Functionalizable Collagen Model Peptides

Proline Analogues

Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.

Carbohydrate Co-Solutes Stabilize Collagen Triple Helices

Carbohydrates are common co-solutes for the stabilization of proteins. The effect of carbohydrate solutions on the stability of collagen, the most abundant protein in mammals, is, however, underexplored. In this work, we studied the thermal stability of collagen triple helices derived from a molecularly defined collagen model peptide (CMP), Ac-(Pro-Hyp-Gly)7 -NH2 , in solutions of six common mono- and disaccharides. We show that the carbohydrates stabilize the collagen triple helix in a concentration-dependent manner, with an increase of the melting temperature of up to 17 °C. In addition, we show that the stabilizing effect is similar for all studied sugars, including trehalose, which is otherwise considered a privileged bioprotectant. The results provided insight into the effects of sugar co-solutes on collagen triple helices and can aid the selection of storage environments for collagen-based materials and probes.

Substitution Effects of Alkene Dipeptide Isosteres on Adjacent Peptide Bond Rotation

Alkene dipeptide isosteres (ADIs) are promising surrogates of peptide bonds that enhance the bioactive peptide resistance to enzymatic hydrolysis in medicinal chemistry. In this study, we investigated the substitution effects of an ADI on the energy barrier of cis-trans isomerization in the acetyl proline methyl ester (Ac-Pro-OMe) model. The (E)-alkene-type proline analog, which favors a cis-amide conformation, exhibits a lower rotational barrier than native Ac-Pro-OMe. A van't Hoff analysis suggests that the energy barrier is primarily reduced by enthalpic repulsion. It was concluded that although carbon-carbon double bonds and pyrrolidine rings individually increase the rigidity of the incorporation site, their combination can provide structural flexibility and disrupt bioactive conformations. This work provides new insights into ADI-based drug design.

Cis-trans isomerization of peptoid residues in the collagen triple-helix

Cis-peptide bonds are rare in proteins, and building blocks less favorable to the trans-conformer have been considered destabilizing. Although proline tolerates the cis-conformer modestly among all amino acids, for collagen, the most prevalent proline-abundant protein, all peptide bonds must be trans to form its hallmark triple-helix structure. Here, using host-guest collagen mimetic peptides (CMPs), we discover that surprisingly, even the cis-enforcing peptoid residues (N-substituted glycines) form stable triple-helices. Our interrogations establish that these peptoid residues entropically stabilize the triple-helix by pre-organizing individual peptides into a polyproline-II helix. Moreover, noting that the cis-demanding peptoid residues drastically reduce the folding rate, we design a CMP whose triple-helix formation can be controlled by peptoid cis-trans isomerization, enabling direct targeting of fibrotic remodeling in myocardial infarction in vivo. These findings elucidate the principles of peptoid cis-trans isomerization in protein folding and showcase the exploitation of cis-amide-favoring residues in building programmable and functional peptidomimetics.

Stabilization of Synthetic Collagen Triple Helices: Charge Pairs and Covalent Capture

Collagen mimetic peptides are composed of triple helices. Triple helical formation frequently utilizes charge pair interactions to direct protein assembly. The design of synthetic triple helices is challenging due to the large number of competing species and the overall fragile nature of collagen mimetics. A successfully designed triple helix incorporates both positive and negative criteria to achieve maximum specificity of the supramolecular assembly. Intrahelical charge pair interactions, particularly those involved in lysine-aspartate and lysine-glutamate pairs, have been especially successful both in driving helix specificity and for subsequent stabilization by covalent capture. Despite this progress, the important sequential and geometric relationships of charged residues in a triple helical context have not been fully explored for either supramolecular assembly or covalent capture stabilization. In this study, we compare the eight canonical axial and lateral charge pairs of lysine and arginine with glutamate and aspartate to their noncanonical, reversed charge pairs. These findings are put into the context of collagen triple helical design and synthesis.

