Metal-directed protein self-assembly

Structural basis of an engineered dual-specific antibody: conformational diversity leads to a hypervariable loop metal-binding site

To explore dual-specificity in a small protein interface, we previously generated a 'metal switch' anti-RNase A VHH antibody using a combinatorial histidine library approach. While most metal-binding sites in proteins are found within rigid secondary structure, the engineered VHH antibody (VHH(metal)), which contained three new histidine residues, possessed metal-binding residues within the flexible hypervariable loops. Here, crystal structure analysis of the free and bound states of VHH(metal) reveals the structural determinants leading to dual-function. Most notably, CDR1 is observed in two distinct conformations when adopting the metal or RNase A bound states. Furthermore, mutagenesis studies revealed that one of the engineered residues, not located in the metal-binding pocket, contributed indirectly to metal recognition, likely through influencing CDR1 conformation. Despite these changes, VHH(metal) possesses a relatively minor energetic penalty toward binding the original antigen, RNase A (~1 kcal/mol), where the engineered gain-of-function metal-binding residues are observed to possess a mix of favorable and unfavorable contributions towards RNase A recognition. Ultimately, the conformationally distinct metal-switch interface architecture reflects the robust, library-based strategy used to produce VHH(metal). These results also suggest that even small protein interfaces, such as VHH, may be structurally and energetically forgiving in adopting novel function, while maintaining original function.

Metal-induced self-assembly of peroxiredoxin as a tool for sorting ultrasmall gold nanoparticles into one-dimensional clusters

Nanomanipulation of matter to create responsive, ordered materials still remains extremely challenging. Supramolecular chemistry has inspired new strategies by which such nanomaterials can be synthesized step by step by exploiting the self-recognition properties of molecules. In this work, the ring-shaped architecture of the 2-Cys peroxiredoxin I protein from Schistosoma mansoni, engineered to have metal ion-binding sites, is used as a template to build up 1D nanoscopic structures through metal-induced self-assembly. Chromatographic and microscopic analyses demonstrate the ability of the protein rings to stack directionally upon interaction with divalent metal ions and form well-defined nanotubes by exploiting the intrinsic recognition properties of the ring surfaces. Taking advantage of such behavior, the rings are then used to capture colloidal Ni(2+)-functionalized ultrasmall gold nanoparticles and arrange them into 1D arrays through stacking into peapod-like complexes. Finally, as the formation of such nano-peapods strictly depends on nanoparticle dimensions, the peroxiredoxin template is used as a colloidal cut-off device to sort by size the encapsulated nanoparticles. These results open up possibilities in developing Prx-based methods to synthesize new advanced functional materials.

Thermodynamic contributions to the stability of the insulin hexamer

The insulin hexamer is resistant to degradation and fibrillation, which makes it an important quaternary structure for its in vivo storage in Zn(2+)- and Ca(2+)-rich vesicles in the pancreas and for pharmaceutical formulations. In addition to the two Zn(2+) ions that are required for its formation, three other species, Zn-coordinating anions (e.g., Cl(-)), Ca(2+), and phenols (e.g., resorcinol), bind to the hexamer and affect the subunit conformation and stability. The contributions of these four species to the thermodynamics of insulin unfolding have been quantified by differential scanning calorimetry and thermal unfolding measurements to determine the extent and nature of their stabilization of the insulin hexamer. Both Zn(2+) and resorcinol make a significant enthalpic contribution, while Ca(2+) primarily affects the protein heat capacity (solvation) by its interactions in the central cation-binding cavity, which is modulated by the surrounding subunit conformations. Coordinating anions have a negligible effect on the stability of the hexamer, even though subunits shift to an alternate conformation when these anions bind to the Zn(2+) ions. Finally, Zn(2+) in excess of the two that are required to form the hexamer further stabilizes the protein by additional enthalpic contributions.

Accurate design of co-assembling multi-component protein nanomaterials

The self-assembly of proteins into highly ordered nanoscale architectures is a hallmark of biological systems. The sophisticated functions of these molecular machines have inspired the development of methods to engineer self-assembling protein nanostructures; however, the design of multi-component protein nanomaterials with high accuracy remains an outstanding challenge. Here we report a computational method for designing protein nanomaterials in which multiple copies of two distinct subunits co-assemble into a specific architecture. We use the method to design five 24-subunit cage-like protein nanomaterials in two distinct symmetric architectures and experimentally demonstrate that their structures are in close agreement with the computational design models. The accuracy of the method and the number and variety of two-component materials that it makes accessible suggest a route to the construction of functional protein nanomaterials tailored to specific applications.

