Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution

Structure-mechanics relationships of collagen fibrils in the osteogenesis imperfecta mouse model

The collagen molecule, which is the building block of collagen fibrils, is a triple helix of two α1(I) chains and one α2(I) chain. However, in the severe mouse model of osteogenesis imperfecta (OIM), deletion of the COL1A2 gene results in the substitution of the α2(I) chain by one α1(I) chain. As this substitution severely impairs the structure and mechanics of collagen-rich tissues at the tissue and organ level, the main aim of this study was to investigate how the structure and mechanics are altered in OIM collagen fibrils. Comparing results from atomic force microscopy imaging and cantilever-based nanoindentation on collagen fibrils from OIM and wild-type (WT) animals, we found a 33% lower indentation modulus in OIM when air-dried (bound water present) and an almost fivefold higher indentation modulus in OIM collagen fibrils when fully hydrated (bound and unbound water present) in phosphate-buffered saline solution (PBS) compared with WT collagen fibrils. These mechanical changes were accompanied by an impaired swelling upon hydration within PBS. Our experimental and atomistic simulation results show how the structure and mechanics are altered at the individual collagen fibril level as a result of collagen gene mutation in OIM. We envisage that the combination of experimental and modelling approaches could allow mechanical phenotyping at the collagen fibril level of virtually any alteration of collagen structure or chemistry.

In vivo studies of ultrafast near-infrared laser tissue bonding and wound healing

Femtosecond (fs) pulse lasers in the near-infrared (NIR) range exhibit very distinct properties upon their interaction with biomolecules compared to the corresponding continuous wave (CW) lasers. Ultrafast NIR laser tissue bonding (LTB) was used to fuse edges of two opposing animal tissue segments in vivo using fs laser photoexcitation of the native vibrations of chomophores. The fusion of the incised tissues was achieved in vivo at the molecular level as the result of the energy–matter interactions of NIR laser radiation with water and the structural proteins like collagen in the target tissues. Nonthermal vibrational excitation from the fs laser absorption by water and collagen induced the formation of cross-links between tissue proteins on either sides of the weld line resulting in tissue bonding. No extrinsic agents were used to facilitate tissue bonding in the fs LTB. These studies were pursued for the understanding and evaluation of the role of ultrafast NIR fs laser radiation in the LTB and consequent wound healing. The fs LTB can be used for difficult to suture structures such as blood vessels, nerves, gallbladder, liver, intestines, and other viscera. Ultrafast NIR LTB yields promising outcomes and benefits in terms of wound closure and wound healing under optimal conditions.

A Natural Interruption Displays Higher Global Stability and Local Conformational Flexibility than a Similar Gly Mutation Sequence in Collagen Mimic Peptides

Natural interruptions in the repeating (Gly-X-Y)n amino acid sequence pattern are found normally in triple helix domains of all nonfibrillar collagens, while any Gly substitution in fibrillar collagens leads to pathological conditions. As revealed by our sequence analysis, two peptides, one modeling a natural G5G interruption (POALO) and the other one mimicking a pathological Gly-to-Ala substitution (LOAPO), are designed. Circular dichroism (CD), NMR, and computational simulation studies have discovered significant differences in stability, conformation, and folding between the two peptides. Compared with the Gly substitution sequence, the natural interruption maintains higher stability, higher triple helix content, and a higher folding rate while introducing more alterations in local triple helical conformation in terms of dihedral angles and hydrogen bonding. The conserved hydrophobic residues at the specific sites of interruptions may provide functional constraints for higher-order assembly as well as biomolecular interactions. These results suggest a molecular basis of different biological roles of natural interruptions and Gly substitutions and may guide the design of collagen mimic peptides containing functional natural interruptions.

Electrostatic Forces Mediated by Choline Dihydrogen Phosphate Stabilize Collagen

Cross-linkers aid in improving biostability of collagen via different mechanisms. Choline dihydrogen phosphate (cDHP), a biocompatible ionic liquid, has been reported as a potential cross-linker for collagen. However, its mechanism is yet unclear. This study explores the effect of cDHP on the physicochemical stability of collagen and nature of its interaction. Dielectric behavior of collagen-cDHP composites signifies that cDHP enhances intermolecular forces. This was demonstrated by an increase in cross-linked groups and high denaturation temperature of collagen-cDHP composites. XRD measurements reveal minor conformational change in helices. Molecular modeling studies illustrate that the force existing between collagen and cDHP is electrostatic in nature. Herein, it is postulated that dihydrogen phosphate anion attaches to cationic functional groups of collagen, resulting in closer vicinity of various side chains of collagen, forming physical and chemical cross-links within collagen, contributing to its structural stability. Our study suggests that dihydrogen phosphate anions can be employed for developing a new class of biocompatible cross-linkers.