Isonitrile-Proline - A Versatile Handle for the Chemoselective Derivatization of Collagen Peptides

Functional groups that allow for chemoselective and bioorthogonal derivatization are valuable tools for the labelling of peptides and proteins. The isonitrile is such a group but synthetic methods for its incorporation into peptides by solid-phase peptide synthesis are not known. Here, we introduce (4S)- and (4R)-isonitrileproline (Inp) as building blocks for solid-phase peptide synthesis. Conformational studies of (4S)- and (4R)-Inp and thermal stability analysis of Inp-containing collagen triple helices revealed that the isonitrile group exerts a stereoelectronic gauche effect. We showcase the value of Inp for bioorthogonal labelling by derivatization of Inp-containing collagen model peptides (CMPs). Dual labelling with a pair of bioorthogonal reactions of a CMP containing Inp and azidoproline residues further highlights the versatility of the new isonitrile-containing amino acids.

Unveiling extracellular matrix assembly: Insights and approaches through bioorthogonal chemistry

Visualizing cells, tissues, and their components specifically without interference with cellular functions, such as biochemical reactions, and cellular viability remains important for biomedical researchers worldwide. For an improved understanding of disease progression, tissue formation during development, and tissue regeneration, labeling extracellular matrix (ECM) components secreted by cells persists is required. Bioorthogonal chemistry approaches offer solutions to visualizing and labeling ECM constituents without interfering with other chemical or biological events. Although biorthogonal chemistry has been studied extensively for several applications, this review summarizes the recent advancements in using biorthogonal chemistry specifically for metabolic labeling and visualization of ECM proteins and glycosaminoglycans that are secreted by cells and living tissues. Challenges, limitations, and future directions surrounding biorthogonal chemistry involved in the labeling of ECM components are discussed. Finally, potential solutions for improvements to biorthogonal chemical approaches are suggested. This would provide theoretical guidance for labeling and visualization of de novo proteins and polysaccharides present in ECM that are cell-secreted for example during tissue remodeling or in vitro differentiation of stem cells.

N-Aminoglycine and Its Derivatives Stabilize PPII Secondary Structure

The identification of unnatural residues that stabilize polyproline type 2 (PPII) folds can aid in the design of peptidomimetics targeting PPII-binding domains. Here, we examine the impact of peptide backbone N-amination on PPII helix stability and find N-aminoglycine (aGly) to be an effective PPII promoter. Further derivatization of an aGly-containing peptide affords N'-alkylated analogues with increased helical propensity. Backbone N-amination of glycine represents a convenient approach to stabilize PPII conformation and allows for the diversity-oriented synthesis of optimally constrained folds.

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.

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.

Predicting Collagen Triple Helix Stability through Additive Effects of Terminal Residues and Caps

Collagen model peptides (CMPs) consisting of proline-(2S,4R)-hydroxyproline-glycine (POG) repeats have provided a breadth of knowledge of the triple helical structure of collagen, the most abundant protein in mammals. Predictive tools for triple helix stability have, however, lagged behind since the effect of CMPs with different frames ([POG]_n , [OGP]_n , or [GPO]_n ) and capped or uncapped termini have so far been underestimated. Here, we elucidated the impact of the frame, terminal functional group and its charge on the stability of collagen triple helices. Combined experimental and theoretical studies with frame-shifted, capped and uncapped CMPs revealed that electrostatic interactions, strand preorganization, interstrand H-bonding, and steric repulsion at the termini contribute to triple helix stability. We show that these individual contributions are additive and allow for the prediction of the melting temperatures of CMP trimers.

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.

Time-Resolved Atomistic Imaging and Statistical Analysis of Daptomycin Oligomers with and without Calcium Ions

Daptomycin (DP) is effective against multiple drug-resistant Gram-positive pathogens because of its distinct mechanism of action. An accepted mechanism includes Ca²⁺-triggered aggregation of the DP molecule to form oligomers. DP and its oligomers have so far defied structural analysis at a molecular level. We studied the ability of DP molecule to aggregate by itself in water, the effects of Ca²⁺ ions to promote the aggregation, and the connectivity of the DP molecules in the oligomers by the combined use of dynamic light scattering in water and atomic-resolution cinematographic imaging of DP molecules captured on a carbon nanotube on which the DP molecule is installed as a fishhook. We found that the DP molecule aggregates weakly into dimers, trimers, and tetramers in water, and strongly in the presence of calcium ions, and that the tetramer is the largest oligomer in homogeneous aqueous solution. The dimer remains as the major species, and we propose a face-to-face stacked structure based on dynamic imaging using millisecond and angstrom resolution transmission electron microscopy. The tetramer in its cyclic form is the largest oligomer observed, while the trimer forms in its linear form. The study has shown that the DP molecule has an intrinsic property of forming tetramers in water, which is enhanced by the presence of calcium ions. Such experimental structural information will serve as a platform for future drug design. The data also illustrate the utility of cinematographic recording for the study of self-organization processes.