Using anchoring motifs for the computational design of protein-protein interactions

The computer-based design of PPIs (protein-protein interactions) is a challenging problem because large desolvation and entropic penalties must be overcome by the creation of favourable hydrophobic and polar contacts at the target interface. Indeed, many computationally designed interactions fail to form when tested in the laboratory. In the present article, we highlight strategies our laboratory has been pursuing to make interface design more tractable. Our general approach has been to make use of structural motifs found in native proteins that are predisposed to interact with a particular binding geometry, and then further bolster these anchor points with favourable hydrophobic contacts. We describe the use of three different anchor points, i.e. β-strand pairing, metal binding and the docking of α-helix into a groove, to successfully design new interfaces. In several cases, high-resolution crystal structures show that the design models closely match the experimental structure. In addition, we have tested the use of buried hydrogen-bond networks as a source of affinity and specificity at interfaces. In these cases, the designed complexes did not form, highlighting the challenges associated with designing buried polar interactions.

Hemoprotein-based supramolecular assembling systems

Hemoproteins are metalloproteins which include iron porphyrin as a cofactor. These proteins have received much attention as promising building blocks for development of new types of biomaterials. This review summarizes recent efforts in the rational design of supramolecular hemoprotein assemblies using myoglobin, horseradish peroxidase, cytochrome b562 and cytochrome c as a monomer unit. The processes of coordination bond-mediated assembly or domain swapping-mediated assembly provide defined oligomers, while hemoprotein reconstitution with synthetic heme derivatives provides submicrometer-sized structures such as fibrils, vesicles/micelles, or networks. Interestingly, several of these assembled structures maintain the intrinsic functions of monomer units. The chemical and/or biological strategies described in this review will lead to the creation of unique hemoprotein-based functional biomaterials.

Designing hydrolytic zinc metalloenzymes

Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up.

Coordinating subdomains of ferritin protein cages with catalysis and biomineralization viewed from the C4 cage axes

Integrated ferritin protein cage function is the reversible synthesis of protein-caged, solid Fe2O3·H2O minerals from Fe(2+) for metabolic iron concentrates and oxidant protection; biomineral order differs in different ferritin proteins. The conserved 432 geometric symmetry of ferritin protein cages parallels the subunit dimer, trimer, and tetramer interfaces, and coincides with function at several cage axes. Multiple subdomains distributed in the self-assembling ferritin nanocages have functional relationships to cage symmetry such as Fe(2+) transport though ion channels (threefold symmetry), biomineral nucleation/order (fourfold symmetry), and mineral dissolution (threefold symmetry) studied in ferritin variants. On the basis of the effects of natural or synthetic subunit dimer cross-links, cage subunit dimers (twofold symmetry) influence iron oxidation and mineral dissolution. 2Fe(2+)/O2 catalysis in ferritin occurs in single subunits, but with cooperativity (n = 3) that is possibly related to the structure/function of the ion channels, which are constructed from segments of three subunits. Here, we study 2Fe(2+) + O2 protein catalysis (diferric peroxo formation) and dissolution of ferritin Fe2O3·H2O biominerals in variants with altered subunit interfaces for trimers (ion channels), E130I, and external dimer surfaces (E88A) as controls, and altered tetramer subunit interfaces (L165I and H169F). The results extend observations on the functional importance of structure at ferritin protein twofold and threefold cage axes to show function at ferritin fourfold cage axes. Here, conserved amino acids facilitate dissolution of ferritin-protein-caged iron biominerals. Biological and nanotechnological uses of ferritin protein cage fourfold symmetry and solid-state mineral properties remain largely unexplored.

Enzyme design from the bottom up: an active nickel electrocatalyst with a structured peptide outer coordination sphere

Catalytic, peptide-containing metal complexes with a well-defined peptide structure have the potential to enhance molecular catalysts through an enzyme-like outer coordination sphere. Here, we report the synthesis and characterization of an active, peptide-based metal complex built upon the well-characterized hydrogen production catalyst [Ni(P(Ph)2N(Ph))2](2+) (P(Ph)2N(Ph)=1,3,6-triphenyl-1-aza-3,6-diphosphacycloheptane). The incorporated peptide maintains its β-hairpin structure when appended to the metal core, and the electrocatalytic activity of the peptide-based metal complex (≈100,000 s(-1)) is enhanced compared to the parent complex ([Ni(P(Ph)2N(APPA))2](2+); ≈50,500 s(-1)). The combination of an active molecular catalyst with a structured peptide provides a scaffold that permits the incorporation of features of an enzyme-like outer-coordination sphere necessary to create molecular electrocatalysts with enhanced functionality.

