Peptidic "Molecular Beacon" for Collagen

Collagen-mimetic peptides (CMP) have been invaluable tools for understanding the structure and function of collagen, which is the most abundant protein in animals. CMPs have also been developed as probes that detect damaged collagen because of the specificity required to form a collagen triple helix. These probes are not, however, ratiometric. Here, we used EPR spectroscopy to determine the end-to-end distances of CMPs that do not form stable homotrimeric helices. We found that those distances are shorter than the distances in the context of a collagen triple helix, suggesting their potential utility as a "molecular beacon" and guiding the choice and location of a pendant fluorophore-quencher pair. We then showed that a molecular beacon based on a glycine-(2S,4S)-4-fluoroproline-(2S,4R)-4-hydroxyproline tripeptide repeat and EDANS-DABCYL pair enabled the ratiometric detection of its binding to both other CMPs and natural mammalian collagen. These results provide guidance for the development of a new modality for detecting damaged collagen in physiological settings.

Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration

Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water-collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H[Formula: see text]O/D[Formula: see text]O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H[Formula: see text]O and D[Formula: see text]O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D[Formula: see text]O than in H[Formula: see text]O, and collagen in D[Formula: see text]O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H[Formula: see text]O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D[Formula: see text]O is less hydrated than in H[Formula: see text]O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen-water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.

Optical clearing of human skin: Molecular modeling and in vivo OCT study

The results of in vivo immersion optical clearing of human skin under the action of two different optical clearing agents (OCAs), such as an aqueous sucrose solution and a radiographic contrast agent Omnipaque™ 300 (iohexol), were obtained with the use of optical coherence tomography (OCT) method. The rate of reduction of light scattering coefficient, obtained through an averaged A-scan of the OCT image in the region of dermis within the depths from 350 to 700 μm, were determined to evaluate the efficiency of optical clearing (EOC). The correlations between the EOC and the energy of intermolecular interaction of OCAs with a fragment of collagen peptide have been established as a result of molecular modeling by quantum chemistry methods HF/STO3G/DFT/B3LYP/6-311G(d) of a number of OCAs (glycerol, iohexol, sucrose, ribose, fructose, glucose) with mimetic peptide of collagen (GPH)3 .

Extraction and Characterization of Human Adipose Tissue-Derived Collagen: Toward Xeno-Free Tissue Engineering

BACKGROUND

Collagen is a key component of connective tissue and has been frequently used in the fabrication of medical devices for tissue regeneration. Human-originated collagen is particularly appealing due to its low immune response as an allograft biomaterial compared to xenografts and its ability to accelerate the regeneration process. Ethically and economically, adipose tissues available from liposuction clinics are a good resource to obtain human collagen. However, studies are still scarce on the extraction and characterization of human collagen, which originates from adipose tissue. The aim of this study is to establish a novel and simple method to extract collagen from human adipose tissue, characterize the collagen, and compare it with commercial-grade porcine collagen for tissue engineering applications.

METHODS

We developed a method to extract the collagen from human adipose tissue under quasi-Good Manufacturing Practice (GMP) conditions, including freezing the tissue, blood removal, and ethanol-based purification. Various techniques, including protein quantification, decellularization assessment, SDS-PAGE, FTIR, and CD spectroscopy analysis, were used for characterization. Amino acid composition was compared with commercial collagen. Biocompatibility and cell proliferation tests were performed, and in vitro tests using collagen sponge scaffolds were conducted with statistical analysis.

RESULTS

Our results showed that this human adipose-derived collagen was equivalent in quality to commercially available porcine collagen. In vitro testing demonstrated high cell attachment and the promotion of cell proliferation.

CONCLUSION

In conclusion, we developed a simple and novel method to extract and characterize collagen and extracellular matrix from human adipose tissue, offering a potential alternative to animal-derived collagen for xeno-free tissue engineering applications.

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.

Ionizing radiation induces cross-linking of two noncovalently bound collagen mimetic peptide triple helices in the absence of a molecular environment

Cross-linking is a fundamental molecular process that is highly important for many applications, in particular, to tune the properties of collagen-based biomaterials. Chemical reagents, the action of enzymes or physical factors such as heat or radiation can facilitate collagen cross-linking. Ionizing radiation has the advantages of being fast, efficient and free from potentially toxic reagents. Collagen cross-linking by ionizing radiation is thought to occur via a water-mediated pathway. In the past, synthesized collagen mimetic peptides have proven to be of great value for understanding the influence of the amino acid sequence on the stability of tertiary (fibrous) as well as secondary (triple helical) structures of collagen. Cross-linking of synthetic collagen mimetic peptides is often used for modifying the properties of biomaterials. In this work, for the first time, we apply radiation-induced cross-linking to synthetic collagen mimetic peptides and present an experimental and theoretical study of peptide hexamers consisting of two noncovalently bound triple helices in the absence of a molecular environment, i.e. in the gas phase. Our results show that X-ray photoabsorption of the hydroxylated hexamer leads to ionization and cross-linking of the two triple helices: thus, we found evidence that cross-linking can be achieved by ionizing radiation, without the presence of any reagent or water. We propose a cross-linking mechanism involving the creation of two radicals on hydroxyproline side-chains and their recombination, ultimately leading to covalent bond formation between the triple helices.

