Self-Assembling Cyclic Peptide Cylinders as Nuclei for Crystal Engineering

Supramolecular chemistry of two new bis(1,2,3-triazolyl)pyridine macrocycles: metal complexation, self-assembly and anion binding

Two new macrocycles containing the bis(1,2,3-triazolyl)pyridine (btp) motif were prepared in high yields from a btp diazide precursor (1). Solution ¹H NMR studies show that this diazide undergoes self-assembly with divalent transition metal ions to form ML₂ complexes with pendant azide groups, apparently suitable for conversion into metal-templated catenanes; however attempts to form these catenanes were unsuccessful. Instead a new macrocycle containing two btp motifs was prepared, which forms a nanotube structure in the solid state. Reduction of the azide groups to amines followed by amide bond formation was used to convert 1 into macrocycle 8 containing btp and isophthalamide functionalities. This macrocycle binds halide and oxalate anions in acetonitrile solely through the isophthalamide motif, and binds aromatic dicarboxylates very strongly through both the isophthalamide amide donors and the btp triazole donors. The macrocycle was complexed with Pd(II) and the resulting complexes were shown to bind strongly to halide anions. The solid state structures of [Pd·8·X]BF₄ (X = Cl^-, Br^-, I^-) were investigated by X-ray crystallography, which showed that [Pd·8·Br] forms an unusual "chain of dimers" structure assembled by metal complexation, N-H⋯Br^- hydrogen bonding and short Pd⋯Pd contacts.

Side-Chain Interactions in d/l Peptide Nanotubes: Studies by Crystallography, NMR Spectroscopy and Molecular Dynamics

Our understanding of the factors affecting the stability of cyclic d/l peptide (CP) nanotubes remains underdeveloped. In this work, we investigate the impact of side chain alignment, hydrophobicity and charge on CP nanotube stability through X-ray crystallography, NMR spectroscopy and molecular dynamics (MD) simulations. We characterise the distinct CP-CP alignments that can form and identify stable and unstable dimers by MD simulation. We measure H-bond half-lives of synthesised CPs by ¹ H-D exchange experiments and find good correlation with predicted CP-CP stabilities. We find that hydrophobic amino acids improve CP dimer stability but experimentally reduce solubility. Charged amino acids either increase or decrease CP dimer stability depending on the relative orientation and composition of charged groups. X-ray crystal structures are solved for two CPs, revealing non-tubular folded conformations. Ultimately, this work will assist the educated design of stable tubular structures for potential applications in biomedicine.

Characteristics and therapeutic applications of antimicrobial peptides

The demand for novel antimicrobial compounds is rapidly growing due to the phenomenon of antibiotic resistance in bacteria. In response, numerous alternative approaches are being taken including use of polymers, metals, combinatorial approaches, and antimicrobial peptides (AMPs). AMPs are a naturally occurring part of the immune system of all higher organisms and display remarkable broad-spectrum activity and high selectivity for bacterial cells over host cells. However, despite good activity and safety profiles, AMPs have struggled to find success in the clinic. In this review, we outline the fundamental properties of AMPs that make them effective antimicrobials and extend this into three main approaches being used to help AMPs become viable clinical options. These three approaches are the incorporation of non-natural amino acids into the AMP sequence to impart better pharmacological properties, the incorporation of AMPs in hydrogels, and the chemical modification of surfaces with AMPs for device applications. These approaches are being developed to enhance the biocompatibility, stability, and/or bioavailability of AMPs as clinical options.

Polymeric Tubular Structures

Nature makes use of tubular structures for the spatial separation of matter on many different length scales, ranging from the nanometer scale (selective channels based on folded proteins) up to the centimeter scale (blood vessels). Today, polymer chemists and engineers can prepare polymeric tubular structures via a variety of different methods also covering many lengthscales, from nanometers to meters. The synthetic approaches described in this chapter vary significantly from the folding of single polymer chains via the self-assembly of DNA fragments to coordinative metal-organic nanotubes to tubes engineerd from bulk polymers using a range of porous or fibrous templates. While all examples reported in this chapter form tubular structures and thereby mimic their naturally occuring counterparts, it is mainly the engineered tubes that are more straightforward to prepare that also show some bio-inspired function.