Interfacial metal coordination in engineered protein and peptide assemblies

Metal ions are frequently found in natural protein-protein interfaces, where they stabilize quaternary or supramolecular protein structures, mediate transient protein-protein interactions, and serve as catalytic centers. Paralleling these natural roles, coordination chemistry of metal ions is being increasingly utilized in creative ways toward engineering and controlling the assembly of functional supramolecular peptide and protein architectures. Here we provide a brief overview of this emerging branch of metalloprotein/peptide engineering and highlight a few select examples from the recent literature that best capture the diversity and future potential of approaches that are being developed.

Computational design of metalloproteins

A number of design strategies exist for the development of novel metalloproteins. These strategies often exploit the inherent symmetry of metal coordination and local topology. Computational design of metal binding sites in flexible regions of proteins is challenging as the number of conformational degrees of freedom is significantly increased. Additionally, without pre-organization of the primary shell ligands by the protein fold, metal binding sites can rearrange according to the coordination constraints of the metal center. Examples of metal incorporation into existing folds, full fold design exploiting symmetry, and fold design in asymmetric scaffolds are presented.

Self-assembly of protein-based biomaterials initiated by titania nanotubes

Protein-based biomaterials are a promising strategy for creating robust highly selective biocatalysts. The assembled biomaterials must sufficiently retain the near-native structure of proteins and provide molecular access to catalytically active sites. These requirements often exclude the use of conventional assembly techniques, which rely on covalent cross-linking of proteins or entrapment within a scaffold. Here we demonstrate that titania nanotubes can initiate and template the self-assembly of enzymes, such as ribonuclease A, while maintaining their catalytic activity. Initially, the enzymes form multilayer thick ellipsoidal aggregates centered on the nanotube surface; subsequently, these nanosized entities assemble into a micrometer-sized enzyme material that has enhanced enzymatic activity and contains as little as 0.1 wt % TiO2 nanotubes. This phenomenon is uniquely associated with the active anatase (001)-like surface of titania nanotubes and does not occur on other anatase nanomaterials, which contain significantly fewer undercoordinated Ti surface sites. These findings present a nanotechnology-enabled mechanism of biomaterial growth and open a new route for creating stable protein-based biomaterials and biocatalysts without the need for chemical modification.

Multivalent protein assembly using monovalent self-assembling building blocks

Discotic molecules, which self-assemble in water into columnar supramolecular polymers, emerged as an alternative platform for the organization of proteins. Here, a monovalent discotic decorated with one single biotin was synthesized to study the self-assembling multivalency of this system in regard to streptavidin. Next to tetravalent streptavidin, monovalent streptavidin was used to study the protein assembly along the supramolecular polymer in detail without the interference of cross-linking. Upon self-assembly of the monovalent biotinylated discotics, multivalent proteins can be assembled along the supramolecular polymer. The concentration of discotics, which influences the length of the final polymers at the same time dictates the amount of assembled proteins.

Simultaneous dual protein labeling using a triorthogonal reagent

Construction of heterofunctional proteins is a rapidly emerging area of biotherapeutics. Combining a protein with other moieties, such as a targeting element, a toxic protein or small molecule, and a fluorophore or polyethylene glycol (PEG) group, can improve the specificity, functionality, potency, and pharmacokinetic profile of a protein. Protein farnesyl transferase (PFTase) is able to site-specifically and quantitatively prenylate proteins containing a C-terminal CaaX-box amino acid sequence with various modified isoprenoids. Here, we describe the design, synthesis, and application of a triorthogonal reagent, 1, that can be used to site-specifically incorporate an alkyne and aldehyde group simultaneously into a protein. To illustrate the capabilities of this approach, a protein was enzymatically modified with compound 1 followed by oxime ligation and click reaction to simultaneously incorporate an azido-tetramethylrhodamine (TAMRA) fluorophore and an aminooxy-PEG moiety. This was performed with both a model protein [green fluorescent protein (GFP)] as well as a therapeutically useful protein [ciliary neurotrophic factor (CNTF)]. Next, a protein was enzymatically modified with compound 1 followed by coupling to an azido-bis-methotrexate dimerizer and aminooxy-TAMRA. Incubation of that construct with a dihydrofolate reductase (DHFR)-DHFR-anti-CD3 fusion protein resulted in the self-assembly of nanoring structures that were endocytosed into T-leukemia cells and visualized therein. These results highlight how complex multifunctional protein assemblies can be prepared using this facile triorthogonal approach.