The use of optical trap and microbeam to investigate the mechanical and transport characteristics of tunneling nanotubes in tumor spheroids

The use of optical trap and microbeam for investigating mechanical and transport properties of inter cellular tunneling nanotubes (TnTs) in tumor spheroids has been demonstrated. TnTs in tumor spheroids have been visualized by manipulating TnT connected cells using optical tweezers. Functionality of the TnTs for transferring cytoplasmic vesicles and injected dye molecules by optoporation method has been studied. Further, the TnTs could be longitudinally stretched by manipulating the connected cells and their elastic response was studied. Manipulation of cells at the surface of tumor spheroid using optical tweezers and injection of fluorescent dye into a trapped cell using optoporation technique.

Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4

Gene product 5 (gp5) of bacteriophage T4 is a spike-shaped protein that functions to disrupt the membrane of the target cell during phage infection. Its C-terminal domain is a long and slender β-helix that is formed by three polypeptide chains wrapped around a common symmetry axis akin to three interdigitated corkscrews. The folding and biophysical properties of such triple-stranded β-helices, which are topologically related to amyloid fibers, represent an unsolved biophysical problem. Here, we report structural and biophysical characterization of T4 gp5 β-helix and its truncated mutants of different lengths. A soluble fragment that forms a dimer of trimers and that could comprise a minimal self-folding unit has been identified. Surprisingly, the hydrophobic core of the β-helix is small. It is located near the C-terminal end of the β-helix and contains a centrally positioned and hydrated magnesium ion. A large part of the β-helix interior comprises a large elongated cavity that binds palmitic, stearic, and oleic acids in an extended conformation suggesting that these molecules might participate in the folding of the complete β-helix.

Metal Stabilization of Collagen and de Novo Designed Mimetic Peptides

We explore the design of metal binding sites to modulate triple-helix stability of collagen and collagen-mimetic peptides. Globular proteins commonly utilize metals to connect tertiary structural elements that are well separated in sequence, constraining structure and enhancing stability. It is more challenging to engineer structural metals into fibrous protein scaffolds, which lack the extensive tertiary contacts seen in globular proteins. In the collagen triple helix, the structural adjacency of the carboxy-termini of the three chains makes this region an attractive target for introducing metal binding sites. We engineered His3 sites based on structural modeling constraints into a series of designed homotrimeric and heterotrimeric peptides, assessing the capacity of metal binding to improve stability and in the case of heterotrimers, affect specificity of assembly. Notable enhancements in stability for both homo- and heteromeric systems were observed upon addition of zinc(II) and several other metal ions only when all three histidine ligands were present. Metal binding affinities were consistent with the expected Irving-Williams series for imidazole. Unlike other metals tested, copper(II) also bound to peptides lacking histidine ligands. Acetylation of the peptide N-termini prevented copper binding, indicating proline backbone amide metal-coordination at this site. Copper similarly stabilized animal extracted Type I collagen in a metal-specific fashion, highlighting the potential importance of metal homeostasis within the extracellular matrix.

Effect of intrinsic and extrinsic factors on the simulated D-band length of type I collagen

A signature feature of collagen is its axial periodicity visible in TEM as alternating dark and light bands. In mature, type I collagen, this repeating unit, D, is 67 nm long. This periodicity reflects an underlying packing of constituent triple-helix polypeptide monomers wherein the dark bands represent gaps between axially adjacent monomers. This organization is visible distinctly in the microfibrillar model of collagen obtained from fiber diffraction. However, to date, no atomistic simulations of this diffraction model under zero-stress conditions have reported a preservation of this structural feature. Such a demonstration is important as it provides the baseline to infer response functions of physiological stimuli. In contrast, simulations predict a considerable shrinkage of the D-band (11-19%). Here we evaluate systemically the effect of several factors on D-band shrinkage. Using force fields employed in previous studies we find that irrespective of the temperature/pressure coupling algorithms, assumed salt concentration or hydration level, and whether or not the monomers are cross-linked, the D-band shrinks considerably. This shrinkage is associated with the bending and widening of individual monomers, but employing a force field whose backbone dihedral energy landscape matches more closely with our computed CCSD(T) values produces a small D-band shrinkage of < 3%. Since this force field also performs better against other experimental data, it appears that the large shrinkage observed in earlier simulations is a force-field artifact. The residual shrinkage could be due to the absence of certain atomic-level details, such as glycosylation sites, for which we do not yet have suitable data.