Fibril-mediated oligomerization of pilin-derived protein nanotubes

BACKGROUND

Self-assembling protein nanotubes (PNTs) are an intriguing alternative to carbon nanotubes for applications in bionanotechnology, in part due to greater inherent biocompatibility. The type IV pilus of the gram negative bacteria Pseudomonas aeruginosa is a protein-based fibre composed of a single subunit, the type IV pilin. Engineered pilin monomers from P. aeruginosa strain K122-4 (ΔK122) have been shown to oligomerize into PNTs both in solution and at surfaces. In order to fully exploit PNTs in bionanotechonological settings, an in-depth understanding of their assembly, physical characteristics and robustness, both in solution and when constrained to surfaces, is required.

RESULTS

This study details the effectiveness of multiple initiators of ΔK122-derived PNT oligomerization and characterize the formation of PNTs in solution. The optimal initiator for the oligomerization of ΔK122 in solution was observed to be 2-methyl-2,4-pentanediol (MPD). Conversely, larger PEG molecules do not trigger oligomerization. Multi-angle light scattering analysis indicates that the pilin protein exists in a monomer-dimer equilibrium in solution, and that an intermediate species forms within three hours that then coalesces over time into high molecular weight PNTs. Transmission Electron Microscopic analysis was used to observe the formation of oligomerized ΔK122 fibrils prior to assembly into full-length PNTs.

CONCLUSIONS

The oligomerization of ΔK122 pilin derived PNTs is a fibril mediated process. The optimal trigger for PNT oligomerization in solution is MPD, and the observation that PEGs do not induce oligomerization may enable the oligomerization of pilin-derived PNTs on PEG-functionalized surfaces for implantable bionanodevices.

Self-assembly in the ferritin nano-cage protein superfamily

Protein self-assembly, through specific, high affinity, and geometrically constraining protein-protein interactions, can control and lead to complex cellular nano-structures. Establishing an understanding of the underlying principles that govern protein self-assembly is not only essential to appreciate the fundamental biological functions of these structures, but could also provide a basis for their enhancement for nano-material applications. The ferritins are a superfamily of well studied proteins that self-assemble into hollow cage-like structures which are ubiquitously found in both prokaryotes and eukaryotes. Structural studies have revealed that many members of the ferritin family can self-assemble into nano-cages of two types. Maxi-ferritins form hollow spheres with octahedral symmetry composed of twenty-four monomers. Mini-ferritins, on the other hand, are tetrahedrally symmetric, hollow assemblies composed of twelve monomers. This review will focus on the structure of members of the ferritin superfamily, the mechanism of ferritin self-assembly and the structure-function relations of these proteins.

Towards functional bionanomaterials based on self-assembling cyclic peptide nanotubes

In recent years, considerable effort has been devoted to the preparation of artificial nanotubular materials. One of the most successful approaches for the construction of noncovalently bonded nanotube entities is the self-assembly of cyclic polypeptides in stacks that are stabilized by hydrogen bonds. This tutorial review covers the history and current situation for synthetic organic nanostructures obtained from self-assembling cyclic peptides. In particular, we describe the evolution to cyclic peptides that not only allow the modification of the outer surface but also the inner cavity by paying special attention to peptide rings that contain cyclic gamma-amino acids. In this respect, we describe the synthesis, properties and application of a new class of homo- and heterodimeric supramolecular assemblies that are precursors of cyclic alpha,gamma-peptide nanotubes.

Molecular Design of beta-Hairpin Peptides for Material Construction

Self-assembled materials composed of beta-sheet forming peptides hold promise as therapeutics and novel biomaterials. This article focuses on the design and engineering of amphiphilic peptide sequences, especially beta-hairpins. Peptides can be designed to intramolecularly fold and then self-assemble on cue, affording hydrogels rich in beta-sheet structure. Hydrogels having distinct material properties can be designed at the molecular level by modulating either the peptide's sequence or the environmental stimulus used to trigger folding and assembly, leading to gelation.

Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics

In order to investigate the structures and properties of cyclic peptide nanotubes of cyclo[(-D: -Phe-L: -Ala)( n = 3,4,5,6)-], cyclo[(-D: -Phe-L: -Ala)( n = 4)-] was synthesized and self-assembled to nanotubes, and its structure and morphology of the nanotube were characterized by mass spectrometry (MS), fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). On the basis of these experimental results, the structures of cyclo[(-D: -Phe-L: -Ala)( n = 3,4,5,6)-] were characterized by molecular dynamics. In addition, the motion behaviors of H(2)O molecules in nanotubes were investigated by molecular dynamics using a COMPASS force field. Experimental results show that cyclo[(-D: -Phe-L: -Ala)( n = 4)-] peptides self-assemble into nanotube bundles. Molecular modeling results indicate that cyclic peptide nanotubes with n = 3, 4, 5 and 6 are very stable; these nanotubes have internal diameters of 5.9 A, 8.1 A, 10.8 A and 13.1 A and outer diameters of 18.2 A, 21.7 A, 23.4 A and 25.9 A respectively. Modeling results demonstrate that H(2)O molecules move in cooperation in single nanotube and they diffuse in one dimension, but they did not diffuse unilaterally due to the antiparallel ring stacking arrangement.

Molecular origin of the self-assembly of lanreotide into nanotubes: a mutational approach

Lanreotide, a synthetic, therapeutic octapeptide analog of somatostatin, self-assembles in water into perfectly hollow and monodisperse (24-nm wide) nanotubes. Lanreotide is a cyclic octapeptide that contains three aromatic residues. The molecular packing of the peptide in the walls of a nanotube has recently been characterized, indicating four hierarchical levels of organization. This is a fascinating example of spontaneous self-organization, very similar to the formation of the gas vesicle walls of Halobacterium halobium. However, this unique peptide self-assembly raises important questions about its molecular origin. We adopted a directed mutation approach to determine the molecular parameters driving the formation of such a remarkable peptide architecture. We have modified the conformation by opening the cycle and by changing the conformation of a Lys residue, and we have also mutated the aromatic side chains of the peptide. We show that three parameters are essential for the formation of lanreotide nanotubes: i), the specificity of two of the three aromatic side chains, ii), the spatial arrangement of the hydrophilic and hydrophobic residues, and iii), the aromatic side chain in the beta-turn of the molecule. When these molecular characteristics are modified, either the peptides lose their self-assembling capability or they form less-ordered architectures, such as amyloid fibers and curved lamellae. Thus we have determined key elements of the molecular origins of lanreotide nanotube formation.

Large-diameter self-assembled dimers of α,γ-cyclic peptides, with the nanotubular solid-state structure of cyclo-[(l-Leu-d-MeN-γ-Acp)4-]·4CHCl2COOH

Dimeric nanotube segments with pore diameters of up to 17 A have been obtained by self-assembly from new alpha,gamma-cyclic peptides.

Old materials with new tricks: multifunctional open-framework materials

The literature on open-framework materials has shown numerous examples of porous solids with additional structural, chemical, or physical properties. These materials show promise for applications ranging from sensing, catalysis and separation to multifunctional materials. This critical review provides an up-to-date survey to this new generation of multifunctional open-framework solids. For this, a detailed revision of the different examples so far reported will be presented, classified into five different sections: magnetic, chiral, conducting, optical, and labile open-frameworks for sensing applications. (413 references.)

Aza-β3-Cyclohexapeptides: Pseudopeptidic Macrocycles with Interesting Conformational and Configurational Properties Slow Pyramidal Nitrogen Inversion in 24-Membered Rings!

Among pseudopeptidic foldamers, aza-beta3-peptides have the unique property to possess nitrogen stereocenters instead of carbon stereocenters. As the result of pyramidal inversion at N(alpha)-atoms along the backbone, they behave as a set of C8-based secondary structures in equilibrium. This structural modulation is exploited here to prepare 24-membered macrocycles with great efficiency. Both crystal structures and spectroscopic data establish that aza-beta3-cyclohexapeptides adopt a highly organized conformation where the relative configuration of chiral nitrogen atoms is alternated. This makes them an interesting scaffold as the stereocontrol occurs spontaneously through the cyclization. These compounds reveal an unprecedented slow pyramidal nitrogen inversion in macrocycles. Pyramidal ground state stabilization, hindered rotation, steric crowding, and H-bond cooperativity are proposed to participate in this striking phenomenon. The equilibrium between invertomers of aza-beta3-cyclohexapeptides is reminiscent of the interchange between the two chair forms of cyclohexane.

