"Belt and braces": a peptide-based linker system of de novo design

Self-Complementary Zwitterionic Peptides Direct Nanoparticle Assembly and Enable Enzymatic Selection of Endocytic Pathways

Supramolecular self-assembly in biological systems holds promise to convert and amplify disease-specific signals to physical or mechanical signals that can direct cell fate. However, it remains challenging to design physiologically stable self-assembling systems that demonstrate tunable and predictable behavior. Here, the use of zwitterionic tetrapeptide modalities to direct nanoparticle assembly under physiological conditions is reported. The self-assembly of gold nanoparticles can be activated by enzymatic unveiling of surface-bound zwitterionic tetrapeptides through matrix metalloprotease-9 (MMP-9), which is overexpressed by cancer cells. This robust nanoparticle assembly is achieved by multivalent, self-complementary interactions of the zwitterionic tetrapeptides. In cancer cells that overexpress MMP-9, the nanoparticle assembly process occurs near the cell membrane and causes size-induced selection of cellular uptake mechanism, resulting in diminished cell growth. The enzyme responsiveness, and therefore, indirectly, the uptake route of the system can be programmed by customizing the peptide sequence: a simple inversion of the two amino acids at the cleavage site completely inactivates the enzyme responsiveness, self-assembly, and consequently changes the endocytic pathway. This robust self-complementary, zwitterionic peptide design demonstrates the use of enzyme-activated electrostatic side-chain patterns as powerful and customizable peptide modalities to program nanoparticle self-assembly and alter cellular response in biological context.

Peptide Design and Self-assembly into Targeted Nanostructure and Functional Materials

Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.

Rational Design of Functional Peptide-Gold Hybrid Nanomaterials for Molecular Interactions

Gold nanoparticles (AuNPs) have been extensively used for decades in biosensing-related development due to outstanding optical properties. Peptides, as newly realized functional biomolecules, are promising candidates of replacing antibodies, receptors, and substrates for specific molecular interactions. Both peptides and AuNPs are robust and easily synthesized at relatively low cost. Hence, peptide-AuNP-based bio-nano-technological approaches have drawn increasing interest, especially in the field of molecular targeting, cell imaging, drug delivery, and therapy. Many excellent works in these areas have been reported: demonstrating novel ideas, exploring new targets, and facilitating advanced diagnostic and therapeutic technologies. Importantly, some of them also have been employed to address real practical problems, especially in remote and less privileged areas. This contribution focuses on the application of peptide-gold hybrid nanomaterials for various molecular interactions, especially in biosensing/diagnostics and cell targeting/imaging, as well as for the development of highly active antimicrobial/antifouling coating strategies. Rationally designed peptide-gold nanomaterials with functional properties are discussed along with future challenges and opportunities.

Self-assembled peptide-inorganic nanoparticle superstructures: from component design to applications

Peptides have become excellent platforms for the design of peptide-nanoparticle hybrid superstructures, owing to their self-assembly and binding/recognition capabilities. Morover, peptide sequences can be encoded and modified to finely tune the structure of the hybrid systems and pursue functionalities that hold promise in an array of high-end applications. This feature article summarizes the different methodologies that have been developed to obtain self-assembled peptide-inorganic nanoparticle hybrid architectures, and discusses how the proper encoding of the peptide sequences can be used for tailoring the architecture and/or functionality of the final systems. We also describe the applications of these hybrid superstructures in different fields, with a brief look at future possibilities towards the development of new functional hybrid materials.