The Yin and Yang of How N-Terminal Acyl Caps Affect Collagen Triple Helices

N-terminal acylation is a common tool for the installation of functional moieties (e.g., sensors or bioactive molecules) on collagen model peptides (CMPs). The N-acyl group and its length are generally assumed to have little or no influence on the properties of the collagen triple helix formed by the CMP. Here, we show that the length of short (C1-C4) acyl capping groups has different effects on the thermal stability of collagen triple helices in POG, OGP, and GPO frames. While the effect of different capping groups on the stability of triple helices in the GPO frame is negligible, longer acyl chains stabilize OGP triple helices but destabilize POG analogues. The observed trends arise from a combination of steric repulsion, the hydrophobic effect, and n → π* interactions. Our study provides a basis for the design of N-terminally functionalized CMPs with predictable effects on triple helix stability.

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.

Gelatin as It Is: History and Modernity

The data concerning the synthesis and physicochemical characteristics of one of the practically important proteins-gelatin, as well as the possibilities of its practical application, are systematized and discussed. When considering the latter, emphasis is placed on the use of gelatin in those areas of science and technology that are associated with the specifics of the spatial/molecular structure of this high-molecular compound, namely, as a binder for the silver halide photographic process, immobilized matrix systems with a nano-level organization of an immobilized substance, matrices for creating pharmaceutical/dosage forms and protein-based nanosystems. It was concluded that the use of this protein is promising in the future.

Gelatin Matrix as Functional Biomaterial for Immobilization of Nanoparticles of Metal-Containing Compounds

The data concerning the synthesis and physicochemical characteristics of specific functional biomaterials-biopolymer-immobilized matrix systems based on gelatin as an array and chemical compounds, which include atoms of various metal elements-are systematized and discussed. The features of this biopolymer which determine the specific properties of the immobilized matrix systems formed by it and their reactivity, are noted. Data on gelatin-immobilized systems in which immobilized substances are elemental metals and coordination compounds formed as a result of redox processes, nucleophilic/electrophilic substitution reactions, and self-assembly (template synthesis), are presented. The possibilities of the practical use of metal-containing gelatin-immobilized systems are promising for the future; in particular, their potential in medicine and pharmacology as a vehicle for "targeted" drug delivery to various internal organs/tissues of the body, and, also, as potential biosensors is noted.

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.

Design of short peptides and peptide amphiphiles as collagen mimics and an investigation of their interactions with collagen using molecular dynamics simulations and docking studies

Short peptide sequences and bolaamphiphiles derived from natural proteins are gaining importance due to their ability to form unique nanoscale architectures for a variety of biological applications. In this work, we have designed six short peptides (triplet or monomeric forms) and two peptide bolaamphiphiles that either incorporate the bioactive collagen motif (Gly-X-Y) or sequences where Gly, Pro, or hydroxyproline (Hyp) are replaced by Ala or His. For the bolaamphiphiles, a malate moiety was used as the aliphatic linker for connecting His with Hyp to create collagen mimics. Stability of the assemblies was assessed through molecular dynamics simulations and results indicated that (Pro-Ala-His)₃ and (Ala-His-Hyp)₃ formed the most stable structures, while the amphiphiles and the monomers showed some disintegration over the course of the 200 ns simulation, though most regained structural integrity and formed fibrillar structures, and micelles by the end of the simulation, likely due to the formation of more thermodynamically stable conformations. Multiple replica simulations (REMD) were also conducted where the sequences were simulated at different temperatures. Our results showed excellent convergence in most cases compared to constant temperature molecular dynamics simulation. Furthermore, molecular docking and MD simulations of the sequences bound to collagen triple helix structure revealed that several of the sequences had a high binding affinity and formed stable complexes, particularly (Pro-Ala-His)₃ and (Ala-His-Hyp)₃. Thus, we have designed new hybrid-peptide-based sequences which may be developed for potential applications as biomaterials for tissue engineering or drug delivery.

A solution structure analysis reveals a bent collagen triple helix in the complement activation recognition molecule mannan-binding lectin

Collagen triple helices are critical in the function of mannan-binding lectin (MBL), an oligomeric recognition molecule in complement activation. The MBL collagen regions form complexes with the serine proteases MASP-1 and MASP-2 in order to activate complement, and mutations lead to common immunodeficiencies. To evaluate their structure-function properties, we studied the solution structures of four MBL-like collagen peptides. The thermal stability of the MBL collagen region was much reduced by the presence of a GQG interruption in the typical (X-Y-Gly)n repeat compared to controls. Experimental solution structural data were collected using analytical ultracentrifugation and small angle X-ray and neutron scattering. As controls, we included two standard Pro-Hyp-Gly collagen peptides (POG)_10-13, as well as three more peptides with diverse (X-Y-Gly)n sequences that represented other collagen features. These data were quantitatively compared with atomistic linear collagen models derived from crystal structures and 12,000 conformations obtained from molecular dynamics simulations. All four MBL peptides were bent to varying degrees up to 85^o in the best-fit molecular dynamics models. The best-fit benchmark peptides (POG)_n were more linear but exhibited a degree of conformational flexibility. The remaining three peptides showed mostly linear solution structures. In conclusion, the collagen helix is not strictly linear, the degree of flexibility in the triple helix depends on its sequence, and the triple helix with the GQG interruption showed a pronounced bend. The bend in MBL GQG peptides resembles the bend in the collagen of complement C1q and may be key for lectin pathway activation.

