Templated Collagen "Double Helices" Maintain Their Structure

Heterotrimeric collagen helix with high specificity of assembly results in a rapid rate of folding

The most abundant natural collagens form heterotrimeric triple helices. Synthetic mimics of collagen heterotrimers have been found to fold slowly, even compared to the already slow rates of homotrimeric helices. These prolonged folding rates are not understood. Here we compare the stabilities, specificities and folding rates of three heterotrimeric collagen mimics designed through a computationally assisted approach. The crystal structure of one ABC-type heterotrimer verified a well-controlled composition and register and elucidated the geometry of pairwise cation-π and axial and lateral salt bridges in the assembly. This collagen heterotrimer folds much faster (hours versus days) than comparable, well-designed systems. Circular dichroism and NMR data suggest the folding is frustrated by unproductive, competing heterotrimer species and these species must unwind before refolding into the thermodynamically favoured assembly. The heterotrimeric collagen folding rate is inhibited by the introduction of preformed competing triple-helical assemblies, which suggests that slow heterotrimer folding kinetics are dominated by the frustration of the energy landscape caused by competing triple helices.

Synthetic Collagen Hydrogels through Symmetric Self-Assembly of Small Peptides

Animal-sourced hydrogels, such as collagen, are widely used as extracellular-matrix (ECM) mimics in tissue engineering but are plagued with problems of reproducibility, immunogenicity, and contamination. Synthetic, chemically defined hydrogels can avoid such issues. Despite the abundance of collagen in the ECM, synthetic collagen hydrogels are extremely rare due to design challenges brought on by the triple-helical structure of collagen. Sticky-ended symmetric self-assembly (SESSA) overcomes these challenges by maximizing interactions between the strands of the triple helix, allowing the assembly of collagen-mimetic peptides (CMPs) into robust synthetic collagen nanofibers. This optimization, however, also minimizes interfiber contacts. In this work, symmetric association states for the SESSA of short CMPs to probe their increased propensity for interfiber association are modelled. It is found that 33-residue CMPs not only self-assemble through sticky ends, but also form hydrogels. These self-assemblies behave with remarkable consistency across multiple scales and present a clear link between their triple-helical architecture and the properties of their hydrogels. The results show that SESSA is an effective and robust design methodology that enables the rational design of synthetic collagen hydrogels.

Controllable and Reversible Assembly of Nanofiber from Natural Macromolecules via Protonation and Deprotonation

Nanofiber is the critical building block for many biological systems to perform various functions. Artificial assembly of molecules into nanofibers in a controllable and reversible manner will create "smart" functions to mimic those of their natural analogues and fabricate new functional materials, but remains an open challenge especially for nature macromolecules. Herein, the controllable and reversible assembly of nanofiber (CSNF) from natural macromolecules with oppositely charged groups are successfully realized by protonation and deprotonation of charged groups. By controlling the electrostatic interaction via protonation and deprotonation, the size and morphology of the assembled nanostructures can be precisely controlled. A strong electrostatic interaction contributes to large nanofiber with high strength, while poor electrostatic interaction produces finer nanofiber or nanoparticle. And especially, the assembly, disassembly, and reassembly of the nanofiber occurs reversibly through protonation and deprotonation, thereby paving a new way for precisely controlling the assembly process and structure of nanofiber. The reversible assembly allows the nanostructure to dynamically reorganize in response to subtle perturbation of environment. The as-prepared CSNF is mechanical strong and can be used as a nano building block to fabricate high-strength film, wire, and straw. This study offers many opportunities for the biomimetic synthesis of new functional materials.

The Chemistry and Biology of Collagen Hybridization

Collagen provides mechanical and biological support for virtually all human tissues in the extracellular matrix (ECM). Its defining molecular structure, the triple-helix, could be damaged and denatured in disease and injuries. To probe collagen damage, the concept of collagen hybridization has been proposed, revised, and validated through a series of investigations reported as early as 1973: a collagen-mimicking peptide strand may form a hybrid triple-helix with the denatured chains of natural collagen but not the intact triple-helical collagen proteins, enabling assessment of proteolytic degradation or mechanical disruption to collagen within a tissue-of-interest. Here we describe the concept and development of collagen hybridization, summarize the decades of chemical investigations on rules underlying the collagen triple-helix folding, and discuss the growing biomedical evidence on collagen denaturation as a previously overlooked ECM signature for an array of conditions involving pathological tissue remodeling and mechanical injuries. Finally, we propose a series of emerging questions regarding the chemical and biological nature of collagen denaturation and highlight the diagnostic and therapeutic opportunities from its targeting.