Self-Assembly, Structures, and Solution Dynamics of Emissive Silver Metallacycles and Helices

Reactions of 9,10-bis(diphenylphosphino)anthracene (PAnP) and AgX (X = OTf-, ClO4-, PF6-, and BF4-) led to luminescent Ag-PAnP complexes with rich structural diversity. Helical polymers [Ag(mu-PAnP)(CH3CN)X]n (X = OTf-, ClO4-, and PF6-) and discrete binuclear [Ag2(mu-PAnP)2(CH3CN)4](PF6)2, trinuclear [Ag3(mu-PAnP)3 supersetBF4](BF4)2, and tetranuclear [Ag4(mu-PAnP)4 superset(ClO4)2](ClO4)2 metallacycles were isolated from different solvents. The tri- and tetranuclear metallacycles exhibited novel puckered-ring and saddlelike structures. Variable-temperature (VT) 31P{1H}-NMR spectroscopy of the complexes was solvent dependent. The dynamics in CD3CN involve two species, but the exchange processes in CD2Cl2 are more complicated. A ring-opening polymerization was proposed for the exchange mechanism in CD3CN.

Synthesis and Self-Assembly of 9,9'-Spirobifluorene-2,2',7,7'-tetracarboxylic Acid and Its Tetraamide. Non-Catenated Formation of Achiral Grid Layers with Large Chiral Pores

The title tetrasubstituted spirobifluorenes 3a, 3b have been designed to serve as convenient achiral tectons for self-assembly of 2D layers with large chiral pores. The underlying stereochemical concept has been confirmed by the results of crystallographic analysis of tetraacid 3a. Self-assembly of isosteric tetraamide 3b led to markedly different results.

Self-Assembled Peptide Tubelets with 7 Å Pores

Here we report the preparation and structural characteristics of self-assembling peptide tubelets composed of 32-membered rings formed of alternating alpha-amino acids and cis-3-aminocyclohexanecarboxylic acids. The tubelets possess a partial hydrophobic core environment, provided by the projection of the cyclohexane C2 methylene moiety into the lumen, and a Van der Waals pore diameter of about 7 A.

Crystal structure of a continuous three-dimensional DNA lattice

DNA has proved to be a versatile material for the rational design and assembly of nanometer scale objects. Here we report the crystal structure of a continuous three-dimensional DNA lattice formed by the self-assembly of a DNA 13-mer. The structure consists of stacked layers of parallel helices with adjacent layers linked through parallel-stranded base pairing. The hexagonal lattice geometry contains solvent channels that appear large enough to allow 3'-linked guest molecules into the crystal. We have successfully used these parallel base pairs to design and produce crystals with greatly enlarged solvent channels. This lattice may have applications as a molecular scaffold for structure determination of guest molecules, as a molecular sieve, or in the assembly of molecular electronics. Predictable non-Watson-Crick base pairs, like those described here, may present a new tool in structural DNA nanotechnology.

Modulating charge transfer through cyclic D,L-alpha-peptide self-assembly

We describe a concise, solid support-based synthetic method for the preparation of cyclic d,l-alpha-peptides bearing 1,4,5,8-naphthalenetetracarboxylic acid diimide (NDI) side chains. Studies of the structural and photoluminescence properties of these molecules in solution show that the hydrogen bond-directed self-assembly of the cyclic d,l-alpha-peptide backbone promotes intermolecular NDI excimer formation. The efficiency of NDI charge transfer in the resulting supramolecular assemblies is shown to depend on the length of the linker between the NDI and the peptide backbone, the distal NDI substituent, and the number of NDIs incorporated in a given structure. The design rationale and synthetic strategies described here should provide a basic blueprint for a series of self-assembling cyclic d,l-alpha-peptide nanotubes with interesting optical and electronic properties.

