A highly controllable protein self-assembly system with morphological versatility induced by reengineered host-guest interactions

Peptide recognition by a synthetic receptor at subnanomolar concentrations

This paper describes the discovery and characterization of a dipeptide sequence, Lys-Phe, that binds to the synthetic receptor cucurbit[8]uril (Q8) in neutral aqueous solution with subnanomolar affinity when located at the N-terminus. The thermodynamic and structural basis for the binding of Q8 to a series of four pentapeptides was characterized by isothermal titration calorimetry, NMR spectroscopy, and X-ray crystallography. Submicromolar binding affinity was observed for the peptides Phe-Lys-Gly-Gly-Tyr (FKGGY, 0.3 μM) and Tyr-Leu-Gly-Gly-Gly (YLGGG, 0.2 μM), whereas the corresponding sequence isomers Lys-Phe-Gly-Gly-Tyr (KFGGY, 0.3 nM) and Leu-Tyr-Gly-Gly-Gly (LYGGG, 1.2 nM) bound to Q8 with 1000-fold and 170-fold increases in affinity, respectively. To our knowledge, these are the highest affinities reported between a synthetic receptor and an unmodified peptide. The high-resolution crystal structures of the Q8·Tyr-Leu-Gly-Gly-Gly and Q8·Leu-Tyr-Gly-Gly-Gly complexes have enabled a detailed analysis of the structural determinants for molecular recognition. The high affinity, sequence-selectivity, minimal size of the target binding site, reversibility in the presence of a competitive guest, compatibility with aqueous media, and low toxicity of Q8 should aid in the development of applications involving low concentrations of target polypeptides.

Cucurbit[8]uril Binds Nonterminal Dipeptide Sites with High Affinity and Induces a Type II β-Turn

In an effort to target polypeptides at nonterminal sites, we screened the binding of the synthetic receptor cucurbit[8]uril (Q8) to a small library of tetrapeptides, each containing a nonterminal dipeptide binding site. The resulting leads were characterized in detail using a combination of isothermal titration calorimetry, 1H NMR spectroscopy, electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS), and X-ray crystallography. The equilibrium dissociation constant values determined for the binding of Q8 to nonterminal dipeptide sites Lys-Phe (KF) and Phe-Lys (FK) were 60 and 86 nm, respectively. These are to the best of our knowledge the highest affinities reported to date for any synthetic receptor targeting a nonterminal site on an unmodified peptide. A 0.79 Å resolution crystal structure was obtained for the complex of Q8 with the peptide Gly-Gly-Leu-Tyr-Gly-Gly-Gly (GGLYGGG) and reveals structural details of the pair-inclusion motif. The molecular basis for recognition is established to be the inclusion of the side chains of Leu and Tyr residues, as well as an extensive network of hydrogen bonds between the peptide backbone, the carbonyl oxygens of Q8, and proximal water molecules. In addition, the crystal structure reveals that Q8 induces a type II β-turn. The sequence-selectivity, high affinity, reversibility, and detailed structural characterization of this system should facilitate the development of applications involving ligand-induced polypeptide folding.

Semisynthesis of Aminomethyl-Insulin: An Atom-Economic Strategy to Increase the Affinity and Selectivity of a Protein for Recognition by a Synthetic Receptor

Advancements in the molecular recognition of insulin by nonantibody-based means would facilitate the development of methodology for the continuous detection of insulin for the management of diabetes mellitus. Herein, we report a novel insulin derivative that binds to the synthetic receptor cucurbit[7]uril (Q7) at a single site and with high nanomolar affinity. The insulin derivative was prepared by a four-step protein semisynthetic method to present a 4-aminomethyl group on the side chain of the Phe^B1 position. The resulting aminomethyl insulin binds to Q7 with an equilibrium dissociation constant value of 99 nM in neutral phosphate buffer, as determined by isothermal titration calorimetry. This 6.8-fold enhancement in affinity versus native insulin was gained by an atom-economical modification (-CH₂NH₂). To the best of our knowledge, this is the highest reported binding affinity for an insulin derivative by a synthetic receptor. This strategy for engineering protein affinity tags induces minimal change to the protein structure while increasing affinity and selectivity for a synthetic receptor.