Peptoid Residues Make Diverse, Hyperstable Collagen Triple-Helices

As the only ribosomally encoded N-substituted amino acid, proline promotes distinct secondary protein structures. The high proline content in collagen, the most abundant protein in the human body, is crucial to forming its hallmark structure: the triple-helix. For over five decades, proline has been considered compulsory for synthetic designs aimed at recapitulating collagen's structure and properties. Here we describe that N-substituted glycines (N-glys), also known as peptoid residues, exhibit a general triple-helical propensity similar to or greater than proline, enabling synthesis of stable triple-helical collagen mimetic peptides (CMPs) with unprecedented side chain diversity. Supported by atomic-resolution crystal structures as well as circular dichroism and computational characterizations spanning over 30 N-gly-containing CMPs, we discovered that N-glys stabilize the triple-helix primarily by sterically preorganizing individual chains into the polyproline-II helix. We demonstrated that N-glys with exotic side chains including a "click"-able alkyne and a photosensitive side chain enable CMPs for functional applications including the spatiotemporal control of cell adhesion and migration. The structural principles uncovered in this study open up opportunities for a new generation of collagen-mimetic therapeutics and materials.

A Proline Mimetic for the Design of New Stable Secondary Structures: Solvent-Dependent Amide Bond Isomerization of (S)-Indoline-2-carboxylic Acid Derivatives

A thorough experimental and computational study on the conformational properties of (S)-indoline-2-carboxylic acid derivatives has been conducted. Methyl (S)-1-acetylindoline-2-carboxylate, both a mimetic of proline and phenylalanine, shows a remarkable tendency toward the cis amide isomer when dissolved in polar solvents. This behavior is opposite to the general preference of proline for the trans isomer, making indoline-2-carboxylic acid a good candidate for the design of different secondary structures and new materials.

Biocasting of an elastin-like recombinamer and collagen bi-layered model of the tunica adventitia and external elastic lamina of the vascular wall

The development of techniques for fabricating vascular wall models will foster the development of preventive and therapeutic therapies for treating cardiovascular diseases. However, the physical and biological complexity of vascular tissue represents a major challenge, especially for the design and the production of off-the-shelf biomimetic vascular replicas. Herein, we report the development of a biocasting technique that can be used to replicate the tunica adventitia and the external elastic lamina of the vascular wall. Type I collagen embedded with neonatal human dermal fibroblast (HDFn) and an elastic click cross-linkable, cell-adhesive and protease-sensitive elastin-like recombinamer (ELR) hydrogel were investigated as readily accessible and tunable layers to the envisaged model. Mechanical characterization confirmed that the viscous and elastic attributes predominated in the collagen and ELR layers, respectively. In vitro maturation confirmed that the collagen and ELR provided a favorable environment for the HDFn viability, while histology revealed the wavy and homogenous morphology of the ELR and collagen layer respectively, the cell polarization towards the cell-attachment sites encoded on the ELR, and the enhanced expression of glycosaminoglycan-rich extracellular matrix and differentiation of the embedded HDFn into myofibroblasts. As a complementary assay, 30% by weight of the collagen layer was substituted with the ELR. This model proved the possibility to tune the composition and confirm the versatile character of the technology developed, while revealing no significant differences with respect to the original construct. On-demand modification of the model dimensions, number and composition of the layers, as well as the type and density of the seeded cells, can be further envisioned, thus suggesting that this bi-layered model may be a promising platform for the fabrication of biomimetic vascular wall models.

Influence of Lipidation on the Folding and Stability of Collagen Triple Helices-An Experimental and Theoretical Study

The folding of triple-helical collagen, the most abundant protein in nature, relies on the nucleation and propagation along the strands. Hydrophobic moieties are crucial for the folding and stability of numerous proteins. Instead, nature uses for collagen a trimerization domain and cis-trans prolyl isomerases to facilitate and accelerate triple helix formation. Yet, pendant hydrophobic moieties endow triple-helical collagen with hyperstability and accelerate the cis-trans isomerization to an extent that thermally induced unfolding and folding of collagen triple helices take place at the same speed. Here, we systematically explored the effect of pendant fatty acids on the folding and stability of collagen triple helices. Thermal denaturation and kinetic studies with a series of collagen mimetic peptides (CMPs) bearing saturated and unsaturated fatty acids with different lengths revealed that longer and more flexible fatty acid appendages increase the stability and the folding rate of collagen triple helices. Molecular dynamics simulations combined with experimental data indicate that the hydrophobic appendages stabilize the triple helix by interaction with the grooves of the collagen triple helix and accelerate the folding and unfolding process by creating a molten globule-like intermediate.