Self-Assembly and Molecular Recognition of a Luminescent Gold Rectangle

A luminescent molecular rectangle [Au(4)(micro-PAnP)(2)(micro-bipy)(2)](OTf)(4) (1.(OTf)(4)) (PAnP = 9,10-bis(diphenylphosphino)anthracene, bipy = 4,4'-bipyridine, X = NO(3)(-) or OTf(-)), synthesized from the self-assembly of the molecular "clip" Au(2)(micro-PAnP)(OTf)(2) and bipy, shows a large rectangular cavity of 7.921(3) x 16.76(3) A. The electronic absorption and emission spectroscopy, and electrochemistry of the metallacyclophane, have been studied. The 1(4+) ions are self-assembled into 2D mosaic in the solid state via complementary edge-to-face interactions between the Ph groups. (1)H NMR titrations ratify the 1:1 complexation between 1(4+) and various aromatic molecules. Comparing the structures of the inclusion complexes indicates an induced-fit mechanism operating in the binding. The emission of 1(4+) is quenched upon the guest binding. The binding constants are determined by both (1)H NMR and fluorescence titrations. Solvophobic and ion-dipole effects are shown to be important in stabilizing the inclusion complexes.

Bottom-up design of biomimetic assemblies

Nature has evolved the ability to assemble a variety of molecules into functional architectures that can specifically bind cellular ligands. Mimicking this strategy requires the design of a set of multifaceted molecules, where elements that direct assembly were conjugated to biologically specific components. The development of functional molecular building-blocks that assemble to form compartments for therapeutics addresses the desire to have controllable morphologies that interact with biological interfaces at nanometer length scales. The practical application of such 'bottom-up' assemblies requires the ability to predict the type of aggregated structure and to synthesize molecules in a highly controlled fashion. This bottom-up approach results in a molecular platform that mimics biological systems with potential for encapsulating and delivering drug molecules.

Efficient macrocyclization of U-turn preorganized peptidomimetics: the role of intramolecular H-bond and solvophobic effects

Simple peptidomimetic molecules derived from amino acids were reacted with meta- and para-bis(bromomethyl)benzene in acetonitrile to very efficiently yield macrocyclic structures. The cyclization reaction does not require high dilution techniques and seems to be insensitive to the size of the formed macrocycle. The analysis of data obtained by (1)H NMR, single-crystal X-ray diffraction, fluorescence measurements, and molecular mechanics indicate that folded conformations can preorganize the system for an efficient cyclization. The role played by intramolecular hydrogen-bonding and solvophobic effects in the presence of folded conformations is analyzed.

New cyclic peptide assemblies with hydrophobic cavities: the structural and thermodynamic basis of a new class of peptide nanotubes

A new class of self-assembling peptides based on cyclic peptides made of alternating 3-aminocyclohexanecarboxylic acid (gamma-Acc) and alpha-amino acids is described. The studied cylindrical assemblies are models for a new class of self-assembling peptide nanotubes (SPN) that present the particular property of having the C2 methylene group pointing toward the lumen of the cavity, modifying the properties of the inner surface of the assembly.

Specific control of peptide assembly with combined hydrophilic and hydrophobic interfaces

Designed coiled-coil heterotrimers are described whose assembly is governed by both hydrophobic and hydrophilic forces. Sterically matched hydrophobic core side-chain packing of alanine and cyclohexylalanine has been shown to promote formation of a 1:1:1 heterotrimer. Manipulation of hydrophilic glutamic acid (Glu)/lysine (Lys) pairs at each of three helical contact interfaces provides a secondary recognition mechanism. Peptides with matched cores and hydrophilic contacts form stable heterotrimers (DeltaG(unf) at 25 degrees C = 17.93 kcal/mol; MW(app) = 11362 vs 11563 calcd for trimer), as do those with a single Lys/Lys (but not Glu/Glu) interface. The additional specificity engendered by simultaneous operation of two interfaces was used to design a system in which six different peptides are mixed to form three specific and independent heterotrimers in the same solution.

Designing supramolecular protein assemblies

Many natural proteins self-assemble, either to fulfill their biological function or as part of a pathogenic process. Biological assembly phenomena such as amyloidogenesis, domain swapping and symmetric oligomerization are inspiring new strategies for designing proteins that self-assemble to form supramolecular complexes. Recent advances include the design of novel proteins that assemble into filaments, symmetric cages and regular arrays.