Designing functional metalloproteins: from structural to catalytic metal sites

Metalloenzymes efficiently catalyze some of the most important and difficult reactions in nature. For many years, coordination chemists have effectively used small molecule models to understand these systems. More recently, protein design has been shown to be an effective approach for mimicking metal coordination environments. Since the first designed proteins were reported, much success has been seen for incorporating metal sites into proteins and attaining the desired coordination environment but until recently, this has been with a lack of significant catalytic activity. Now there are examples of designed metalloproteins that, although not yet reaching the activity of native enzymes, are considerably closer. In this review, we highlight work leading up to the design of a small metalloprotein containing two metal sites, one for structural stability (HgS3) and the other a separate catalytic zinc site to mimic carbonic anhydrase activity (ZnN3O). The first section will describe previous studies that allowed for a high affinity thiolate site that binds heavy metals in a way that stabilizes three-stranded coiled coils. The second section will examine ways of preparing histidine rich environments that lead to metal based hydrolytic catalysts. We will also discuss other recent examples of the design of structural metal sites and functional metalloenzymes. Our work demonstrates that attaining the proper first coordination geometry of a metal site can lead to a significant fraction of catalytic activity, apparently independent of the type of secondary structure of the surrounding protein environment. We are now in a position to begin to meet the challenge of building a metalloenzyme systematically from the bottom-up by engineering and analyzing interactions directly around the metal site and beyond.

In vitro and cellular self-assembly of a Zn-binding protein cryptand via templated disulfide bonds

Simultaneously strong and reversible through redox chemistry, disulfide bonds play a unique and often irreplaceable role in the formation of biological and synthetic assemblies. In an approach inspired by supramolecular chemistry, we report here that engineered noncovalent interactions on the surface of a monomeric protein can template its assembly into a unique cryptand-like protein complex ((C81/C96)RIDC14) by guiding the selective formation of multiple disulfide bonds across different interfaces. Owing to its highly interconnected framework, (C81/C96)RIDC14 is well preorganized for metal coordination in its interior, can support a large internal cavity surrounding the metal sites, and can withstand significant alterations in inner-sphere metal coordination. (C81/C96)RIDC14 self-assembles with high fidelity and yield in the periplasmic space of E. coli cells, where it can successfully compete for Zn(II) binding.

Practical approaches to designing novel protein assemblies

Molecular self-assembly offers a means by which sophisticated materials can be constructed with unparalleled precision. Designing self-assembling protein structures is of particular interest as a result of the unique functional capabilities of proteins. Custom-designed protein materials could lead to new possibilities in therapeutics, bioenergy, and materials science. Although the field was long hampered by the challenges involved in designing such complex molecules, novel approaches and computational tools have recently led to remarkable progress. Here we review recent design studies in the context of three fundamental aspects of self-assembling materials: subunit organization, subunit interactions, and regulation of assembly.

One-step photo synthesis of protein-drug nanoassemblies for drug delivery

Upon controlled UV illumination, disulfide bonds in bovine α-lactalbumin (BLA) are selectively broken, leading to self-assembly of the BLA and doxorubicin (DOX) molecules into nanoparticles via hydrophobic interactions and intermolecular disulfide bonds. Such protein-drug nanoparticles have synergistic anticancer activity in vitro and tumor-homing specificity in vivo, which are of great potential for systemic drug delivery in cancer therapy.

Covalent core-shell architecture of hemoglobin and human serum albumin as an artificial O2 carrier

Covalent core-shell structured protein clusters of hemoglobin (Hb) and human serum albumin (HSA) (HbX-HSAm) (m = 2, 3) with novel physiological properties were generated by linkage of Hb surface lysins to HSA cysteine-34 via an α-succinimidyl-ε-maleimide cross-linker (X: 1 or 2). The isoelectric points of HbX-HSAm (pI = 5.0-5.2) were markedly lower than that of Hb and almost identical to that of HSA. AFM and TEM measurements revealed a triangular Hb1-HSA3 cluster in aqueous medium. The complete 3D structure of Hb1-HSA3 based on TEM data was reconstructed, revealing two possible conformer variants. All HbX-HSAm clusters showed a moderately higher O2 affinity than the native Hb. Furthermore, the exterior HSA units possess a remarkable ability to bind lumiflavin (LF). The addition of NADH to an aqueous solution of the met-Hb2-(HSA-LF)3 cluster reduced the inactive ferric Hb center to the functional ferrous Hb. This O2-carrying hemoprotein cluster with strongly negative surface net charge, high O2 affinity, and NADH-dependent reductase unit can support a new generation of molecular architecture for red blood cell substitutes.