Molecular Engineering of Rigid Hydrogels Co-assembled from Collagenous Helical Peptides Based on a Single Triplet Motif

The potential of ultra-short peptides to self-assemble into well-ordered functional nanostructures makes them promising minimal components for mimicking the basic ingredient of nature and diverse biomaterials. However, selection and modular design of perfect de novo sequences are extremely tricky due to their vast possible combinatorial space. Moreover, a single amino acid substitution can drastically alter the supramolecular packing structure of short peptide assemblies. Here, we report the design of rigid hybrid hydrogels produced by sequence engineering of a new series of ultra-short collagen-mimicking tripeptides. Connecting glycine with different combinations of proline and its post-translational product 4-hydroxyproline, the single triplet motif, displays the natural collagen-helix-like structure. Improved mechanical rigidity is obtained via co-assembly with the non-collagenous hydrogelator, fluorenylmethoxycarbonyl (Fmoc) diphenylalanine. Characterizations of the supramolecular interactions that promote the self-supporting and self-healing properties of the co-assemblies are performed by physicochemical experiments and atomistic models. Our results clearly demonstrate the significance of sequence engineering to design functional peptide motifs with desired physicochemical and electromechanical properties and reveal co-assembly as a promising strategy for the utilization of small, readily accessible biomimetic building blocks to generate hybrid biomolecular assemblies with structural heterogeneity and functionality of natural materials.

Cation-π Interactions and Their Role in Assembling Collagen Triple Helices

Cation-π interactions play a significant role in the stabilization of globular proteins. However, their role in collagen triple helices is less well understood and they have rarely been used in de novo designed collagen mimetic systems. In this study, we analyze the stabilizing and destabilizing effects in pairwise amino acid interactions between cationic and aromatic residues in both axial and lateral sequential relationships. Thermal unfolding experiments demonstrated that only axial pairs are stabilizing, while the lateral pairs are uniformly destabilizing. Molecular dynamics simulations show that pairs with an axial relationship can achieve a near-ideal interaction distance, but pairs in a lateral relationship do not. Arginine-π systems were found to be more stabilizing than lysine-π and histidine-π. Arginine-π interactions were then studied in more chemically diverse ABC-type heterotrimeric helices, where arginine-tyrosine pairs were found to form the best helix. This work helps elucidate the role of cation-π interactions in triple helices and illustrates their utility in designing 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.

Walking on water: revisiting the role of water in articular cartilage biomechanics in relation to tissue engineering and regenerative medicine

The importance, and the difficulty, of generating biosynthetic articular cartilage is widely recognized. Problems arise from obtaining sufficient stiffness, toughness and longevity in the material and integration of new material into existing cartilage and bone. Much work has been done on chondrocytes and tissue macromolecular components while water, which comprises the bulk of the tissue, is largely seen as a passive component; the ‘solid matrix’ is believed to be the main load-bearing element most of the time. Water is commonly seen as an inert filler whose restricted flow through the tissue is believed to be sufficient to generate the properties measured. We propose that this model should be turned on its head. Water comprises 70–80% of the matrix and has a bulk modulus considerably greater than that of cartilage. We suggest that the macromolecular components structure the water to support the loads applied. Here, we shall examine the structure and organization of the main macromolecules, collagen, aggrecan and hyaluronan, and explore how water interacts with their polyelectrolyte nature. This may inform the biosynthetic process by identifying starting points to enable developing tissue properties to guide the cells into producing the appropriate macromolecular composition and structure.

Supramolecular assembly of protein building blocks: from folding to function

Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.

The effects of glycine to alanine mutations on the structure of GPO collagen model peptides

Collagen proteins are the main constituents of the extracellular matrix (ECM), and fulfil a number of wide-ranging functions, including contributions to the mechanical and biological behaviour of the ECM. Due to the heterogeneous nature of collagen in tissue samples it is difficult to fully explain the experimental observation, and hence the study of shorter model peptides is common place. Here, the computational energy landscape framework is employed to study Gly to Ala mutations in a GPO model peptide. The results show good agreement with the experimental observations for the GPO reference and a triply mutated peptide, demonstrating the validity of the approach. The modelling predicts that changes in structure are moderate and localised, with an increased dynamic in the backbone and alterations to the hydrogen bonding pattern. Two mechanisms for adjusting to the mutations are observed, with potential consequences regarding protein binding. Finally, in line with a hypothesis that proline puckering allows controlled flexibility (Chow et al., Sci. Rep., 2018, 8, 13809), alterations in the puckering preferences are observed in the strained residues surrounding the mutational sites.

