCPO strategy has proven successful in designing diverse topologies, no high-resolution structural information been available about these novel folds. Here we report crystal structure a single-chain shape triangle. neither cyclization nor addition nanobodies enabled crystallization, it was ultimately facilitated by inclusion GCN2 homodimer. Triangle edges are formed orthogonal parallel dimers P1:P2, P3:P4, connected short linkers. A triangle large central cavity is additionally stabilized side-chain interactions between neighboring segments at each vertex. The lattice densely packed number contacts triangles. Interestingly, polypeptide chain folds into trefoil-type knot topology, AlphaFold2 fails predict correct fold. validates CC-based strategy, providing molecular insight underlying stabilization new opportunities for design.

Language: Английский

---

Applicability of AlphaFold2 in the modelling of coiled-coil domains

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 10, 2024

Abstract Coiled coils are a common protein structural motif involved in cellular functions ranging from mediating protein-protein interactions to facilitating processes such as signal transduction or regulation of gene expression. They formed by two more alpha helices that wind around central axis form buried hydrophobic core. Various forms coiled-coil bundles have been reported, each characterized the number, orientation, and degree winding constituent helices. This variability is underpinned short sequence repeats coiled whose properties determine both their overall topology local geometry The strikingly repetitive has enabled development accurate sequence-based prediction methods; however, modeling domains remains challenging task. In this work, we evaluated accuracy AlphaFold2 domains, predicting global topological properties. Furthermore, show oligomeric state can be achieved using internal representations AlphaFold2, with performance better than any previous state-of-the-art method (code available at https://github.com/labstructbioinf/dc2_oligo ).

Language: Английский

---

Computational Prediction of Coiled–Coil Protein Gelation Dynamics and Structure

Biomacromolecules, Journal Year: 2023, Volume and Issue: 25(1), P. 258 - 271

Published: Dec. 18, 2023

Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics drug delivery. We have previously explored the ability to engineer thermoresponsive supramolecular assembly coiled–coil proteins into with varying gelation properties, where we defined parameters in hydrogel design. Using Rosetta energy scores Poisson–Boltzmann electrostatic energies, iterate computational design strategy predict while simultaneously exploring five new protein sequences. Provided this library, explore impact silico energies on structure kinetics, also reveal range blue autofluorescence that enables disassembly recovery. As result identify sequence, Q5, capable within 24 h at 4 °C, more than 2-fold increase over our previous iteration Q2. The fast time Q5 assessment structural transition real using small-angle X-ray scattering (SAXS) is correlated coarse-grained atomistic molecular dynamics simulations revealing assembling behavior coiled–coils toward nanofiber gelation. This work represents first system predictable self-assembly, autofluorescent capability, model fiber formation.

Language: Английский

---

Computational protein design

Nature Reviews Methods Primers, Journal Year: 2025, Volume and Issue: 5(1)

Published: Feb. 27, 2025

---

Parallel Temperature Replica-Exchange Molecular Dynamics Simulations Capture the Observed Impact of Stapling on Coiled-Coil Conformational Stability

The Journal of Physical Chemistry B, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 9, 2025

Macrocyclization or stapling is an important strategy for increasing the conformational stability and target-binding affinity of peptides proteins, especially in therapeutic contexts. Atomistic simulations such stapled proteins could help rationalize existing experimental data provide predictive tools design new proteins. Standard approaches exist incorporating nonstandard amino acids functional groups into force fields required MD have been used context more than a decade. However, enthusiasm their use has limited by time-intensive nature concerns about whether resulting would be physically realistic. Here, we report development field parameters two unnatural triazole staples, which incorporated implicit-solvent parallel temperature replica-exchange molecular dynamics several coiled-coil variants nonstapled counterparts. We these to calculate melting temperatures (Tm) each variant along with impact on relative its counterpart (ΔΔG). Trends among simulated Tm ΔΔG values closely match those observed previous experiments, suggesting that developed staples are sufficiently realistic useful predicting protein/peptide other