Combined computational design of a zinc-binding site and a protein-protein interaction: one open zinc coordination site was not a robust hotspot for de novo ubiquitin binding

We computationally designed a de novo protein-protein interaction between wild-type ubiquitin and a redesigned scaffold. Our strategy was to incorporate zinc at the designed interface to promote affinity and orientation specificity. A large set of monomeric scaffold surfaces were computationally engineered with three-residue zinc coordination sites, and the ubiquitin residue H68 was docked to the open coordination site to complete a tetrahedral zinc site. This single coordination bond was intended as a hotspot and polar interaction for ubiquitin binding, and surrounding residues on the scaffold were optimized primarily as hydrophobic residues using a rotamer-based sequence design protocol in Rosetta. From thousands of independent design simulations, four sequences were selected for experimental characterization. The best performing design, called Spelter, binds tightly to zinc (Kd  < 10 nM) and binds ubiquitin with a Kd of 20 µM in the presence of zinc and 68 µM in the absence of zinc. Mutagenesis studies and nuclear magnetic resonance chemical shift perturbation experiments indicate that Spelter interacts with H68 and the target surface on ubiquitin; however, H68 does not form a hotspot as intended. Instead, mutation of H68 to alanine results in tighter binding. Although a 3/1 zinc coordination arrangement at an interface cannot be ruled out as a means to improve affinity, our study led us to conclude that 2/2 coordination arrangements or multiple-zinc designs are more likely to promote high-affinity protein interactions.

Designing enzyme-like catalysts: a rhodium(II) metallopeptide case study

Chemists have long been fascinated by metalloenzymes and their chemistry. Because enzymes are essential for biological processes and to life itself, they present a key to understanding the world around us. At the same time, if chemists could harness the reactivity and selectivity of enzymes in designed transition-metal catalysts, we would have access to a powerful practical advance in chemistry. But the design of enzyme-like catalysts from scratch presents enormous challenges. Simplified, designed systems often don't provide the opportunity to mimic the complex features of enzymes such as selectivity in polyfunctional environments and access to reactive intermediates incompatible with bulk aqueous solution. Extensive efforts by numerous groups have led to remarkable designed metalloproteins that contain complex folds, including well-defined secondary and tertiary structure surrounding complex polymetallic centers. These structural achievements, however, have not yet led to general approaches to useful catalysts; continued efforts and new insights are needed. Our efforts have combined the attributes of enzymatic and traditional catalysis, bringing the benefits of polypeptide ligands to bear on completely nonbiological transition-metal centers. With a focus on designing useful catalytic activity, we have examined rhodium(II) carboxylates, bound to peptide chains through carboxylate side chains. Among other advantages, these complexes are stable and catalytically active in water. Our efforts have centered on two main interests: (1) understanding how Nature's ligand of choice, polypeptides, can be used to control the chemistry of nonbiological metal centers, and (2) mimicking metalloenzyme characteristics in designed, nonbiological catalysts. This Account conveys our motivation and goals for these studies, outlines progress to date, and discusses the future of enzyme-like catalyst design. In particular, these studies have resulted in on-bead, high-throughput screens for asymmetric metallopeptide catalysts. In addition, peptide-based molecular recognition strategies have facilitated the site-specific modification of protein substrates. Molecular recognition enables site-specific, proximity-driven modification of a broad range of amino acids, and the concepts outlined here are compatible with natural protein substrates and with complex, cell-like environments. We have also explored rhodium metallopeptides as hybrid organic-inorganic inhibitor molecules that block protein-protein interactions.

Femtomolar Zn(II) affinity of minimal zinc hook peptides--a promising small tag for protein engineering

The minimal zinc hook peptide of Rad50 and its alanine mutants form highly stable Zn(II) complexes. These peptides were successfully used as a small, efficient tag for reversible Zn(II)-mediated protein homodimerization. The high stability, its biological consequences and potential applications in protein engineering are discussed.