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.

Decellularized pericardium tissues at increasing glucose, galactose and ribose concentrations and at different time points studied using scanning X-ray microscopy

Diseases like widespread diabetes or rare galactosemia may lead to high sugar concentrations in the human body, thereby promoting the formation of glycoconjugates. Glycation of collagen, i.e. the formation of glucose bridges, is nonenzymatic and therefore cannot be prevented in any other way than keeping the sugar level low. It relates to secondary diseases, abundantly occurring in aging populations and diabetics. However, little is known about the effects of glycation of collagen on the molecular level. We studied in vitro the effect of glycation, with d-glucose and d-galactose as well as d-ribose, on the structure of type 1 collagen by preparing decellularized matrices of bovine pericardia soaked in different sugar solutions, at increasing concentrations (0, 2.5, 5, 10, 20 and 40 mg ml-1), and incubated at 37°C for 3, 14, 30 and 90 days. The tissue samples were analyzed with small- and wide-angle X-ray scattering in scanning mode. We found that glucose and galactose produce similar changes in collagen, i.e. they mainly affect the lateral packing between macromolecules. However, ribose is much faster in glycation, provoking a larger effect on the lateral packing, but also seems to cause qualitatively different effects on the collagen structure.

Antibody responses to collagen peptides and streptococcal collagen-like 1 proteins in acute rheumatic fever patients

Acute rheumatic fever (ARF) is a serious post-infectious immune sequelae of Group A streptococcus (GAS). Pathogenesis remains poorly understood, including the events associated with collagen autoantibody generation. GAS express streptococcal collagen-like proteins (Scl) that contain a collagenous domain resembling human collagen. Here, the relationship between antibody reactivity to GAS Scl proteins and human collagen in ARF was investigated. Serum IgG specific for a representative Scl protein (Scl1.1) together with collagen-I and collagen-IV mimetic peptides were quantified in ARF patients (n = 36) and healthy matched controls (n = 36). Reactivity to Scl1.1 was significantly elevated in ARF compared to controls (P < 0.0001) and this was mapped to the collagen-like region of the protein, rather than the N-terminal non-collagenous region. Reactivity to collagen-1 and collagen-IV peptides was also significantly elevated in ARF cases (P < 0.001). However, there was no correlation between Scl1.1 and collagen peptide antibody binding, and hierarchical clustering of ARF cases by IgG reactivity showed two distinct clusters, with Scl1.1 antigens in one and collagen peptides in the other, demonstrating that collagen autoantibodies are not immunologically related to those targeting Scl1.1. Thus, anti-collagen antibodies in ARF appear to be generated as part of the autoreactivity process, independent of any mimicry with GAS collagen-like proteins.

Mechanism of collagen folding propagation studied by Molecular Dynamics simulations

Collagen forms a characteristic triple helical structure and plays a central role for stabilizing the extra-cellular matrix. After a C-terminal nucleus formation folding proceeds to form long triple-helical fibers. The molecular details of triple helix folding process is of central importance for an understanding of several human diseases associated with misfolded or unstable collagen fibrils. However, the folding propagation is too rapid to be studied by experimental high resolution techniques. We employed multiple Molecular Dynamics simulations starting from unfolded peptides with an already formed nucleus to successfully follow the folding propagation in atomic detail. The triple helix folding was found to propagate involving first two chains forming a short transient template. Secondly, three residues of the third chain fold on this template with an overall mean propagation of ~75 ns per unit. The formation of loops with multiples of the repeating unit was found as a characteristic misfolding event especially when starting from an unstable nucleus. Central Gly→Ala or Gly→Thr substitutions resulted in reduced stability and folding rates due to structural deformations interfering with folding propagation.

The extracellular matrix is stabilized by collagen, a fibrillar protein structure, which represents the most abundant protein of the human body. Collagen consists of three peptide chains that form an elongated triple helix with a repeating and largely conserved sequence pattern of two proline (or hydroxyproline) residues followed by a glycine. Several human diseases are associated with mutations in collagen. The folding propagation is the most critical step in the collagen structure formation and not well understood. We have used multiple Molecular Dynamics simulations to specifically investigate the mechanism of triple helix propagation and how it is affected by mutations. The folding propagation was found to involve first two chains forming a short transient template followed by three residues of the third chain to fold on this template. Additional simulations were used to characterize misfolding events such as loop formation and the effect of glycine substitutions on collagen folding.