NMR studies demonstrate a unique AAB composition and chain register for a heterotrimeric type IV collagen model peptide containing a natural interruption site

All non-fibrillar collagens contain interruptions in the (Gly-X-Y)n repeating sequence, such as the more than 20 interruptions found in chains of basement membrane type IV collagen. Two selectively doubly labeled peptides are designed to model a site in type IV collagen with a GVG interruption in the α1(IV) and a corresponding GISLK sequence within the α2(IV) chain. CD and NMR studies on a 2:1 mixture of these two peptides support the formation of a single-component heterotrimer that maintains the one-residue staggering in the triple-helix, has a unique chain register, and contains hydrogen bonds at the interruption site. Formation of hydrogen bonds at interruption sites may provide a driving force for self-assembly and chain register in type IV and other non-fibrillar collagens. This study illustrates the potential role of interruptions in the structure, dynamics, and folding of natural collagen heterotrimers and forms a basis for understanding their biological role.

A Single Stereodynamic Center Modulates the Rate of Self-Assembly in a Biomolecular System

Chirality is a property of asymmetry important to both physical and abstract systems. Understanding how molecular systems respond to perturbations in their chiral building blocks can provide insight into diverse areas such as biomolecular self-assembly, protein folding, drug design, materials, and catalysis. Despite the fundamental importance of stereochemical preorganization in nature and designed materials, the ramifications of replacing chiral centers with stereodynamic atomic mimics in the context of biomolecular systems is unknown. Herein, we demonstrate that replacement of a single amino acid stereocenter with a stereodynamic nitrogen atom has profound consequences on the self-assembly of a biomolecular system. Our results provide insight into how the fundamental biopolymers of life would behave if their chiral centers were not configurationally stable, highlighting the vital importance of stereochemistry as a pre-organizing element in biomolecular folding and assembly events.

Hydroxyproline-induced Helical Disruption in Conantokin Rl-B Affects Subunit-selective Antagonistic Activities toward Ion Channels of N-Methyl-d-aspartate Receptors

Conantokins are ~20-amino acid peptides present in predatory marine snail venoms that function as allosteric antagonists of ion channels of the N-methyl-d-aspartate receptor (NMDAR). These peptides possess a high percentage of post-/co-translationally modified amino acids, particularly γ-carboxyglutamate (Gla). Appropriately spaced Gla residues allow binding of functional divalent cations, which induces end-to-end α-helices in many conantokins. A smaller number of these peptides additionally contain 4-hydroxyproline (Hyp). Hyp should prevent adoption of the metal ion-induced full α-helix, with unknown functional consequences. To address this disparity, as well as the role of Hyp in conantokins, we have solved the high resolution three-dimensional solution structure of a Gla/Hyp-containing 18-residue conantokin, conRl-B, by high field NMR spectroscopy. We show that Hyp(10) disrupts only a small region of the α-helix of the Mn(2+)·peptide complex, which displays cation-induced α-helices on each terminus of the peptide. The function of conRl-B was examined by measuring its inhibition of NMDA/Gly-mediated current through NMDAR ion channels in mouse cortical neurons. The conRl-B displays high inhibitory selectivity for subclasses of NMDARs that contain the functionally important GluN2B subunit. Replacement of Hyp(10) with N(8)Q results in a Mg(2+)-complexed end-to-end α-helix, accompanied by attenuation of NMDAR inhibitory activity. However, replacement of Hyp(10) with Pro(10) allowed the resulting peptide to retain its inhibitory property but diminished its GluN2B specificity. Thus, these modified amino acids, in specific peptide backbones, play critical roles in their subunit-selective inhibition of NMDAR ion channels, a finding that can be employed to design NMDAR antagonists that function at ion channels of distinct NMDAR subclasses.

Local amino acid sequence patterns dominate the heterogeneous phenotype for the collagen connective tissue disease Osteogenesis Imperfecta resulting from Gly mutations

