Biomolecular Assemblies: Moving from Observation to Predictive Design.

Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.

Understanding the Coacervate-to-Vesicle Transition of Globular Fusion Proteins to Engineer Protein Vesicle Size and Membrane Heterogeneity.

Protein-rich coacervates are liquid phases separate from the aqueous bulk phase that are used by nature for compartmentalization and more recently have been exploited by engineers for delivery and formulation applications. They also serve as an intermediate phase in an assembly path to more complex structures, such as vesicles. Recombinant fusion protein complexes made from a globular protein fused with a glutamic acid-rich leucine zipper (globule-ZE) and an arginine-rich leucine zipper fused with an elastin-like polypeptide (ZR-ELP) show different phases from soluble, through an intermediate coacervate phase, and finally to vesicles with increasing temperature of the aqueous solution. We investigated the phase transition kinetics of the fusion protein complexes at different temperatures using dynamic light scattering and microscopy, along with mathematical modeling. We controlled coacervate growth by aging the solution at an intermediate temperature that supports coacervation and confirmed that the size of the coacervate droplets dictates the size of vesicles formed upon further heating. With this understanding of the phase transition, we developed strategies to induce heterogeneity in the organization of globular proteins in the vesicle membrane through simple mixing of coacervates containing two different globular fusion proteins prior to the vesicle transition. This study gives fundamental insights and practical strategies for development of globular protein-rich coacervates and vesicles for drug delivery, microreactors, and protocell applications.

Multistep Conformation Selection in Amyloid Assembly.

Defining pathways for amyloid assembly could impact therapeutic strategies for as many as 50 disease states. Here we show that amyloid assembly is subject to different forces regulating nucleation and propagation steps and provide evidence that the more global ß-sheet/ß-sheet facial complementarity is a critical determinant for amyloid nucleation and structural selection.

Expanding the informational chemistries of life: peptide/RNA networks.

The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA. Peptide conformational networks are known to be capable of evolution in disease states and of co-opting metal ions, aromatic heterocycles and lipids to extend their emergent behaviours. The coexistence and association of dynamic peptide and RNA networks appear to have driven the emergence of higher-order informational systems in biology that are not available to either scaffold independently, and such mutualistic interdependence poses critical questions regarding the search for life across our Solar System and beyond.This article is part of the themed issue 'Reconceptualizing the origins of life'.

Stent grafts improved patency of ruptured hemodialysis vascular accesses.

This study aimed to compare stent graft with balloon tamponade for ruptured dialysis access during percutaneous transluminal angioplasty. Patients over an 8-year period (2010-2018) were identified from a database of 11,609 procedures. The primary endpoint was target lesion primary patency at 12 months. A total of 143 patients who had rupture dialysis access were enrolled, of whom 52 were salvaged by stent grafts and 91 were salvaged by balloon tamponade. The 6-month target lesion primary patency was greater in the stent graft group than in the balloon tamponade group (66.7% vs. 29.5%, P < 0.001). The benefit of stent grafts was sustained for 12 months (52.5% vs. 9.0%, P < 0.001). The stent grafts increased the median time from the index procedure to the next intervention in the ruptured area by 171 days (260 vs. 89 days) at 12 months. There was no significant difference in the access circuit patency rates at 6 months (25.5% vs. 19.8%, P = 0.203) and 12 months (12.0% vs. 5.8%, P = 0.052). The patency results of the stent grafts remained after the multivariable adjustment analysis. Compared to balloon tamponade alone, stent grafts provided superior target lesion primary patency at 6 and 12 months. The access circuit patency rates were similar.

Chemical control of peptide material phase transitions.

Progressive solute-rich polymer phase transitions provide pathways for achieving ordered supramolecular assemblies. Intrinsically disordered protein domains specifically regulate information in biological networks via conformational ordering. Here we consider a molecular tagging strategy to control ordering transitions in polymeric materials and provide a proof-of-principle minimal peptide phase network captured with a dynamic chemical network.

Use of the Viabahn covered stent for the treatment of venous rupture during interventions of dysfunctional or thrombosed hemodialysis vascular access.

BACKGROUND: Angioplasty-related vessel rupture is a common complication of interventions. The effect of covered stents to treat venous rupture has been evaluated in smaller series, but should be further evaluated. OBJECTIVE: To report the immediate outcomes and patency rates of a covered stent to rescue angioplasty-related venous rupture of hemodialysis vascular access. METHODS: From January 2013 to December 2018, 113 procedures complicated with vessel ruptures were retrospectively analyzed from a prospectively collected database of 8146 hemodialysis access interventions. The strategies to salvage vessel ruptures were based on the discretion of the treating physicians. Follow-up outcomes were obtained via review of the angiographic images, procedural notes, and medical and dialysis records within 12 months after the index procedures. RESULTS: A total of 52 vessel ruptures (21 fistulas, 31 grafts) salvaged by using Viabahn covered stents were enrolled. Vessel ruptures developed in 28 (53.8%) thrombectomy procedures. Device success was achieved in all procedures (100%) and clinical success was achieved in 50 (96.2%). The primary patency of the stent area was 66.0% at 6 months and 50.0% at 12 months. The primary patency of the entire access circuit was 27.4% at 6 months and 16.0% at 12 months. The most common cause of access circuit primary patency loss was thrombotic occlusion for graft accesses and restenosis at stent area for native accesses. Eleven vascular accesses were abandoned within 12 months after vessel ruptures, and the secondary patency rate of the entire access circuit was 78.0% at 12 months. CONCLUSIONS: Treatment of angioplasty-induced vessel rupture of hemodialysis vascular accesses by using Viabahn covered stents has good immediate outcomes and patency results at the stent area. Nonetheless, the patency rate of entire access circuit was still below the threshold recommended by guidelines.