Controllably Adjusting the Hydrophobicity of Collagen Fibers for Enhancing the Adsorption Rate, Retention Capacity, and Separation Performance of Flavonoid Aglycones

Collagen fibers (CFs) were previously used as packing materials for the separation of flavonoids based on hydrogen bond and hydrophobic interactions. However, as for flavonoid aglycones, CFs presented unsatisfactory adsorption capacity and separation efficiency due to the fact that they include limited hydroxyls and phenyls. In order to improve the adsorption capacity and separation efficiency, the hydrophobic modification strategy was employed in this research to enhance the hydrophobic interaction of CF with flavonoid aglycones by using silane coupling agents with different alkyl chains (isobutyl, octyl, and dodecyl). FT-IR analysis, DSC, TG, SEM, EDS mapping, water contact angle, and absorption time of solvent proved the successful grafting of alkyl chains on the CF without disturbing its special fiber structure, leading to the significantly enhanced hydrophobicity of the CF. The dynamic adsorption and elution behavior of kaempferol and quercetin (the typical flavonoid aglycones) on the hydrophobic CF showed that the adsorption rate and retention rate were largely increased in comparison with the CF without modification. Molecular dynamic simulations indicated that the CF grafted with isobutyls could interact with flavonoid aglycones through the highest synergetic effect of hydrophobic and hydrogen bond interactions, which exhibited the strongest retention to flavonoid aglycones. On further increasing the alkyl length (octyl and dodecyl), the hydrophobic interaction was further enhanced, but the hydrogen bonds were significantly weakened by steric hindrance, which showed that the retention to flavonoid aglycones was appropriately increased but without causing peak tailing. In the column separation of kaempferol and quercetin, the CF with hydrophobic modification presented a greater separation efficiency, with the purity of kaempferol increased from 71.99 to 86.57-97.50% and the purity of quercetin increased from 82.69 to 88.07-99.37%, which was much better than that of polyamide and close to that of sephadex LH 20. Therefore, the hydrophobicity of the CF could be controllably adjusted to enhance the adsorption rate and retention capacity, specifically improving the separation efficiency of flavonoid aglycones.

Controlling the Trimerization of the Collagen Triple-Helix by Solvent Switching

Collagen hybridizing peptides (CHPs) are a powerful tool for targeting collagen damage in pathological tissues due to their ability to specifically form a hybrid collagen triple-helix with the denatured collagen chains. However, CHPs have a strong tendency to self-trimerize, requiring preheating or complicated chemical modifications to dissociate their homotrimers into monomers, which hinders their applications. To control the self-assembly of CHP monomers, we evaluated the effects of 22 cosolvents on the triple-helix structure: unlike typical globular proteins, the CHP homotrimers (as well as the hybrid CHP-collagen triple helix) cannot be destabilized by the hydrophobic alcohols and detergents (e.g., SDS) but can be effectively dissociated by the cosolvents that dominate hydrogen bonds (e.g., urea, guanidinium salts, and hexafluoroisopropanol). Our study provided a reference for the solvent effects on natural collagen and a simple effective solvent-switch method, enabling CHP utilization in automated histopathology staining and in vivo imaging and targeting of collagen damage.

Hollow Octadecameric Self-Assembly of Collagen-like Peptides

The folding of collagen is a hierarchical process that starts with three peptides associating into the characteristic triple helical fold. Depending on the specific collagen in question, these triple helices then assemble into bundles reminiscent of α-helical coiled-coils. Unlike α-helices, however, the bundling of collagen triple helices is very poorly understood with almost no direct experimental data available. In order to shed light on this critical step of collagen hierarchical assembly, we have examined the collagenous region of complement component 1q. Thirteen synthetic peptides were prepared to dissect the critical regions allowing for its octadecameric self-assembly. We find that short peptides (under 40 amino acids) are able to self-assemble into specific (ABC)6 octadecamers. This requires the ABC heterotrimeric composition as the self-assembly subunit, but does not require disulfide bonds. Self-assembly into this octadecamer is aided by short noncollagenous sequences at the N-terminus, although they are not entirely required. The mechanism of self-assembly appears to begin with the very slow formation of the ABC heterotrimeric helix, followed by rapid bundling of triple helices into progressively larger oligomers, terminating in the formation of the (ABC)6 octadecamer. Cryo-electron microscopy reveals the (ABC)6 assembly as a remarkable, hollow, crown-like structure with an open channel approximately 18 Å at the narrow end and 30 Å at the wide end. This work helps to illuminate the structure and assembly mechanism of a critical protein in the innate immune system and lays the groundwork for the de novo design of higher order collagen mimetic peptide assemblies.