Osteogenesis Imperfecta (OI), a hereditary connective tissue disease in collagen that arises from a single Gly → X mutation in the collagen chain, varies widely in phenotype from perinatal lethal to mild. It is unclear why there is such a large variation in the severity of the disease considering the repeating (Gly-X-Y)n sequence and the uniform rod-like structure of collagen. We systematically evaluate the effect of local (Gly-X-Y)n sequence around the mutation site on OI phenotype using integrated bio-statistical approaches, including odds ratio analysis and decision tree modeling. We show that different Gly → X mutations have different local sequence patterns that are correlated with lethal and nonlethal phenotypes providing a mechanism for understanding the sensitivity of local context in defining lethal and non-lethal OI. A number of important trends about which factors are related to OI phenotypes are revealed by the bio-statistical analyses; most striking is the complementary relationship between the placement of Pro residues and small residues and their correlation to OI phenotype. When Pro is present or small flexible residues are absent nearby a mutation site, the OI case tends to be lethal; when Pro is present or small flexible residues are absent further away from the mutation site, the OI case tends to be nonlethal. The analysis also reveals the dominant role of local sequence around mutation sites in the Major Ligand Binding Regions that are primarily responsible for collagen binding to its receptors and shows that non-lethal mutations are highly predicted by local sequence considerations alone whereas lethal mutations are not as easily predicted and may be a result of more complex interactions. Understanding the sequence determinants of OI mutations will enhance genetic counseling and help establish which steps in the collagen hierarchy to target for drug therapy.

Collagenolytic Matrix Metalloproteinase Activities toward Peptomeric Triple-Helical Substrates

Although collagenolytic matrix metalloproteinases (MMPs) possess common domain organizations, there are subtle differences in their processing of collagenous triple-helical substrates. In this study, we have incorporated peptoid residues into collagen model triple-helical peptides and examined MMP activities toward these peptomeric chimeras. Several different peptoid residues were incorporated into triple-helical substrates at subsites P3, P1, P1', and P10' individually or in combination, and the effects of the peptoid residues were evaluated on the activities of full-length MMP-1, MMP-8, MMP-13, and MMP-14/MT1-MMP. Most peptomers showed little discrimination between MMPs. However, a peptomer containing N-methyl Gly (sarcosine) in the P1' subsite and N-isobutyl Gly (NLeu) in the P10' subsite was hydrolyzed efficiently only by MMP-13 [nomenclature relative to the α1(I)772-786 sequence]. Cleavage site analysis showed hydrolysis at the Gly-Gln bond, indicating a shifted binding of the triple helix compared to the parent sequence. Favorable hydrolysis by MMP-13 was not due to sequence specificity or instability of the substrate triple helix but rather was based on the specific interactions of the P7' peptoid residue with the MMP-13 hemopexin-like domain. A fluorescence resonance energy transfer triple-helical peptomer was constructed and found to be readily processed by MMP-13, not cleaved by MMP-1 and MMP-8, and weakly hydrolyzed by MT1-MMP. The influence of the triple-helical structure containing peptoid residues on the interaction between MMP subsites and individual substrate residues may provide additional information about the mechanism of collagenolysis, the understanding of collagen specificity, and the design of selective MMP probes.

Tissue-engineered acellular small diameter long-bypass grafts with neointima-inducing activity

Researchers have attempted to develop efficient antithrombogenic surfaces, and yet small-caliber artificial vascular grafts are still unavailable. Here, we demonstrate the excellent patency of tissue-engineered small-caliber long-bypass grafts measuring 20-30 cm in length and having a 2-mm inner diameter. The inner surface of an acellular ostrich carotid artery was modified with a novel heterobifunctional peptide composed of a collagen-binding region and the integrin α4β1 ligand, REDV. Six grafts were transplanted in the femoral-femoral artery crossover bypass method. Animals were observed for 20 days and received no anticoagulant medication. No thrombogenesis was observed on the luminal surface and five cases were patent. In contrast, all unmodified grafts became occluded, and severe thrombosis was observed. The vascular grafts reported here are the first successful demonstrations of short-term patency at clinically applicable sizes.

Evaluation of polyvinyl alcohol composite membranes containing collagen and bone particles

Composite biomaterials provide alternative materials that improve on the properties of the individual components and can be used to replace or restore damaged or diseased tissues. Typically, a composite biomaterial consists of a matrix, often a polymer, with one or more fillers that can be made up of particles, sheets or fibres. The polymer matrix can be chosen from a wide range of compositions and can be fabricated easily and rapidly into complex shapes and structures. In the present study we have examined three size fractions of collagen-containing particles embedded at up to 60% w/w in a poly(vinyl alcohol) (PVA) matrix. The particles used were bone particles, which are a mineral-collagen composite and demineralised bone, which gives naturally cross-linked collagen particles. SEM showed well dispersed particles in the PVA matrix for all concentrations and sizes of particles, with FTIR suggesting collagen to PVA hydrogen bonding. Tg of membranes shifted to a slightly lower temperature with increasing collagen content, along with a minor amount of melting point depression. The modulus and tensile strength of membranes were improved with the addition of both particles up to 10 wt%, and were clearly strengthened by the addition, although this effect decreased with higher collagen loadings. Elongation at break decreased with collagen content. Cell adhesion to the membranes was observed associated with the collagen particles, indicating a lack of cytotoxicity.