Triple-Helix-Stabilizing Effects in Collagen Model Peptides Containing PPII-Helix-Preorganized Diproline Modules

Collagen model peptides (CMPs) serve as tools for understanding stability and function of the collagen triple helix and have a potential for biomedical applications. In the past, interstrand cross-linking or conformational preconditioning of proline units through stereoelectronic effects have been utilized in the design of stabilized CMPs. To further study the effects determining collagen triple helix stability we investigated a series of CMPs containing synthetic diproline-mimicking modules (ProMs), which were preorganized in a PPII-helix-type conformation by a functionalizable intrastrand C2 bridge. Results of CD-based denaturation studies were correlated with calculated (DFT) conformational preferences of the ProM units, revealing that the relative helix stability is mainly governed by an interplay of main-chain preorganization, ring-flip preference, adaptability, and steric effects. Triple helix integrity was proven by crystal structure analysis and binding to HSP47.

Studying biomolecular folding and binding using temperature-jump mass spectrometry

Characterizing folding and complex formation of biomolecules provides a view into their thermodynamics, kinetics and folding pathways. Deciphering kinetic intermediates is particularly important because they can often be targeted by drugs. The key advantage of native mass spectrometry over conventional methods that monitor a single observable is its ability to identify and quantify coexisting species. Here, we show the design of a temperature-jump electrospray source for mass spectrometry that allows one to perform fast kinetics experiments (0.16-32 s) at different temperatures (10-90 °C). The setup allows recording of both folding and unfolding kinetics by using temperature jumps from high to low, and low to high, temperatures. Six biological systems, ranging from peptides to proteins to DNA complexes, exemplify the use of this device. Using temperature-dependent experiments, the folding and unfolding of a DNA triplex are studied, providing detailed information on its thermodynamics and kinetics.

Photo-responsive azobenzene interactions promote hierarchical self-assembly of collagen triple-helical peptides to various higher-order structures

Collagen is an essential structural protein in animal tissues and plays key roles in cellular modulation. We investigated methods to discover collagen model peptides (CMPs) that would self-assemble into triple helices and then grow into supramolecular organizations with diverse morphological features, which would be valuable as biomaterials. This challenging undertaking was achieved by placing azobenzene groups on the ends of the CMPs, (GPO)_n (n = 3–10), Azo-(GPO)_n. In a dilute aqueous solution (80 μM), CD spectra indicated that the Azo-(GPO)_n (n > 4) formed triple helices due to strong hydrophobic azobenzene interactions, and that helix stability was increased with the peptide segment length. The resulting triple helices induced a specific azobenzene orientation through turned and twisted configurations as shown by CD spectra. TEM observations for the same solutions disclosed the morphologies for the Azo-CMPs. Azo-(GPO)₃, having the shortest peptide segment, showed no nanostructure, both Azo-(GPO)₄ and Azo-(GPO)₅ provided consistent well-developed nanofiber structures resembling the natural collagen fibers, and Azo-(GPO)_ns (n = 6–10) grew into flexible rod-like micelle fibers. In addition, alkyl chain-attached C_mAzo-(GPO)₅ displayed a toroidal morphology, and Azp-deg-(GPO)₅ having a hydrophilic spacer assembled into a bilayer vesicle structure. These diverse morphological features are considered to be due to the characteristics of the pre-organized triple helix units. Photo-isomerization of the azobenzene moiety brought about the disappearance of such characteristic nano-architectures. When the solution concentration was increased up to 1 wt%, only Azo-(GPO)₄ and Azo-(GPO)₅ spontaneously formed hydrogels exhibiting a satisfactory gel-to-sol transition upon UV irradiation.

Collagen is an essential structural protein in animal tissues and plays key roles in cellular modulation.