Charge-Free, Stabilizing Amide-π Interactions Can Be Used to Control Collagen Triple-Helix Self-Assembly

There is a noted lack of understood, controllable interactions for directing the organization of collagen triple helices. While the field has had success using charge-pair interactions and cation-π interactions in helix design, these alone are not adequate for achieving the degree of specificity desirable for these supramolecular structures. Furthermore, because of the reliance on electrostatic interactions, designed heterotrimeric systems have been heavily charged, a property undesirable in some applications. Amide-π interactions are a comparatively understudied class of charge-free interactions, which could potentially be harnessed for triple-helix design. Herein, we propose, validate, and utilize pairwise amino acid amide-π interactions in collagen triple-helix design. Glutamine-phenylalanine pairs, when arranged in an axial geometry, are found to exhibit a moderately stabilizing effect, while in the lateral geometry, this pair is destabilizing. Together this allows glutamine-phenylalanine pairs to effectively set the register of triple helices. In contrast, interactions between asparagine and phenylalanine appear to have little effect on triple-helical stability. After deconvoluting the contributions of these amino acids to triple-helix stability, we demonstrate these new glutamine-phenylalanine interactions in the successful design of a heterotrimeric triple helix. The results of all of these analyses are used to update our collagen triple-helix thermal stability prediction algorithm, Scoring function for Collagen Emulating Peptides' Temperature of Transition (SCEPTTr).

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.

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.

Defining the Extracellular Matrix of Rhabdomyosarcoma

Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood with a propensity to metastasize. Current treatment for patients with RMS includes conventional systemic chemotherapy, radiation therapy, and surgical resection; nevertheless, little to no improvement in long term survival has been achieved in decades-underlining the need for target discovery and new therapeutic approaches to targeting tumor cells or the tumor microenvironment. To evaluate cross-species sarcoma extracellular matrix production, we have used murine models which feature knowledge of the myogenic cell-of-origin. With focus on the RMS/undifferentiated pleomorphic sarcoma (UPS) continuum, we have constructed tissue microarrays of 48 murine and four human sarcomas to analyze expression of seven different collagens, fibrillins, and collagen-modifying proteins, with cross-correlation to RNA deep sequencing. We have uncovered that RMS produces increased expression of type XVIII collagen alpha 1 (COL18A1), which is clinically associated with decreased long-term survival. We have also identified significantly increased RNA expression of COL4A1, FBN2, PLOD1, and PLOD2 in human RMS relative to normal skeletal muscle. These results complement recent studies investigating whether soft tissue sarcomas utilize collagens, fibrillins, and collagen-modifying enzymes to alter the structural integrity of surrounding host extracellular matrix/collagen quaternary structure resulting in improved ability to improve the ability to invade regionally and metastasize, for which therapeutic targeting is possible.

Effect of Collagen Tripeptide and Adjusting for Climate Change on Skin Hydration in Middle-Aged Women: A Randomized, Double-Blind, Placebo-Controlled Trial

Introduction: Although collagen is widely used in various forms as a functional ingredient in skin care products, the effect of oral supplementation of collagen tripeptides (CTPs) on human skin is unclear. Moreover, the majority of the positive outcomes of CTP reported so far have not considered the effect of weather conditions. Therefore, we tested the effect of CTP and adjusting for climate change on skin properties in middle-aged women.

Materials and Methods: A randomized controlled trial was conducted with 84 women between 40 and 60 years of age. Participants were randomized to receive placebo or 1,000 mg CTP daily for 12 weeks. CTP was prepared from the skin of Nile Tilapia by the digestion method using collagenase from non-pathogenic bacteria of the genus Bacillus. Skin hydration, wrinkling, and elasticity were assessed at baseline and after 6 and 12 weeks with adjustments for temperature, humidity, and ultraviolet A exposure during the evaluation time using weather data from the regional meteorological office.

Results: Of the 82 participants, 74 completed the trial without adverse effects. Compared with the control group, trans-epidermal water loss was reduced more in the CTP group after 12 weeks (P < 0.05). At 12 weeks, even after adjustment for humidity, temperature, and UVA in the region, the difference of the two groups in TEWL remained statistically significant (adjusted for humidity and temperature, P = 0.024; adjusted for UVA, P = 0.032; adjusted for temperature, high temperature, and ultraviolet A, P = 0.031). In terms of skin hydration, more improvement was evident in the CTP group than in the control group. In the subgroup analysis, subjects under 50 years of age showed a significant improvement in total score and moisture in the subjective skin improvement questionnaire after taking CTP for 12 weeks. Application of CTP was well-tolerated, and no notable adverse effect was reported from both groups.

Discussion: Our findings suggest that oral ingestion of CTP from the Skin of Nile Tilapia (Oreochromis niloticus) is well-tolerated and helps reduce water loss in in middle-aged women.

Clinical Trial Registration:www.clinicaltrials.gov/, Identifier: NCT03505684.