Language: Английский

---

High‐Throughput Evaluation of Natural Diversity of F‐Type ATP Synthase Rotor Ring Stoichiometries

Proteins Structure Function and Bioinformatics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 15, 2025

Adenosine triphosphate (ATP) synthases are large enzymes present in every living cell. They consist of a transmembrane and soluble domain, each comprising multiple subunits. The part contains an oligomeric rotor ring (c-ring), whose stoichiometry defines the ratio between number synthesized ATP molecules ions transported through membrane. Currently, c-rings F-Type consisting 8-17 (except 16) subunits have been experimentally demonstrated, but it is not known whether other stoichiometries natural organisms. Here, we easy-to-use high-throughput computational approach based on AlphaFold that allows us to estimate all homo-oligomeric c-rings, sequences genomic databases. We validate available experimental data, obtaining correlation as high 0.94 for reference dataset use predict existence with varying at least from 8 27. then conduct molecular dynamics simulations two above 17 corroborate machine learning-based predictions. Our work strongly suggests rings previously undescribed organisms highlights utility AlphaFold-based approaches studying proteins.

Language: Английский

---

Emergence of binding and catalysis from a designed generalist binding protein

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

Abstract The evolution of proteins that bind to small molecules and catalyze chemical transformations played a central role in the emergence life. While natural have finely tuned affinity for their primary ligands, they also often weak affinities other molecules. These interactions serve as starting points new specificities functions. Inspired by this concept, we determined ability simple de novo protein set diverse (< 300 Da) crystallographic fragment screening. We then used information design one variant binds fluorogenic molecule another acts highly efficient Kemp eliminase enzyme. Collectively, our work illuminates how novel functions can emerge from existing proteins.

Language: Английский

---

Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: March 5, 2025

Coiled-coil proteins provide an excellent scaffold for multistate de novo protein design due to their established sequence-to-structure relationships and ability switch conformations in response external stimuli, such as changes pH or temperature. However, the computational of coiled-coil assemblies is challenging, it requires accurate estimates free energy differences between multiple alternative conformations. Here, we demonstrate how this challenge can be tackled using metadynamics simulations with orientational, positional conformational restraints. We show that, even subtle sequence variations, our protocol predict preferred topology dimers trimers, oligomerization states dimers, tetramers, well switching behavior a pH-dependent system. Our approach provides method predicting stability designs offers new framework computing binding energies protein-protein multiprotein complexes.

Language: Английский

---

Hierarchical Assembly of Conductive Fibers from Coiled-Coil Peptide Building Blocks

ACS Nano, Journal Year: 2025, Volume and Issue: unknown

Published: March 7, 2025

Biology provides many sources of inspiration for synthetic and multifunctional nanomaterials. Naturally evolved proteins exhibit specialized, sequence-defined functions self-assembly behavior. Recapitulating their molecularly defined behavior, however, is challenging in de novo proteins. Peptides, on the other hand, represent a more well-defined rationally designable space with potential sequence-programmable, stimuli-responsive design structure function, making them ideal building blocks bioelectronic interfaces. In this work, we peptides that capacity to transport electrical current over micrometer-long distances. A lysine-lysine (KK) motif inserted at solvent-exposed positions coiled-coil-forming peptide sequence introduces pH-dependent control transition from unordered α-helical structure. The ordered state serves as block assembly coiled coils higher-order assemblies. Cryo-EM structures these reveal hierarchical organization cross coil (CCC) arrangement. Structural analysis also reveals β-sheet fiber phase under certain conditions placements KK motif, revealing complex sensitive pathway. Both solid-state solution-based electrochemical characterizations show CCC fibers are electronically conductive. Single-fiber conductive AFM measurement indicates conductivity comparable bacterial cytochrome filaments. Solution-deposited films approximately doubled electroactive surface area electrode, confirming aqueous environments. This work establishes element balancing order-disorder transitions into highly organized nanofibers.

Language: Английский

---