Temperature-controlled electrospray ionization mass spectrometry as a tool to study collagen homo- and heterotrimers

Collagen model peptides are useful for understanding the assembly and structure of collagen triple helices. The design of self-assembling heterotrimeric helices is particularly challenging and often affords mixtures of non-covalent assemblies that are difficult to characterize by conventional NMR and CD spectroscopic techniques. This can render a detailed understanding of the factors that control heterotrimer formation difficult and restrict rational design. Here, we present a novel method based on electrospray ionization mass spectrometry to investigate homo- and heterotrimeric collagen model peptides. Under native conditions, the high resolving power of mass spectrometry was used to access the stoichiometric composition of different triple helices in complex mixtures. A temperature-controlled electrospray ionization source was built to perform thermal denaturation experiments and provided melting temperatures of triple helices. These were found to be in good agreement with values obtained from CD spectroscopic measurements. Importantly, for mixtures of coexisting homo- and heterotrimers, which are difficult to analyze by conventional methods, our technique allowed for the identification and monitoring of the unfolding of each individual species. Their respective melting temperatures could easily be accessed in a single experiment, using small amounts of sample.

Reversible Covalent End-Capping of Collagen Model Peptides

The combination of supramolecular aggregation of collagen model peptides with reversible covalent end‐capping of the formed triple helix in a single experimental set‐up yielded minicollagens, which were characterized by a single melting temperature. In spite of the numerous possible reaction intermediates, a specific synthetic collagen with a leading, middle and trailing strand is formed in a highly cooperative self‐assembly process.

A self-assembly and higher order structure forming triple helical protein as a novel biomaterial for cell proliferation

Collagen plays a critical role in the structural design of the extracellular matrix (ECM) and cell signaling in mammals, which makes it one of the most promising biomaterials with versatile applications. However, there is considerable concern regarding the purity and predictability of the product performance. At present, it is mainly derived as a mixture of collagen (different types) from animal tissues, where the selective enrichment of a particular type of collagen is generally difficult and expensive. Collagen derived from bovine sources poses the risk of transmitting diseases and can cause adverse immunologic and inflammatory responses. Hence, recombinant collagen can be a good alternative. Nevertheless, the necessity of post-translational hydroxyproline (Hyp) modification limits large-scale recombinant collagen production. Here, we recombinantly expressed the collagen-like protein (CLTP) and genetically introduced the Hyp in the CLTP to form a higher order self-assembled fibril structure, similar to human collagen. During the current study, it was observed that the Hyp incorporated CLTP protein (CLTHP) formed a stable triple helical polyproline-II like structure and self-assembled to form fibrils at neutral pH, which had an initial lag phase followed by a growth phase similar to animal collagen. In contrast, the higher order fibrillar assembly was missing in the nonhydroxylated CLTP. This study demonstrated that CLTHP self-association is based on the common underlying lateral interactions between triple helical structured proteins, where the hydroxyproline forms the significantly stable hydration network. Hence, this work will be the first fundamental empirical research for flexible modifications of recombinant collagen for structural analysis and biomedical applications.

Promotion of the collagen triple helix in a hydrophobic environment

The collagen triple helix is better suited for octanol than for water.

Isolated Collagen Mimetic Peptide Assemblies Have Stable Triple-Helix Structures

The origin of the triple-helix structure and high stability of collagen has been debated for many years. As models of the triple helix and building blocks for new biomaterials, collagen mimetic peptide (CMP) assemblies have been deeply studied in the condensed phase. In particular, it was found that hydroxylation of proline, an abundant post-translational modification in collagen, increases its stability. Two main hypotheses emerged to account for this behavior: 1) intra-helix stereoelectronic effects, and 2) the role of water molecules H-bound to hydroxyproline side-chains. However, in condensed-phase investigations, the influence of water cannot be fully removed. Therefore, we employed a combination of tandem ion mobility and mass spectrometries to assess the structure and stability of CMP assemblies in the gas phase. These results show a conservation of the structure and stability properties of triple helix models in the absence of solvent, supporting an important role of stereoelectronic effects. Moreover, evidence that small triple helix assemblies with controlled stoichiometry can be studied in the gas phase is given, which opens new perspectives in the understanding of the first steps of collagen fiber growth.