Supramolecular assembling systems formed by heme-heme pocket interactions in hemoproteins

A native protein in a biological system spontaneously produces large and elegant assemblies via self-assembly or assembly with various biomolecules which provide non-covalent interactions. In this context, the protein plays a key role in construction of a unique supramolecular structure operating as a functional system. Our group has recently highlighted the structure and function of hemoproteins reconstituted with artificially created heme analogs. The heme molecule is a replaceable cofactor of several hemoproteins. Here, we focus on the successive supramolecular protein assemblies driven by heme-heme pocket interactions to afford various examples of protein fibers, networks and three-dimensional clusters in which an artificial heme moiety is introduced onto the surface of a hemoprotein via covalent linkage and the native heme cofactor is removed from the heme pocket. This strategy is found to be useful for constructing hybrid materials with an electrode or with nanoparticles. The new systems described herein are expected to lead to the generation of various biomaterials with functions and characteristic physicochemical properties similar to those of hemoproteins.

Self-assembly of glutathione S-transferase into nanowires

This study presents the Ni-ion-directed self-assembly of a C(2)-symmetric homodimeric enzyme into nanowires. A genetically introduced His-tag arm stretches out of the central structure of a C(2)-symmetric homodimer of glutathione S-transferase, which is used as a linker to recruit a second building block through interprotein metal coordination, forming self-assembled one-dimensional nanostructures with excellent enzymatic activity.

Principles for designing ordered protein assemblies

In nature, many proteins have evolved to have self-complementary shapes. This drives them to assemble into supramolecular structures, sometimes of great complexity, and often carrying out sophisticated cellular functions. Designing novel proteins that can self-assemble into similarly complex structures is a longstanding goal in bioengineering. New ideas, combined with continually improving computer algorithms, are making it possible to advance on that goal, bringing wide-ranging applications in synthetic biology within reach. Prospective applications range from vaccine design to molecular delivery to bioactive materials. Recent strategies and examples of successfully designed protein cages, layers, and crystals are reviewed.

Protein-induced structural evolution of silver sulfide at the nanoscale: from hollow particles to solid spheres

Herein, a novel structural transformation of Ag(2)S nanoparticles from hollow particles to solid spheres is reported. The features of these structures are identified through a set of characterizations based on which the formation mechanism is also investigated.

Hybrid organic-inorganic inhibitors of a PDZ interaction that regulates the endocytic fate of CFTR

Together strong: Cooperative binding of organic (see picture, red) and inorganic fragments provides a strategy for the potent inhibition of protein-protein interactions. By targeting specific Lewis basic side chains in peripheral regions of the binding site for coordination to a rhodium(II) center, the affinity of otherwise weak ligands is improved.

Computational design of self-assembling protein nanomaterials with atomic level accuracy

We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.

Biological stimuli and biomolecules in the assembly and manipulation of nanoscale polymeric particles

Living systems are replete with complex, stimuli-responsive nanoscale materials and molecular self-assemblies. There is an ever increasing and intense interest within the chemical sciences to understand, mimic and interface with these biological systems utilizing synthetic and/or semi-synthetic tools. Our aim in this review is to give perspective on this emerging field of research by highlighting examples of polymeric nanoparticles and micelles that are prepared utilizing biopolymers together with synthetic polymers for the purpose of developing nanomaterials capable of interacting and responding to biologically relevant stimuli. It is expected that with the merging of evolved biological molecules with synthetic materials, will come the ability to prepare complex, functional devices. A variety of applications will become accessible including self-healing materials, self-replicating systems, biodiagnostic tools, drug targeting materials and autonomous, adaptive sensors. Most importantly, the success of this type of strategy will impact how biomolecules are stabilized and incorporated into synthetic devices and at the same time, will influence how synthetic materials are utilized within biomedical applications.

Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays

Proteins represent the most sophisticated building blocks available to an organism and to the laboratory chemist. Yet, in contrast to nearly all other types of molecular building blocks, the designed self-assembly of proteins has largely been inaccessible because of the chemical and structural heterogeneity of protein surfaces. To circumvent the challenge of programming extensive non-covalent interactions to control protein self-assembly, we have previously exploited the directionality and strength of metal coordination interactions to guide the formation of closed, homoligomeric protein assemblies. Here, we extend this strategy to the generation of periodic protein arrays. We show that a monomeric protein with properly oriented coordination motifs on its surface can arrange, on metal binding, into one-dimensional nanotubes and two- or three-dimensional crystalline arrays with dimensions that collectively span nearly the entire nano- and micrometre scale. The assembly of these arrays is tuned predictably by external stimuli, such as metal concentration and pH.