Systems Analysis for Peptide Systems Chemistry.

Living systems employ both covalent chemistry and physical assembly to achieve complex behaviors. The emerging field of systems chemistry, inspired by these biological systems, attempts to construct and analyze systems that are simpler than biology, while still embodying biological design principles. Due to the multiple phenomena at play, it can be difficult to predict which phenomena will dominate and when. Conversely, there may be no single rate-limiting step, but rather a reaction network that is difficult to intuit from a purely experimental approach. Mathematical modeling can help to sort out these issues, although it can be challenging to build such models, especially for assembly kinetics. Numerical and statistical methods can play an important role to facilitate the synergistic and iterative use of modeling and experiment, and should be part of a systems chemistry curriculum. Three case studies are presented here, from our work in peptide-based systems, to illustrate some of the tools available for model construction, model simulation, and experimental design. Examples are provided in which these tools help to evaluate hypotheses, uncover design principles, and design new experiments.

Conformational evolution of polymorphic amyloid assemblies.

The morphological diversity of amyloid assemblies has complicated the development of disease therapies and the design of novel biomaterials for decades. Here we review the conformational evolution of amyloids from the initial liquid-liquid phase separation into the oligomeric particle phase to the nucleation of the more ordered assembly phases. With mounting evidence that the assemblies emerging from the oligomeric phases may not be stable in solution and undergo further structural transitions, we propose the concept of conformational evolution, where mutations may occur at the ends or on the surface of the pre-existing fibers and different morphologies are under selection throughout the assembly process.

Kinetic Model for Two-Step Nucleation of Peptide Assembly.

Intermediate dynamic assemblies are increasingly seen as necessary for the initial desolvation and organization of biomaterials to achieve their final crystalline order. Here we present a general peptide assembly model for two-step nucleation. The model predicts the phase transitions and equilibria between different phases by employing a combination of the Flory-Huggins parameter, the particle growth constant, and the binding energy to assemblies. Monte Carlo simulations are used to demonstrate how the system evolves from pure solution phases to the final thermodynamic assembly phase via an intermediate metastable particle phase. The final state of the system is determined by the solubility of the particle and assembly phases, where the phase with the lower solubility accumulates. A rare three-phase equilibrium exists when the solubilities of the particles and assemblies are similar. Experimental support for this model is achieved with assembly of the amyloid peptide Ac-KLVFFAE-NH2 (Aß(16-22)) in mixed acetonitrile/water systems. Increasing the acetonitrile concentration decreases the number of particles, increases the particle size, and accelerates the assembly rate, all consistent with acetonitrile increasing the Aß(16-22) peptide's solubility of particles but with little influence on the stability of the assemblies. Taken together, our model captures the transition from the metastable particle phase to the higher order peptide assembly through two-step nucleation.

Catalytic diversity in self-propagating peptide assemblies.

The protein-only infectious agents known as prions exist within cellular matrices as populations of assembled polypeptide phases ranging from particles to amyloid fibres. These phases appear to undergo Darwinian-like selection and propagation, yet remarkably little is known about their accessible chemical and biological functions. Here we construct simple peptides that assemble into well-defined amyloid phases and define paracrystalline surfaces able to catalyse specific enantioselective chemical reactions. Structural adjustments of individual amino acid residues predictably control both the assembled crystalline order and their accessible catalytic repertoire. Notably, the density and proximity of the extended arrays of enantioselective catalytic sites achieve template-directed polymerization of new polymers. These diverse amyloid templates can now be extended as dynamic self-propagating templates for the construction of even more complex functional materials.

Design of multi-phase dynamic chemical networks.

Template-directed polymerization reactions enable the accurate storage and processing of nature's biopolymer information. This mutualistic relationship of nucleic acids and proteins, a network known as life's central dogma, is now marvellously complex, and the progressive steps necessary for creating the initial sequence and chain-length-specific polymer templates are lost to time. Here we design and construct dynamic polymerization networks that exploit metastable prion cross-ß phases. Mixed-phase environments have been used for constructing synthetic polymers, but these dynamic phases emerge naturally from the growing peptide oligomers and create environments suitable both to nucleate assembly and select for ordered templates. The resulting templates direct the amplification of a phase containing only chain-length-specific peptide-like oligomers. Such multi-phase biopolymer dynamics reveal pathways for the emergence, self-selection and amplification of chain-length- and possibly sequence-specific biopolymers.