"On/Off" Switchable Sequential Light-Harvesting Systems Based on Controllable Protein Nanosheets for Regulation of Photocatalysis

A controllable protein nanostructures-based "On/Off" switchable artificial light-harvesting system (LHS) with sequential multistep energy transfer and photocatalysis was reported herein for mimicking the natural LHS in both structure and function. Single-layered protein nanosheets were first constructed via a reversible covalent self-assembly strategy using cricoid stable protein one (SP1) as building blocks to realize an ordered arrangement of pigments. Fluorescent chromophores like carbon dots (CDs) can be precisely distributed on the protein nanosheets superficially via electrostatic interactions and make the ratio between donors and acceptors adjustable. After being anchored with a photocatalysis center (eosin-5-isothiocyanate, EY), the constructed LHS could sequentially transfer energy between two kinds of chromophores (CD1 and CD2), and further transfer to EY center with a high efficiency of 84%. Interestingly, the Förster resonance energy transfer (FRET) process of our LHS could be reversibly "On/Off" switched by the redox regulated assembly and disassembly of SP1 building blocks. Moreover, the LHS has been further proved to promote the yield of a model cross-coupling hydrogen evolution reaction and regulate the process of the reaction with the FRET process "On/Off" state.

Morphological Selectivity of a Protein Self-Assembly System with a Repertoire of Diverse Interaction Modes

Multiple metal chelating sites were incorporated onto the second mitochondria-derived activator of caspase (SMAC) building blocks. The combination of different binding sites generated a repertoire of diverse binding modes, among which two different microfilament types (small and large) with distinct patterns were selected under thermodynamic control. Furthermore, the two microfilaments exhibited a pronounced secondary assembly trend due to the potential noncovalent interactions on the protein surfaces. Coupled with stereoselectivity, they presented a strong self-recognition effect and underwent two distinct reassembly patterns. That is, the large filaments self-associated in pairs to form "interlocked chain" structures, while the small ones twisted to form protein helical bundles. This work represents one of the few studies of selective self-assembly of self-assembled protein assemblies. Such an idea may provide inspiration for constructing more sophisticated protein architectures in the future.

Rational Design of Self-Assembling Supramolecular Protein Nanostructures Utilizing the Cucurbit[8]Uril Macrocyclic Host

Self-assembly is a phenomenon that governs molecular structural organization in nature, therefore raising research interest for the fabrication of novel nanomaterials with diverse applications in biocatalysis, biomedicine, material templating, and biosensor development. In this chapter we provide protocols for the development of supramolecular protein complexes based on host-guest interactions in the presence of the macrocyclic host, cucurbit[8]uril (CB[8]). CB[8] is reported to exhibit high binding affinity towards the tripeptide Phe-Gly-Gly (FGG), therefore it can be utilized as a selective adhesive of protein molecules, after fusion of FGG to an accessible protein surface.

Formation of β-Lactoglobulin Self-Assemblies via Liquid-Liquid Phase Separation for Applications beyond the Biological Functions

Proteins are like miracle machines, playing important roles in living organisms. They perform vital biofunctions by further combining together and/or with other biomacromolecules to form assemblies or condensates such as membraneless organelles. Therefore, studying the self-assembly of biomacromolecules is of fundamental importance. In addition to their biological activities, protein assemblies also exhibit extra properties that enable them to achieve applications beyond their original functions. Herein, this study showed that in the presence of monosaccharides, ethylene glycols, and amino acids, β-lactoglobulin (β-LG) can form assemblies with specific structures, which were highly reproducible. The mechanism of the assembly process was studied through multi-scale observations and theoretical analysis, and it was found that the assembling all started from the formation of solute-rich liquid droplets via liquid-liquid phase separation (LLPS). These droplets then combined together to form condensates with elaborate structures, and the condensates finally evolved to form assemblies with various morphologies. Such a mechanism of the assembly is valuable for studying the assembly processes that frequently occur in living organisms. Detailed studies concerning the properties and applications of the obtained β-LG assemblies showed that the assemblies exhibited significantly better performances than the protein itself in terms of autofluorescence, antioxidant activity, and metal ion absorption, which indicates broad applications of these assemblies in bioimaging, biodetection, biodiagnosis, health maintenance, and pollution treatment. This study revealed that biomacromolecules, especially proteins, can be assembled via LLPS, and some unexpected application potentials could be found beyond their original biological functions.

Design and recognition of cucurbituril-secured platinum-bound oligopeptides

Platinum terpyridyl complexes, stacked on top of one another and secured as dimers with cucurbit[8]uril (CB[8]) in aqueous medium, were functionalized quantitatively and in situ with a pair of pentapeptides Phe-(Gly)₃-Cys by grafting their cysteine residues to the Pt centers. The resulting CB[8]·(Pt·peptide)₂ assemblies were used to target secondary hosts CB[7] and CB[8] via their pair of phenylalanine residues, again in situ. A series of well-defined architectures, including a supramolecular “pendant necklace” with hybrid head-to-head and head-to-tail arrangements inside CB[8], were obtained during the self-sorting process after combining only 3 or 4 simple building units.

A platinum terpyridyl complex, pentapeptide Phe-(Gly)₃-Cys and cucurbit[8]uril assemble into a “pendant necklace” with hybrid head-to-head and head-to-tail arrangements in aqueous medium.