Taking Advantage of the Morpheein Behavior of Peroxiredoxin in Bionanotechnology

Morpheeins are proteins that reversibly assemble into different oligomers, whose architectures are governed by conformational changes of the subunits. This property could be utilized in bionanotechnology where the building of nanometric and new high-ordered structures is required. By capitalizing on the adaptability of morpheeins to create patterned structures and exploiting their inborn affinity toward inorganic and living matter, “bottom-up” creation of nanostructures could be achieved using a single protein building block, which may be useful as such or as scaffolds for more complex materials. Peroxiredoxins represent the paradigm of a morpheein that can be applied to bionanotechnology. This review describes the structural and functional transitions that peroxiredoxins undergo to form high-order oligomers, e.g., rings, tubes, particles, and catenanes, and reports on the chemical and genetic engineering approaches to employ them in the generation of responsive nanostructures and nanodevices. The usefulness of the morpheeins’ behavior is emphasized, supporting their use in future applications.

Preparation and Characterization of Electrospun Collagen Based Composites for Biomedical Applications

Electrospinning is a widely used technology for obtaining nanofibers from synthetic and natural polymers. In this study, electrospun mats from collagen (C), polyethylene terephthalate (PET) and a blend of the two (C-PET) were prepared and stabilized through a cross-linking process. The aim of this research was to prepare and characterize the nanofiber structure by Fourier-transform infrared with attenuated total reflectance spectroscopy (FTIR-ATR) in close correlation with dynamic vapor sorption (DVS). The studies indicated that C-PET nanofibrous mats shows improved mechanical properties compared to collagen samples. A correlation between morphological, structural and cytotoxic proprieties of the studied samples were emphasized and the results suggest that the prepared nanofiber mats could be a promising candidate for tissue-engineering applications, especially dermal applications.

Collagen-Inspired Helical Peptide Coassembly Forms a Rigid Hydrogel with Twisted Polyproline II Architecture

Collagen, the most abundant protein in mammals, possesses notable cohesion and elasticity properties and efficiently induces tissue regeneration. The Gly-Pro-Hyp canonical tripeptide repeating unit of the collagen superhelix has been well-characterized. However, to date, the shortest tripeptide repeat demonstrated to attain a helical conformation contained 3-10 peptide repeats. Here, taking a minimalistic approach, we studied a single repeating unit of collagen in its protected form, Fmoc-Gly-Pro-Hyp. The peptide formed single crystals displaying left-handed polyproline II superhelical packing, as in the native collagen single strand. The crystalline assemblies also display head-to-tail H-bond interactions and an "aromatic zipper" arrangement at the molecular interface. The coassembly of this tripeptide, with Fmoc-Phe-Phe, a well-studied dipeptide hydrogelator, produced twisted helical fibrils with a polyproline II conformation and improved hydrogel mechanical rigidity. The design of these peptides illustrates the possibility to assemble superhelical nanostructures from minimal collagen-inspired peptides with their potential use as functional motifs to introduce a polyproline II conformation into hybrid hydrogel assemblies.

Sub-Ångstrom structure of collagen model peptide (GPO)10 shows a hydrated triple helix with pitch variation and two proline ring conformations

Collagens are large structural proteins that are prevalent in mammalian connective tissue. Peptides designed to include a glycine-proline-hydroxyproline (GPO) amino acid triad are biomimetic analogs of the collagen triple helix, a fold that is a hallmark of collagen-like sequences. To inform the rational engineering of collagen-like peptides and proteins for food systems, we report the crystal structure of the (GPO)₁₀ peptide at 0.89-Å resolution, solved using direct methods. We determined that a single chain in the asymmetric unit forms a pseudo-hexagonal network of triple helices that have a pitch variation consistent with the model 7/2 helix (3.5 residues per turn). The proline rings occupied one of two states, while the helix was found to have a well-defined hydration shell involved in the stabilization of the inter-helix crystal network. This structure offers a new high-resolution basis for understanding the hierarchical assembly of native collagens, which will aid the food industry in engineering new sustainable food systems.

Corrosion of Heritage Objects: Collagen-Like Triple Helix Found in the Calcium Acetate Hemihydrate Crystal Structure

Helical motifs are common in nature, for example, the DNA double or the collagen triple helix. In the latter proteins, the helical motif originates from glycine, the smallest amino acid, whose molecular confirmation is closely related to acetic acid. The combination of acetic acid with calcium and water, which are also omnipresent in nature, materializing as calcium acetate hemihydrate, was now revealed to exhibit a collagen‐like triple helix structure. This calcium salt is observed as efflorescence phase on calcareous heritage objects, like historic Mollusca shells, pottery or marble reliefs. In a model experiment pure calcium acetate hemihydrate was crystallized on the surface of a terracotta vessel. Calcium acetate hemihydrate crystallizes in a surprisingly large unit cell with a volume of 11,794.5(3) ų at ambient conditions. Acetate ions bridge neighboring calcium cations forming spiral chains, which are arranged in a triple helix motif.