Peptide-induced super-assembly of biocatalytic metal-organic frameworks for programmed enzyme cascades

Despite the promise of metal-organic frameworks (MOFs) as functional matrices for enzyme stabilization, the development of a stimulus-responsive approach to induce a multi-enzyme cascade reaction in MOFs remains a critical challenge. Here, a novel method using peptide-induced super-assembly of MOFs is developed for programmed enzyme cascade reactions on demand. The super-assembled MOF particles containing different enzymes show remarkable 7.3-fold and 4.4-fold catalytic activity enhancements for the two-enzyme and three-enzyme cascade reactions, respectively, as compared with the unassembled MOF nanoparticles. Further digestion of the coiled-coil forming peptides on the MOF surfaces leads to the MOF superstructure disassembly and the programmed enzyme cascade reaction being "switched-off". Research on these stimuli-responsive materials with controllable and predictable biocatalytic functions/properties provide a concept to facilitate the fabrication of next-generation smart materials based on precision chemistry.

Logical design and application of prodrug platforms

This review summarizes the current state of prodrugs and elaborates the logical design and future development of the prodrug platform.

Protein-Mediated Colloidal Assembly

Programmable colloidal assembly enables the creation of mesoscale materials in a bottom-up manner. Although DNA oligonucleotides have been used extensively as the programmable units in this paradigm, proteins, which exhibit more diverse modes of association and function, have not been widely used to direct colloidal assembly. Here we use protein-protein interactions to drive controlled aggregation of polystyrene microparticles, either through reversible coiled-coil interactions or through intermolecular isopeptide linkages. The sizes of the resulting aggregates are tunable and can be controlled by the concentration of immobilized surface proteins. Moreover, particles coated with different protein pairs undergo orthogonal assembly. We demonstrate that aggregates formed by association of coiled-coil proteins, in contrast to those linked by isopeptide bonds, are dispersed by treatment with chemical denaturants or soluble competing proteins. Finally, we show that protein-protein interactions can be used to assemble complex core-shell aggregates. This work illustrates a versatile strategy for engineering colloidal systems for use in materials science and biotechnology.

pH sensitive coiled coils: a strategy for enhanced liposomal drug delivery

Stimuli responsive controlled release from liposome based vesicles is a promising strategy for the site specific delivery of drugs. Herein, we report the design of pH sensitive coiled coils and their incorporation into the liposome as triggers for the controlled release of encapsulated drugs. The designed coiled coil peptides with the incorporation of environment sensitive fluorescent amino acids were found to be stable at physiological pH and unstructured while changing the pH of the environment to either acidic or basic. This pH dependent conformational switch of the coiled-coil polypeptides was exploited as triggers for the enhanced release of the encapsulated drug molecules from liposomes. The SEM, DLS and TEM analysis revealed the uniform morphology of the peptide liposome hybrid vesicles. Further, the drug encapsulated liposome internalization experiments with cancer cells revealed the enhanced release and accumulation of drugs in the acidic lysosomal compartments in comparison with liposomes without coiled coils.

The Trypanosome Flagellar Pocket Collar and Its Ring Forming Protein-TbBILBO1

Sub-species of Trypanosoma brucei are the causal agents of human African sleeping sickness and Nagana in domesticated livestock. These pathogens have developed an organelle-like compartment called the flagellar pocket (FP). The FP carries out endo- and exocytosis and is the only structure this parasite has evolved to do so. The FP is essential for parasite viability, making it an interesting structure to evaluate as a drug target, especially since it has an indispensible cytoskeleton component called the flagellar pocket collar (FPC). The FPC is located at the neck of the FP where the flagellum exits the cell. The FPC has a complex architecture and division cycle, but little is known concerning its organization. Recent work has focused on understanding how the FP and the FPC are formed and as a result of these studies an important calcium-binding, polymer-forming protein named TbBILBO1 was identified. Cellular biology analysis of TbBILBO1 has demonstrated its uniqueness as a FPC component and until recently, it was unknown what structural role it played in forming the FPC. This review summarizes the recent data on the polymer forming properties of TbBILBO1 and how these are correlated to the FP cytoskeleton.

Dynamic covalent assembly and disassembly of nanoparticle aggregates

A new type of dynamic covalent nanoparticle (NP) building block is reported, exhibiting rapid constitutional adaptation in a NP-bound monolayer of boronate esters, and formation of covalently linked NP assemblies, which despite being connected by covalent bonds, can be fully disassembled on application of a chemical stimulus.