Inviting C5-Trifluoromethylated Pseudoprolines into Collagen Mimetic Peptides

Numerous collagen mimetic peptides (CMPs) have been engineered using proline derivatives substituted at their C(3) and/or C(4) position in order to stabilize or functionalize collagen triple-helix mimics. However, no example has been reported so far with C(5) substitutions. Here, we introduce a fluorinated CMP incorporating trifluoromethyl groups at the C(5) position of pseudoproline residues. In tripeptide models, our CD, NMR, and molecular dynamics (MD) studies have shown that, when properly arranged, these residues meet the structural requirements for a triple-helix assembly. Two host-guest CMPs were synthesized and analyzed by CD spectroscopy. The NMR analysis in solution of the most stable confirmed the presence of structured homotrimers that we interpret as triple helices. MD calculations showed that the triple-helix model remained stable throughout the simulation with all six trifluoromethyl groups pointing outward from the triple helix. Pseudoprolines substituted at the C(5) positions appeared as valuable tools for the design of new fluorinated collagen mimetic peptides.

Frame Shifts Affect the Stability of Collagen Triple Helices

Collagen model peptides (CMPs), composed of proline-(2S,4R)-hydroxyproline-glycine (POG) repeat units, have been extensively used to study the structure and stability of triple-helical collagen─the dominant structural protein in mammals─at the molecular level. Despite the more than 50-year history of CMPs and numerous studies on the relationship between the composition of single-stranded CMPs and the thermal stability of the assembled triple helices, little attention has been paid to the effects arising from their terminal residues. Here, we show that frame-shifted CMPs, which share POG repeat units but terminate with P, O, or G, form triple helices with vastly different thermal stabilities. A melting temperature difference as high as 16 °C was found for triple helices from 20-mers Ac-OG[POG]₆-NH₂ and Ac-[POG]₆PO-NH₂, and triple helices of the constitutional isomers Ac-[POG]₇-NH₂ and Ac-[GPO]₇-NH₂ melt 10 °C apart. A combination of thermal denaturation, circular dichroism and NMR spectroscopic studies, and molecular dynamics simulations revealed that the stability differences originate from the propensity of the peptide termini to preorganize into a polyproline-II helical structure. Our results advise that care must be taken when designing peptide mimics of structural proteins, as subtle changes in the terminal residues can significantly affect their properties. Our findings also provide a general and straightforward tool for tuning the stability of CMPs for applications as synthetic materials and biological probes.

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.

Rapid Production of Multifunctional Self-Assembling Peptides for Incorporation and Visualization within Hydrogel Biomaterials

Peptides are of continued interest for therapeutic applications, from soluble and immobilized ligands that promote desired binding or uptake to self-assembled supramolecular structures that serve as scaffolds in vitro and in vivo. These applications require efficient and scalable synthetic approaches because of the large amounts of material that often are needed for studies of bulk material properties and their translation. In this work, we establish new methods for the synthesis, purification, and visualization of assembling peptides, with a focus on multifunctional collagen mimetic peptides (mfCMPs) relevant for formation and integration within hydrogel-based biomaterials. First, a methodical approach useful for the microwave-assisted synthesis of assembling peptide sequences prone to deletions was established, beginning with the identification of the deleted residues and their locations and followed by targeted use of dual chemistry couplings for those specific residues. Second, purification techniques that integrate the principles of heating and ion displacement with traditional chromatography and dialysis were implemented to improve separation and isolation of the desired multifunctional peptide product, which contained blocks for thermoresponsiveness and ionic interactions. Third, an approach for fluorescent labeling of these mfCMPs, which is orthogonal to their assembly and their covalent incorporation into a bulk hydrogel material, was established, allowing visualization of the resulting hierarchical fibrillar structures in three dimensions within hydrogels using confocal microscopy. The methods presented in this work allow the production of multifunctional peptides in scalable quantities and with minimal deletions, enabling future studies for better understanding of composition-structure-property relationships and for translating these biomaterials into a range of applications. Although mfCMPs are the focus of this work, the methods demonstrated could prove useful for other assembling peptide systems and for the production of peptides more broadly for therapeutic applications.