Mannoside and 1,2-mannobioside β-cyclodextrin-scaffolded NO-photodonors for targeting antibiotic resistant bacteria

Two β-cyclodextrin derivatives randomly appended on the primary face with both the nitric oxide (NO) photodonor 4-nitro-3-(trifluoromethyl)aniline and a mannose or α(1→2)mannobioside residue are reported to construct targeted NO photoreleasing nanocarriers. 2D ROESY and PGSE NMR suggested supramolecular homodimerization in water by inclusion of the nitroaniline group into the facing macrocycle cavities. Isothermal titration calorimetry on their concanavalin A lectin binding showed an exothermic binding event to the lectin and an endothermic process during the dilution of the conjugates. Both α(1→2)mannobioside and the nitroaniline moieties significantly enhanced the binding to the lectin. These effects might arise from a better fit within the carbohydrate-recognition site in the former case and a multivalent effect caused by homodimerization in the latter. Direct detection of NO by amperometric technique shows that both β-cyclodextrin derivatives release this radical upon excitation with visible light with higher efficiency than the unfunctionalized NO photodonor.

Conformation Analysis of GalNAc-Appended Sugar Amino Acid Foldamers as Glycopeptide Mimics

Sugar amino acid (SAA)-based foldamers with well-defined secondary structures were appended with N-acetylgalactosamine (GalNAc) sugars to access sequence-defined, multidentate glycoconjugates with full control over number, spacing and position. Conformation analysis of these glycopeptides by extensive NMR spectroscopic studies revealed that the appended GalNAc units had a profound influence on the native conformational behaviour of the SAA foldamers. Whereas the 2,5-cis glycoconjugate showed a helical structure in water, comprising of two consecutive 16-membered hydrogen bonds, its 2,5-trans congener displayed an unprecedented 16/10-mixed turn structure not seen before in any glycopeptide foldamer.

Direct/Reversible Amidation of Troponyl Alkylglycinates via Cationic Troponyl Lactones and Mechanistic Insights

The conversion of troponyl alkylglycinate acid/ester/amide derivatives (Trag acid/ester/amide) into cationic troponyl lactones (CTLs) in the presence of trifluoroacetic acid and their amidation with amines is described. The reversible amidation of Trag amides, that is, the cleavage and reformation of the Trag amide bond via CTLs is demonstrated. The direct amidation of Trag esters with the amino group of amino acid esters/peptide esters via CTLs is achieved. The direct amidation of the amine group of hydroxyl amino acid esters is selective over esterification. The Trag amide bond is stable under basic ester hydrolysis and Fmoc removal conditions. Hence, the troponyl alkylglycinates could be applicable as protecting groups for amine functionality of amino acids and peptides. The reaction mechanism was investigated by using a deuterium probe and studied by NMR and electrospray ionisation mass spectrometry techniques. Deuterium incorporation at α-CH₂ strongly supported the formation of CTLs via ketene intermediates.

Modeling Glyco-Collagen Conjugates Using a Host-Guest Strategy To Alter Phenotypic Cell Migration and in Vivo Wound Healing

The constructs and study of combinatorial libraries of structurally defined homologous extracellular matrix (ECM) glycopeptides can significantly accelerate the identification of cell surface markers involved in a variety of physiological and pathological processes. Herein, we present a simple and reliable host-guest approach to design a high-throughput glyco-collagen library to modulate the primary and secondary cell line migration process. 4-Amidoadamantyl-substituted collagen peptides and β-cyclodextrin appended with mono- or disaccharides were used to construct self-assembled glyco-collagen conjugates (GCCs), which were found to be thermally stable, with triple-helix structures and nanoneedles-like morphologies that altered cell migration processes. We also investigated the glycopeptide's mechanisms of action, which included interactions with integrins and cell signaling kinases. Finally, we report murine wound models to demonstrate the real-time application of GCCs. As a result of our observations, we claim that the host-guest model of ECM glycopeptides offers an effective tool to expedite identification of specific glycopeptides to manipulate cell morphogenesis, cell differentiation metastatic processes, and their biomedical applications.