Construction of Ultralarge Two-Dimensional Fluorescent Protein Arrays via a Reengineered Rhodamine B-Based Molecular Tool

The self-luminous property of enhanced green fluorescent protein (EGFP) makes it an extremely attractive building block for creating functional biomaterials. A practical challenge in the design of EGFP-based materials, however, stems from the structural and chemical heterogeneity of the EGFP surface. In this study, a maleimide-functionalized rhodamine B molecule (RhG₂M) was designed as a versatile molecular tool to overcome this obstacle. Site-specific modification of an EGFP variant (EGFP-4C) with RhG₂M allowed for the fabrication of a series of well-defined two-dimensional (2D) arrays that span nano- and micrometer scales. Furthermore, the resulting ultralarge 2D EGFP-4C arrays feature both structural uniformity and flexibility, together with the inherent optical properties, making them advanced materials with great potential for practical applications. In addition, this strategy can be further extended into three dimensions and applied to the modular generation of periodic functional materials with more complex structures.

Oligomeric Cucurbituril Complexes: from Peculiar Assemblies to Emerging Applications

Proteins are an endless source of inspiration. By carefully tuning the amino-acid sequence of proteins, nature made them evolve from primary to quaternary structures, a property specific to protein oligomers and often crucial to accomplish their function. On the other hand, the synthetic macrocycles cucurbiturils (CBs) have shown outstanding recognition properties in water, and a growing number of (host)_n :(guest)_n supramolecular polymers involving CBs have been reported. However, the burgeoning field of discrete (n:n) host:guest oligomers has just started to attract attention. While 2:2 complexes are the major oligomers, 3:3 and up to 6:6 oligomers have been described, some associated with emerging applications, specific to the (n:n) arrangements. Design rules to target (n:n) host:guest oligomers are proposed toward new advanced host:guest systems.

Hierarchical Self-Assembly of Proteins Through Rationally Designed Supramolecular Interfaces

With the increasing advances in the basic understanding of pathogenesis mechanism and fabrication of advanced biological materials, protein nanomaterials are being developed for their potential bioengineering research and biomedical applications. Among different fabrication strategies, supramolecular self-assembly provides a versatile approach to construct hierarchical nanostructures from polyhedral cages, filaments, tubules, monolayer sheets to even cubic crystals through rationally designed supramolecular interfaces. In this mini review, we will briefly recall recent progress in reconstituting protein interfaces for hierarchical self-assembly and classify by the types of designed protein-protein interactions into receptor-ligand recognition, electrostatic interaction, metal coordination, and non-specific interaction networks. Moreover, some attempts on functionalization of protein superstructures for bioengineering and/or biomedical applications are also shortly discussed. We believe this mini review will outline the stream of hierarchical self-assembly of proteins through rationally designed supramolecular interfaces, which would open minds in visualizing protein-protein recognition and assembly in living cells and organisms, and even constructing multifarious functional bionanomaterials.

Engineering protein polymers of ultrahigh molecular weight via supramolecular polymerization: towards mimicking the giant muscle protein titin

Utilizing protein fragment reconstitution of a small protein GB1, we developed an efficient, supramolecular polymerization strategy to engineer protein polymers with ultrahigh molecular weight that mimic the giant muscle protein titin.

The giant muscle protein titin is the largest protein in cells and responsible for the passive elasticity of muscles. Titin, made of hundreds of individually folded globular domains, is a protein polymer with folded globular domains as its macromonomers. Due to titin's ultrahigh molecular weight, it has been challenging to engineer high molecular weight artificial protein polymers that mimic titin. Taking advantage of protein fragment reconstitution (PFR) of a small protein GB1, which can be reconstituted from its two split fragments G_N and G_C, here we report the development of an efficient, PFR-based supramolecular polymerization strategy to engineer protein polymers with ultrahigh molecular weight. We found that the engineered bifunctional protein macromonomers (G_C-macromonomer-G_N) can undergo supramolecular polymerization, in a way similar to condensation polymerization, via the reconstitution of G_N and G_C to produce protein polymers with ultrahigh molecular weight (with an average molecular weight of 0.5 MDa). Such high molecular weight linear protein polymers closely mimic titin and provide protein polymer building blocks for the construction of biomaterials with improved physical and mechanical properties.