Infrared harmonic features of collagen models at B3LYP-D3: From amide bands to the THz region

In this paper, we have studied the vibrational spectral features for the collagen triple helix using a dispersion corrected hybrid density functional theory (DFT-D) approach. The protein is simulated by an infinite extended polymer both in the gas phase and in a water micro-solvated environment. We have adopted proline-rich collagen models in line with the high content of proline in natural collagens. Our scaled harmonic vibrational spectra are in very good agreement with the experiments and allow for the peak assignment of the collagen amide I and III bands, supporting or questioning the experimental interpretation by means of vibrational normal modes analysis. Furthermore, we demonstrated that IR spectroscopy in the THz region can detect the small variations inherent to the triple helix helicity (10/3 over 7/2), thus elucidating the packing state of the collagen. So far, identifying the collagen helicity is only possible by means of crystal x-ray diffraction.

Insertion of Pro-Hyp-Gly provides 2 kcal mol-1 stability but attenuates the specific assembly of ABC heterotrimeric collagen triple helices

Collagen is a major structural component of the extracellular matrix and connective tissue. The key structural feature of collagen is the collagen triple helix, with a Xaa-Yaa-Gly (glycine) repeating pattern. The most frequently occurring triplet is Pro (proline)-Hyp (hydroxyproline)-Gly. The reversible thermal folding and unfolding of a series of heterotrimeric collagen triple helices with varying number of Pro-Hyp-Gly triplets were monitored by circular dichroism spectroscopy to determine the unfolding thermodynamic parameters Tm (midpoint transition temperature), ΔHTm (unfolding enthalpy), and ΔGunfold (unfolding free energy). The Tm and ΔGunfold of the heterotrimeric collagen triple helices increased with increasing number of Pro-Hyp-Gly triplets. The ΔGunfold increased by 2.0 ± 0.2 kcal mol-1 upon inserting one Pro-Hyp-Gly triplet into all three chains. The Tm difference between the most stable ABC combination and the second most stable BCC combination decreased with increasing number of Pro-Hyp-Gly triplets, even though the ΔGunfold difference remained the same. These results should be useful for tuning the stability of collagen triple helical peptides for hydrogel formation, recognition of denatured collagen triple helices as diagnostics and therapeutics, and targeted drug delivery.

Role for Cell-Surface Collagen of Streptococcus pyogenes in Infections

Group A Streptococcus (GAS) displays cell-surface proteins that resemble human collagen. We find that a fluorophore-labeled collagen mimetic peptide (CMP) labels GAS cells but not Escherichia coli or Bacillus subtilis cells, which lack such proteins. The CMP likely engages in a heterotrimeric helix with endogenous collagen, as the nonnatural d enantiomer of the CMP does not label GAS cells. To identify a molecular target, we used reverse genetics to "knock-in" the GAS genes that encode two proteins with collagen-like domains, Scl1 and Scl2, into B. subtilis. The fluorescent CMP labels the cells of these B. subtilis strains. Moreover, these strains bind tightly to a surface of mammalian collagen. These data are consistent with streptococcal collagen forming triple helices with damaged collagen in a wound bed and thus have implications for microbial virulence.

Cyclic Peptide Mimetic of Damaged Collagen

Collagen is the most abundant protein in humans and the major component of human skin. Collagen mimetic peptides (CMPs) can anneal to damaged collagen in vitro and in vivo. A duplex of CMPs was envisioned as a macromolecular mimic for damaged collagen. The duplex was synthesized on a solid support from the amino groups of a lysine residue and by using olefin metathesis to link the N termini. The resulting cyclic peptide, which is a monomer in solution, binds to CMPs to form a triple helix. Among these, CMPs that are engineered to avoid the formation of homotrimers but preorganized to adopt the conformation of a collagen strand exhibit enhanced association. Thus, this cyclic peptide enables the assessment of CMPs for utility in annealing to damaged collagen. Such CMPs have potential use in the diagnosis and treatment of fibrotic diseases and wounds.