Cross-Linked Collagen Triple Helices by Oxime Ligation

Covalent cross-links are crucial for the folding and stability of triple-helical collagen, the most abundant protein in nature. Cross-linking is also an attractive strategy for the development of synthetic collagen-based biocompatible materials. Nature uses interchain disulfide bridges to stabilize collagen trimers. However, their implementation into synthetic collagen is difficult and requires the replacement of the canonical amino acids (4R)-hydroxyproline and proline by cysteine or homocysteine, which reduces the preorganization and thereby stability of collagen triple helices. We therefore explored alternative covalent cross-links that allow for connecting triple-helical collagen via proline residues. Here, we present collagen model peptides that are cross-linked by oxime bonds between 4-aminooxyproline (Aop) and 4-oxoacetamidoproline placed in coplanar Xaa and Yaa positions of neighboring strands. The covalently connected strands folded into hyperstable collagen triple helices (T_m ≈ 80 °C). The design of the cross-links was guided by an analysis of the conformational properties of Aop, studies on the stability and functionalization of Aop-containing collagen triple helices, and molecular dynamics simulations. The studies also show that the aminooxy group exerts a stereoelectronic effect comparable to fluorine and introduce oxime ligation as a tool for the functionalization of synthetic collagen.

The n→π* Interaction

The carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group. Mixing of these orbitals releases energy, resulting in an attractive interaction. Hints of such interactions were evident in small-molecule crystal structures as early as the 1970s, but not until 2001 was the role of such interactions articulated clearly. These non-covalent interactions were first discovered during investigations into the thermostability of the proline-rich protein collagen, which achieves a robust structure despite a relatively low potential for hydrogen bonding. It was found that by modulating the distance between two carbonyl groups in the peptide backbone, one could alter the conformational preferences of a peptide bond to proline. Specifically, only the trans conformation of a peptide bond to proline allows for an attractive interaction with an adjacent carbonyl group, so when one increases the proximity of the two carbonyl groups, one enhances their interaction and promotes the trans conformation of the peptide bond, which increases the thermostability of collagen. More recently, attention has been paid to the nature of these interactions. Some have argued that rather than resulting from electron donation, carbonyl interactions are a particular example of dipolar interactions that are well-approximated by classical mechanics. However, experimental evidence has demonstrated otherwise. Numerous examples now exist where an increase in the dipole moment of a carbonyl group decreases the strength of its interactions with other carbonyl groups, demonstrating unequivocally that a dipolar mechanism is insufficient to describe these interactions. Rather, these interactions have important quantum-mechanical character that can be evaluated through careful experimental analysis and judicious use of computation. Although individual n→π* interactions are relatively weak (∼0.3-0.7 kcal/mol), the ubiquity of carbonyl groups across chemistry and biology gives the n→π* interaction broad impact. In particular, the n→π* interaction is likely to play an important role in dictating protein structure. Indeed, bioinformatics analysis suggests that approximately one-third of residues in folded proteins satisfy the geometric requirements to engage in an n→π* interaction, which is likely to be of particular importance for the α-helix. Other carbonyl-dense polymeric materials like polyesters and peptoids are also influenced by n→π* interactions, as are a variety of small molecules, some with particular medicinal importance. Research will continue to identify molecules whose conformation and activity are affected by the n→π* interaction and will clarify their specific contributions to the structures of biomacromolecules.

The effects of thioamide backbone substitution on protein stability: a study in α-helical, β-sheet, and polyproline II helical contexts

Thioamides are single atom substitutions of the peptide bond that serve as versatile probes of protein structure. Effective use of thioamides requires a robust understanding of the impact that the substitution has on a protein of interest. However, the thermodynamic effects of thioamide incorporation have only been studied in small structural motifs, and their influence on secondary structure in the context of full-length proteins is not known. Here we describe a comprehensive survey of thioamide substitutions in three benchmark protein systems (calmodulin, the B1 domain of protein G, and collagen) featuring the most prevalent secondary structure motifs: α-helix, β-sheet, and polyproline type II helix. We find that in most cases, effects on thermostability can be understood in terms of the positioning and local environment of the thioamide relative to proximal structural elements and hydrogen bonding networks. These observations set the stage for the rational design of thioamide substituted proteins with predictable stabilities.

Effect of N- and C-terminal functional groups on the stability of collagen triple helices

The effect of chargedversusneutral N- and C-termini on the stability of the collagen triple helix was examined.

Incorporation of ‘click’ chemistry glycomimetics dramatically alters triple-helix stability in an adiponectin model peptide

A striking decrease in thermal stability was observed upon incorporation of triazole-linked galactosylated-lysine into an adiponectin model peptide, suggesting possible applications of ‘click’ glycomimetics in bioengineering.