Template-Free Construction of Highly Ordered Monolayered Fluorescent Protein Nanosheets: A Bioinspired Artificial Light-Harvesting System

Using biological materials for light-harvesting applications has attracted considerable attention in recent years. Such materials provide excellent environmental compatibility and often exhibit superior properties over synthetic materials. Herein, inspired by the outstanding energy transfer performance in coelenterates, we constructed a template-free, highly ordered two-dimensional light-harvesting system by covalent-induced coassembly of EBFP2 (donor) and EGFP (acceptor), in which the fluorescent chromophores were well distributed and adopted a fixed orientation. By introducing approximate square planar binding sites on the side surface of protein, assembly pattern was pin down and self-assembly extended in orthogonal directions to achieve monolayered and tessellated protein nanoarrays. The excellent antiself-quenching property of fluorescent proteins endowed the coassembled system with attractive light-harvesting capability. Even at high local concentrations, a low resonance energy transfer self-quenching was observed and, therefore, energy can be efficiently transferred. More importantly, the distance between adjacent chromophores is continuously adjustable. By making minor changes to the length of the inducing linker, we have achieved significant control over the size of the assembly. A micron-sized light-harvesting system with satisfactory energy transfer efficiency was finally obtained. This work developed a template-free light-harvesting system completely based on fluorescent proteins (FPs), which overcame the restriction of using templates. Not limited to this work, the special core-shell structure of FPs may be expected to direct the optimization of fluorescent dyes by cladding.

Functional protein nanostructures: a chemical toolbox

Nature has evolved an optimal synthetic factory in the form of translational and posttranslational processes by which millions of proteins with defined primary sequences and 3D structures can be built. Nature's toolkit gives rise to protein building blocks, which dictates their spatial arrangement to form functional protein nanostructures that serve a myriad of functions in cells, ranging from biocatalysis, formation of structural networks, and regulation of biochemical processes, to sensing. With the advent of chemical tools for site-selective protein modifications and recombinant engineering, there is a rapid development to develop and apply synthetic methods for creating structurally defined, functional protein nanostructures for a broad range of applications in the fields of catalysis, materials and biomedical sciences. In this review, design principles and structural features for achieving and characterizing functional protein nanostructures by synthetic approaches are summarized. The synthetic customization of protein building blocks, the design and introduction of recognition units and linkers and subsequent assembly into structurally defined protein architectures are discussed herein. Key examples of these supramolecular protein nanostructures, their unique functions and resultant impact for biomedical applications are highlighted.

Cucurbit[8]uril-Based Polymers and Polymer Materials

Cucurbit[8]uril (CB[8]) is unique and notable in the cucurbit[n]uril family, since it has a relatively large cavity and thus is able to simultaneously accommodate two guest molecules. Typically, an electron-deficient first guest and an electron-rich second guest can be bound by CB[8] to form a stable 1:1:1 heteroternary supramolecular complex. Additionally, two homo guests can also be strongly dimerized inside the cavity of CB[8] to form a 2:1 homoternary supramolecular complex. During the past decade, by combining polymer science and CB[8] host-guest chemistry, a variety of systems have been established to construct supramolecular polymers with polymer chains typically at the nanoscale/sub-microscale, and CB[8]-based micro/nanostructured polymer materials in the form of polymer networks and hydrogels, microcapsules, micelles, vesicles, and colloidal particles, normally in solution and occasionally on surfaces. This Review summarizes the noncovalent interactions and strategies used for the preparation of CB[8]-based polymers and polymer materials with a focus on the representative and latest developments, followed by a brief discussion of their characterization, properties, and applications.

Donor-acceptor interaction-driven self-assembly of amphiphilic rod-coil molecules into supramolecular nanoassemblies

Rigid-flexible amphiphilic molecules consisting of an aromatic segment based on pyrene and biphenyl units and hydrophilic polyethylene oxide chains self-assemble into lamellar, hexagonal columnar, and two-dimensional columnar nanostructures in the bulk state. In aqueous solution, these molecules self-assemble into nanofibers, spherical micelles, and multilayer nanotubes, depending on the chain or rod length of the molecules. Notably, ordered nanostructures of supramolecular polymers, such as single-layer curving fragments, nanofibers, and nanosheets, were constructed through charge-transfer interactions between the nanoobjects and an electron-acceptor molecule, 2,4,5,7-tetranitrofluorenone. These experimental results reveal that diverse supramolecular morphologies can be controlled by tuning rod-coil molecular interactions or charge-transfer interactions between the donor and acceptor molecules.

Supramolecular Chemistry Targeting Proteins

The specific recognition of protein surface elements is a fundamental challenge in the life sciences. New developments in this field will form the basis of advanced therapeutic approaches and lead to applications such as sensors, affinity tags, immobilization techniques, and protein-based materials. Synthetic supramolecular molecules and materials are creating new opportunities for protein recognition that are orthogonal to classical small molecule and protein-based approaches. As outlined here, their unique molecular features enable the recognition of amino acids, peptides, and even whole protein surfaces, which can be applied to the modulation and assembly of proteins. We believe that structural insights into these processes are of great value for the further development of this field and have therefore focused this Perspective on contributions that provide such structural data.