Impact of multivalent charge presentation on peptide-nanoparticle aggregation

Strategies to achieve controlled nanoparticle aggregation have gained much interest, due to the versatility of such systems and their applications in materials science and medicine. In this article we demonstrate that coiled-coil peptide-induced aggregation based on electrostatic interactions is highly sensitive to the length of the peptide as well as the number of presented charges. The quaternary structure of the peptide was found to play an important role in aggregation kinetics. Furthermore, we show that the presence of peptide fibers leads to well-defined nanoparticle assembly on the surface of these macrostructures.

Hierarchical Self-Assembled Peptide Nano-ensembles

A variety of peptides can be self-assembled, i.e. self-organized spontaneously, into large and complex hierarchical structures, reproducibly by regulating a range of parameters that can be environment driven, process driven, or peptide driven. These supramolecular peptide aggregates yield different shapes and structures like nanofibers, nanotubes, nanobelts, nanowires, nanotapes, and micelles. These peptide nanostructures represent a category of materials that bridge biotechnology and nanotechnology and are found suitable not only for biomedical applications such as tissue engineering and drug delivery but also in nanoelectronics.

Short peptide based self-assembled nanostructures: implications in drug delivery and tissue engineering

Self-assembling peptides with many potential biomedical applications.

Anti-antimicrobial peptides: folding-mediated host defense antagonists

Antimicrobial or host defense peptides are innate immune regulators found in all multicellular organisms. Many of them fold into membrane-bound α-helices and function by causing cell wall disruption in microorganisms. Herein we probe the possibility and functional implications of antimicrobial antagonism mediated by complementary coiled-coil interactions between antimicrobial peptides and de novo designed antagonists: anti-antimicrobial peptides. Using sequences from native helical families such as cathelicidins, cecropins, and magainins we demonstrate that designed antagonists can co-fold with antimicrobial peptides into functionally inert helical oligomers. The properties and function of the resulting assemblies were studied in solution, membrane environments, and in bacterial culture by a combination of chiroptical and solid-state NMR spectroscopies, microscopy, bioassays, and molecular dynamics simulations. The findings offer a molecular rationale for anti-antimicrobial responses with potential implications for antimicrobial resistance.

SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains

The synthetic biology toolkit contains a growing number of parts for regulating transcription and translation, but very few that can be used to control protein association. Here we report characterization of 22 previously published heterospecific synthetic coiled-coil peptides called SYNZIPs. We present biophysical analysis of the oligomerization states, helix orientations, and affinities of 27 SYNZIP pairs. SYNZIP pairs were also tested for interaction in two cell-based assays. In a yeast two-hybrid screen, >85% of 253 comparable interactions were consistent with prior in vitro measurements made using coiled-coil microarrays. In a yeast-signaling assay controlled by coiled-coil mediated scaffolding, 12 SYNZIP pairs were successfully used to down-regulate the expression of a reporter gene following treatment with α-factor. Characterization of these interaction modules dramatically increases the number of available protein interaction parts for synthetic biology and should facilitate a wide range of molecular engineering applications. Summary characteristics of 27 SYNZIP peptide pairs are reported in specification sheets available in the Supporting Information and at the SYNZIP Web site [http://keatingweb.mit.edu/SYNZIP/].