Chemical Synthesis of Peptides Containing Site-Specific Advanced Glycation Endproducts

In nature, proteins, lipids, and nucleic acids can nonenzymatically react with sugars and sugar degradation products to give rise to a diverse range of modifications, known as advanced glycation endproducts (AGEs). These AGEs typically occur at lysine and arginine residues of long-lived proteins, such as collagen, and can modify the structure and function of the native protein. AGEs accumulate during the normal aging process, and AGE formation is dramatically accelerated with diabetes. AGEs have also been implicated in a wide range of debilitating conditions including cardiovascular, renal failure, and neurodegenerative diseases. Thus, there is an ongoing interest in studying the role of AGEs in different aspects of these disorders. Typically, glycated proteins are prepared using nonspecific in vitro incubation techniques. However, this method results in a complex mixture of products which is then employed without further purification. In order to determine the effect of individual AGEs in a peptide sequence, in this Account, we highlight our synthetic methods for site-specifically introducing five frequently occurring AGEs, namely, N^ε-(carboxymethyl)lysine (CML), N^ε-(carboxyethyl)lysine (CEL), pyrraline, glyoxal-lysine dimer (GOLD), and methylglyoxal-lysine dimer (MOLD) into collagen peptides. Both a collagen model peptide (CMP) and the telopeptide region of human type I α1 collagen (CTP) were chosen due to being prone to glycation and cross-linking in vivo. For the preparation of the AGE-modified collagen peptides, we investigated both the initial preparation of AGE building blocks in solution followed by incorporation into Fmoc-SPPS, as well as an on-resin method whereby AGEs were selectively introduced by modification of the side-chain of an unprotected resin-bound lysine. Both of our synthetic methods enabled the site-specifically modified AGE-containing collagen peptides to be obtained in high purity and yield. In addition, the on-resin method had the added advantage of requiring fewer synthetic steps. We then evaluated the impact of the specific AGEs on the properties of the native protein and found that the AGE modifications protected against proteolytic digestion, enhanced copper binding at physiological pH, and, for the cross-linking AGEs, disrupted the triple helical structure of CMPs. Overall these synthetic methods offered a new strategy for preparing peptides site-specifically modified by AGEs, which can be applied to other peptidic systems, thereby enabling further insights into the biochemical consequences of AGEs.

Enantioselective Nucleophilic β-Carbon-Atom Amination of Enals: Carbene-Catalyzed Formal [3+2] Reactions

An enantioselective β-carbon amination for enals is disclosed. The nitrogen atom from a protected hydrazine with suitable electronic properties readily behaves as a nucleophile. Addition of the nitrogen nucleophile to a catalytically generated N-heterocyclic-carbene-bound α,β-unsaturated acyl azolium intermediate constructs a new carbon-nitrogen bond asymmetrically. The pyrazolidinone products from our catalytic reactions are common scaffolds in bioactive molecules, and can be easily transformed into useful compounds such as β(3) -amino-acid derivatives.

Collagen structure: new tricks from a very old dog

The main features of the triple helical structure of collagen were deduced in the mid-1950s from fibre X-ray diffraction of tendons. Yet, the resulting models only could offer an average description of the molecular conformation. A critical advance came about 20 years later with the chemical synthesis of sufficiently long and homogeneous peptides with collagen-like sequences. The availability of these collagen model peptides resulted in a large number of biochemical, crystallographic and NMR studies that have revolutionized our understanding of collagen structure. High-resolution crystal structures from collagen model peptides have provided a wealth of data on collagen conformational variability, interaction with water, collagen stability or the effects of interruptions. Furthermore, a large increase in the number of structures of collagen model peptides in complex with domains from receptors or collagen-binding proteins has shed light on the mechanisms of collagen recognition. In recent years, collagen biochemistry has escaped the boundaries of natural collagen sequences. Detailed knowledge of collagen structure has opened the field for protein engineers who have used chemical biology approaches to produce hyperstable collagens with unnatural residues, rationally designed collagen heterotrimers, self-assembling collagen peptides, etc. This review summarizes our current understanding of the structure of the collagen triple helical domain (COL×3) and gives an overview of some of the new developments in collagen molecular engineering aiming to produce novel collagen-based materials with superior properties.