Comparative analysis of the viscoelastic properties of collagen-like proteins by virtual creep test

Viscoelasticity of collagen is essential for the integrity of connective tissue and its aberrancy may result in collagen dysfunction and the emergence of connective tissue diseases. Precise identification of viscoelastic properties of collagens, and affecting factors are necessary to understand collagen behavior in the extracellular matrix as well as the mechanism of collagen-related diseases. The aim of this study is to investigate the mechanical and viscoelastic properties and time-lapse changes of protein-protein and protein-solvent hydrogen bonds of proline-rich and hydroxyproline-rich collagens by molecular dynamics simulation applying a virtual creep test. To this end, ten different collagen-like protein structures including [(Gly-Pro-Ala)₇]₃, [(Gly-Pro-Arg)₇]₃, [(Gly-Pro-Asp)₇]₃, [(Gly-Pro-Lys)₇]₃, [(Gly-Pro-Ser)₇]₃, [(Gly-Pro-Hyp)₇]₃, [(Gly-Ala-Hyp)₇]₃, [(Gly-Glu-Hyp)₇]₃, [(Gly-Leu-Hyp)₇]₃ and [(Gly-Val-Hyp)₇]₃ were virtually built and the viscoelastic properties of the structures were determined by virtual creep test according to Kelvin-Voigt model with various constant pulling forces. Different pulling forces ranged from 500 piconewton (pN) to 5000 pN were applied. As a result, Young's modulus of the collagens was found positively correlated with the pulling force. The viscosity values and relaxation times were negatively correlated. Results also revealed a decreased number of intramolecular hydrogen bonds in hydroxyproline-rich collagens (but not in proline-rich collagens) and an increased number of protein-solvent hydrogen bonds in response to the increasing pulling force. Our results also confirmed that proline and hydroxyproline are the most critical amino acids in determining the collagen viscoelasticity. We suggest that collagen length and mechanical force may be additional important factors for biomechanical properties and behavior of collagen in the extracellular matrix.Communicated by Ramaswamy H. Sarma.

Elucidating the Nature of Interactions in Collagen Triple-Helix Wrapping

Collagen is the most abundant protein family in the animal kingdom. Its structural motif envisages three polypeptide chains coiled in the so-called collagen triple helix. Depending on the triplet amino acid sequence of the chains, collagen has different helical arrangements. Such atomic-scale structural variations have a large impact on the large-scale structure of collagen. In this Letter, we elucidate the interactions that are responsible for a specific helical pattern of the collagen protein by means of DFT-D-based computer simulations. We demonstrate that interchain interactions and solvation effects stabilize compact helices over elongated ones. Conversely, elongated helices are stabilized by less geometrical strain and entropic factors. Our computational procedure predicts the collagen helical pattern in agreement with the experimental evidence.

Production of protein-based polymers in Pichia pastoris

Materials science and genetic engineering have joined forces over the last three decades in the development of so-called protein-based polymers. These are proteins, typically with repetitive amino acid sequences, that have such physical properties that they can be used as functional materials. Well-known natural examples are collagen, silk, and elastin, but also artificial sequences have been devised. These proteins can be produced in a suitable host via recombinant DNA technology, and it is this inherent control over monomer sequence and molecular size that renders this class of polymers of particular interest to the fields of nanomaterials and biomedical research. Traditionally, Escherichia coli has been the main workhorse for the production of these polymers, but the methylotrophic yeast Pichia pastoris is finding increased use in view of the often high yields and potential bioprocessing benefits. We here provide an overview of protein-based polymers produced in P. pastoris. We summarize their physicochemical properties, briefly note possible applications, and detail their biosynthesis. Some challenges that may be faced when using P. pastoris for polymer production are identified: (i) low yields and poor process control in shake flask cultures; i.e., the need for bioreactors, (ii) proteolytic degradation, and (iii) self-assembly in vivo. Strategies to overcome these challenges are discussed, which we anticipate will be of interest also to readers involved in protein expression in P. pastoris in general.

A structural prospective for collagen receptors such as DDR and their binding of the collagen fibril

The structure of the collagen fibril surface directly effects and possibly assists the management of collagen receptor interactions. An important class of collagen receptors, the receptor tyrosine kinases of the Discoidin Domain Receptor family (DDR1 and DDR2), are differentially activated by specific collagen types and play important roles in cell adhesion, migration, proliferation, and matrix remodeling. This review discusses their structure and function as it pertains directly to the fibrillar collagen structure with which they interact far more readily than they do with isolated molecular collagen. This prospective provides further insight into the mechanisms of activation and rational cellular control of this important class of receptors while also providing a comparison of DDR-collagen interactions with other receptors such as integrin and GPVI. When improperly regulated, DDR activation can lead to abnormal cellular proliferation activities such as in cancer. Hence how and when the DDRs associate with the major basis of mammalian tissue infrastructure, fibrillar collagen, should be of keen interest.