Polypeptide folding-mediated tuning of the optical and structural properties of gold nanoparticle assemblies

Responsive hybrid nanomaterials with well-defined properties are of significant interest for the development of biosensors with additional applications in tissue engineering and drug delivery. Here, we present a detailed characterization using UV-vis spectroscopy and small angle X-ray scattering of a hybrid material comprised of polypeptide-decorated gold nanoparticles with highly controllable assembly properties. The assembly is triggered by a folding-dependent bridging of the particles mediated by the heteroassociation of immobilized helix-loop-helix polypeptides and a complementary nonlinear polypeptide present in solution. The polypeptides are de novo designed to associate and fold into a heterotrimeric complex comprised of two disulfide-linked four-helix bundles. The particles form structured assemblies with a highly defined interparticle gap (4.8±0.4 nm) that correlates to the size of the folded polypeptides. Transitions in particle aggregation dynamics, mass-fractal dimensions and ordering, as a function of particle size and the concentration of the bridging polypeptide, are observed; these have significant effects on the optical properties of the assemblies. The assembly and ordering of the particles are highly complex processes that are affected by a large number of variables including the number of polypeptides bridging the particles and the particle mobility within the aggregates. A fundamental understanding of these processes is of paramount interest for the development of novel hybrid nanomaterials with tunable structural and optical properties and for the optimization of nanoparticle-based colorimetric biodetection strategies.

Alpha-helical peptide assemblies giving new function to designed structures

The design of alpha-helical tectons for self-assembly is maturing as a science. We have now reached the point where many different coiled-coil topologies can be reliably produced and validated in synthetic systems and the field is now moving on towards more complex, discrete structures and applications. Similarly the design of infinite or fiber assemblies has also matured, with the creation fibers that have been modified or functionalized in a variety of ways. This chapter discusses the progress made in both of these areas as well as outlining the challenges still to come.

Self-assembly of coiled coils in synthetic biology: inspiration and progress

Biological self-assembly is very complex and results in highly functional materials. In effect, it takes a bottom-up approach using biomolecular building blocks of precisely defined shape, size, hydrophobicity, and spatial distribution of functionality. Inspired by, and drawing lessons from self-assembly processes in nature, scientists are learning how to control the balance of many small forces to increase the complexity and functionality of self-assembled nanomaterials. The coiled-coil motif, a multipurpose building block commonly found in nature, has great potential in synthetic biology. In this review we examine the roles that the coiled-coil peptide motif plays in self-assembly in nature, and then summarize the advances that this has inspired in the creation of functional units, assemblies, and systems.

Complexity in nanoparticle assembly and function obtained by direct-grafted peptides

We synthesize peptide-functionalized nanoparticles by growing the peptide directly from the nanoparticles in a grafting-from process. We demonstrate the procedure by grafting a short, pH and oxidation responsive peptide sequence from 300 nm silica nanoparticles. The peptide allows destabilization of the particles in response to pH by neutralization of electrostatic charge, while manipulation of oxidizing conditions in the system offers the ability to select for irreversible, covalent bonding between the particles. In one system, we show the assembly of an asymmetrically functionalized set of particles, which may have applications in the formation of binary particle networks. The method of preparing peptide-coated particles should greatly simplify existing processes used to create peptide-functionalized nanoparticles.

Environmentally responsive peptides as anticancer drug carriers

The tumor microenvironment provides multiple cues that may be exploited to improve the efficacy of established chemotherapeutics; furthermore, polypeptides are uniquely situated to capitalize on these signals. Peptides provide: 1) a rich repertoire of biologically specific interactions to draw upon; 2) environmentally responsive phase behaviors, which may be tuned to respond to signatures of disease; 3) opportunities to direct self-assembly; 4) control over routes of biodegradation; 5) the option to seamlessly combine functionalities into a single polymer via a one-step biosynthesis. As development of cancer-targeted nanocarriers expands, peptides provide a unique source of functional units that may target disease. This review explores potential microenvironmental physiology indicative of tumors and peptides that have demonstrated an ability to target and deliver to these signals.