Collagen degradation in tuberculosis pathogenesis: the biochemical consequences of hosting an undesired guest

The scenario of chemical reactions prompted by the infection by Mycobacterium tuberculosis is huge. The infection generates a localized inflammatory response, with the recruitment of neutrophils, monocytes, and T-lymphocytes. Consequences of this immune reaction can be the eradication or containment of the infection, but these events can be deleterious to the host inasmuch as lung tissue can be destroyed. Indeed, a hallmark of tuberculosis (TB) is the formation of lung cavities, which increase disease development and transmission, as they are sites of high mycobacterial burden. Pulmonary cavitation is associated with antibiotic failure and the emergence of antibiotic resistance. For cavities to form, M. tuberculosis induces the overexpression of host proteases, like matrix metalloproteinases and cathepsin, which are secreted from monocyte-derived cells, neutrophils, and stromal cells. These proteases destroy the lung parenchyma, in particular the collagen constituent of the extracellular matrix (ECM). Namely, in an attempt to destroy infected cells, the immune reactions prompted by mycobacterial infections induce the destruction of vital regions of the lung, in a process that can become fatal. Here, we review structure and function of the main molecular actors of ECM degradation due to M. tuberculosis infection and the proposed mechanisms of tissue destruction, mainly attacking fibrillar collagen. Importantly, enzymes responsible for collagen destruction are emerging as key targets for adjunctive therapies to limit immunopathology in TB.

High pressure Raman study of type-I collagen

The high pressure response of type-I collagen from bovine Achilles tendon is investigated with micro-Raman spectroscopy. Fluorinert™ and methanol-ethanol mixtures were used as pressure transmitting media (PTM) in a diamond anvil cell. The Raman spectrum of collagen is dominated by three bands centred at approximately 1450, 1660 and 2930 cm^-1 , attributed to C-H deformation, C=O stretching of the peptide bond (amide-I band) and C-H stretching modes respectively. Upon pressure increase, using Fluorinert™ as PTM, a shift towards higher frequencies of the C-H stretching and deformation peaks is observed. Contrary, the amide-I band peaks are shifted to lower frequencies with moderate pressure slopes. On the other hand, when using the alcohol mixture as PTM, the amide-I band exhibits more pronounced C=O bond softening, deduced from the shift to lower frequencies, suggesting a strengthening of the hydrogen bonds between glycine and proline residues of different collagen chains due to the presence of the polar alcohol molecules. Furthermore, some of the peaks exhibit abrupt changes in their pressure slopes at approximately 2 GPa, implying a variation in the compressibility of the collagen fibres. This could be attributed to a pitch change from 10/3 to 7/2, sliding of the tropocollagen molecules, twisting variation at the molecular level and/or elimination of the D-gaps induced by kink compression. All spectral changes are reversible upon pressure release, which indicates that denaturation has not taken place. Finally, a minor lipid phase contamination was detected in some sample spots. Its pressure response is also monitored.

Extraction and physicochemical characterization of broiler (Gallus gallus domesticus) skin gelatin compared to commercial bovine gelatin

Gelatin was extracted from broiler (Gallus gallus domesticus) skins and analyzed to compare its physicochemical properties with those of commercial bovine gelatin. The average yield of broiler skin gelatin was 6.5% on a wet weight basis. Broiler skin gelatin had more α1-and α2-chains than β-chain and contained high molecular weight (γ-chain) polymers. Glycine was the dominant amino acid in broiler skin gelatin (20.26%), followed by proline (Pro) (15.12%) then hydroxyproline (Hyp) (11.36%). Compared to commercial bovine gelatin, broiler skin gelatin had less total imino acids (Pro and Hyp) but a higher (33.65 vs. 31.38°C) melting temperature (P < 0.01). The differences in physical properties between the broiler and commercial bovine gelatins appeared to be associated with differences in their amino acid composition and molecular weight distribution. The sensory evaluation results revealed that broiler skin gelatin could be a potential alternative to commercial bovine gelatin, useful in various food products.

Unique Conformation in a Natural Interruption Sequence of Type XIX Collagen Revealed by Its High-Resolution Crystal Structure

Naturally occurring interruptions in nonfibrillar collagen play key roles in molecular flexibility, collagen degradation, and ligand binding. The structural feature of the interruption sequences and the molecular basis for their functions have not been well studied. Here, we focused on a G5G type natural interruption sequence G-POALO-G from human type XIX collagen, a homotrimer collagen, as this sequence possesses distinct properties compared with those of a pathological similar Gly mutation sequence in collagen mimic peptides. We determined the crystal structures of the host-guest peptide (GPO)₃-GPOALO-(GPO)₄ to 1.03 Å resolution in two crystal forms. In these structures, the interruption zone brings localized disruptions to the triple helix and introduces a light 6-8° bend with the same directional preference to the whole molecule, which may correspond structurally to the first physiological kink site in type XIX collagen. Furthermore, at the G5G interruption site, the presence of Ala and Leu residues, both with free N-H groups, allows the formation of more direct and water-mediated interchain hydrogen bonds than in the related Gly → Ala structure. These could partly explain the difference in thermal stability between the different interruptions. In addition, our structures provide a detailed view of the dynamic property of such an interrupted zone with respect to hydrogen bonding topology, torsion angles, and helical parameters. Our results, for the first time, also identified the binding of zinc to the end of the triple helix. These findings will shed light on how the interruption sequence influences the conformation of the collagen molecule and provide a structural basis for further functional studies.