Cooperative dual-stimuli-triggered aggregation of poly-L-histidine-functionalized au nanoparticles

Nanoparticles that are responsive to multiple stimuli allow more precise control over the aggregation process and thus the structures and properties of the resulting aggregates. Au nanoparticles functionalized by poly-L-histidine (PLH), a simple polypeptide with a pK(a) value (approximately 6.2) around the physiological pH, are sensitive to pH and temperature simultaneously. The dual stimuli, pH and temperature, must act in a cooperative way to switch the hydrophobic beta-sheet structure of PLH and thus trigger the assembly/disassembly of the Au nanoparticles. The aggregation process and thus the conformation change of PLH can be well recognized by the color change of the Au nanoparticles by naked eyes.

The leucine zipper as a building block for self-assembled protein fibers

Nanostructured materials are receiving increased attention from both academia and industry. For example, the fundamental understanding of fiber formation by peptides and proteins both is of interest in itself and may lead to a range of applications. A key idea here is that the folding and subsequent supramolecular assembly of the monomers can be programmed within polypeptide chains. Thus, with an understanding of so-called sequence-to-structure relationships for these peptide assemblies, it may be possible to design novel nanostructures from the bottom up that exhibit properties determined by, but not characteristic of, their component building blocks. In this respect, the alpha-helical leucine zipper presents an excellent place to start in the rational design of ordered nanostructures that span several length scales. Indeed, such systems have been put forward and developed to different degrees. Despite their apparent diversity, they employ similar assembly routes that can be compiled into one basic methodology. This chapter gives examples and provides methods of what can be achieved through leucine zipper-based assembly of fibrous structures.

Protein cages, rings and tubes: useful components of future nanodevices?

There is a great deal of interest in the possibility that complex nanoscale devices can be designed and engineered. Such devices will lead to the development of new materials, electronics and smart drugs. Producing complex nanoscale devices, however will present many challenges and the components of such devices will require a number of special features. Devices will be engineered to incorporate desired functionalities but, because of the difficulties of controlling matter precisely at the nanoscale with current technology, the nanodevice components must self-assemble. In addition, nanocomponents that are to have wide applicability in various devices must have enough flexibility to integrate into a large number of potentially very different environments. These challenges are daunting and complex, and artificial nanodevices have not yet been constructed. However, the existence of nanomachines in nature in the form of proteins (eg, enzymes) suggests that they will be possible to produce. As the material from which nature's nanomachines are made, proteins seem ideal to form the basis of engineered components of such nanodevices. Initially, engineering projects may focus on building blocks such as rings, cages and tubes, examples of which exist in nature and may act as a useful start point for modification and further development. This review focuses on the recent research and possible future development of such protein building blocks.

A new peptide-based method for the design and synthesis of nanoparticle superstructures: construction of highly ordered gold nanoparticle double helices

Left-handed gold nanoparticle double helices were prepared using a new method that allows simultaneous synthesis and assembly of discrete nanoparticles. This method involves coupling the processes of peptide self-assembly of and peptide-based biomineralization of nanoparticles. In this study, AYSSGAPPMPPF (PEPAu), an oligopeptide with an affinity for gold surfaces, was modified with an aliphatic tail to generate C12-PEPAu. In the presence of buffers and gold salts, amphiphilic C12-PEPAu was used to both control the formation of monodisperse gold nanoparticles and simultaneously direct their assembly into left-handed gold nanoparticle double helices. The gold nanoparticle double helices are highly regular, spatially complex, and they exemplify the utility of this methodology for rationally controlling the topology of nanoparticle superstructures and the stereochemical organization of discrete nanoparticles within these structures.

Assembly of polypeptide-functionalized gold nanoparticles through a heteroassociation- and folding-dependent bridging

Gold nanoparticles were functionalized with a synthetic polypeptide, de novo-designed to associate with a charge complementary linker polypeptide in a folding-dependent manner. A heterotrimeric complex that folds into two disulphide-linked four-helix bundles is formed when the linker polypeptide associates with two of the immobilized peptides. The heterotrimer forms in between separate particles and induces a rapid and extensive aggregation with a well-defined interparticle spacing. The aggregated particles are redispersed when the disulphide bridge in the linker polypeptide is reduced.