Tuning cellular response by modular design of bioactive domains in collagen

Collagen's ability to direct cellular behavior suggests that redesigning it at the molecular level could enable manipulation of cells residing in an engineered microenvironment. However, the fabrication of full-length collagen mimics of specified sequence de novo has been elusive, and applications still rely on material from native tissues. Using a bottom-up strategy, we synthesized modular genes and expressed recombinant human collagen variants in Saccharomyces cerevisiae. The resulting biopolymers contained prescribed cell-interaction sites that can direct and tune cellular responses, with retention of the important triple-helical self-assembled structure. Removal of the native integrin-binding sites GROGER, GAOGER, GLOGEN, GLKGEN, and GMOGER in human collagen III yielded collagen that did not support adhesion of mammalian cells. Introduction of GFOGER sequences to this scaffold at specified locations and densities resulted in varying degrees of cellular attachment. The recruitment of focal adhesion complexes on the different collagens ranged from a 96% reduction to a 56% increase over native collagen I. Adhesion to the GFOGER-containing variants was entirely dependent and partially dependent on the β1 and α2 subunits of integrin, respectively, with cell adhesion on average reduced by 86% with anti-β1 and 38% with anti-α2 integrin antibody incubation. Results support the importance of local context in collagen-cell interactions. The investigation demonstrates the flexibility of this approach to introduce targeted changes throughout the collagen polymer for producing fully-prescribed variants with tailored properties.

Structure of collagen adsorbed on a model implant surface resolved by polarization modulation infrared reflection-absorption spectroscopy

The polarization modulation infrared reflection-absorption spectra of collagen adsorbed on a titania surface and quantum chemical calculations are used to describe components of the amide I mode to the protein structure at a sub-molecular level. In this study, imino acid rich and poor fragments, representing the entire collagen molecule, are taken into account. The amide I mode of the collagen triple helix is composed of three absorption bands which involve: (i) (∼1690cm(-1)) the CO stretching modes at unhydrated groups, (ii) (1655-1673cm(-1)) the CO stretching at carbonyl groups at imino acids and glycine forming intramolecular hydrogen bonds with H atoms at both NH2 and, unusual for proteins, CH2 groups at glycine at a neighbouring chain and (iii) (∼1640cm(-1)) the CO stretching at carbonyl groups forming hydrogen bonds between two, often charged, amino acids as well as hydrogen bonds to water along the entire helix. The IR spectrum of films prepared from diluted solutions (c<50μgml(-1)) corresponds to solution spectra indicating that native collagen molecules interact with water adsorbed on the titania surface. In films prepared from solutions (c⩾50μgml(-1)) collagen multilayers are formed. The amide I mode is blue-shifted by 18cm(-1), indicating that intramolecular hydrogen bonds at imino acid rich fragments are weakened. Simultaneous red-shift of the amide A mode implies that the strength of hydrogen bonds at the imino acid poor fragments increases. Theoretically predicted distortion of the collagen structure upon adsorption on the titania surface is experimentally confirmed.

The self-assembly of a mini-fibril with axial periodicity from a designed collagen-mimetic triple helix

In this work we describe the self-assembly of a collagen-like periodic mini-fibril from a recombinant triple helix. The triple helix, designated Col108, is expressed in Escherichia coli using an artificial gene and consists of a 378-residue triple helix domain organized into three pseudo-repeating sequence units. The peptide forms a stable triple helix with a melting temperature of 41 °C. Upon increases of pH and temperature, Col108 self-assembles in solution into smooth mini-fibrils with the cross-striated banding pattern typical of fibrillar collagens. The banding pattern is characterized by an axially repeating feature of ∼35 nm as observed by transmission electron microscopy and atomic force microscopy. Both the negatively stained and the positively stained transmission electron microscopy patterns of the Col108 mini-fibrils are consistent with a staggered arrangement of triple helices having a staggering value of 123 residues, a value closely connected to the size of one repeat sequence unit. A mechanism is proposed for the mini-fibril formation of Col108 in which the axial periodicity is instigated by the built-in sequence periodicity and stabilized by the optimized interactions between the triple helices in a 1-unit staggered arrangement. Lacking hydroxyproline residues and telopeptides, two factors implicated in the fibrillogenesis of native collagen, the Col108 mini-fibrils demonstrate that sequence features of the triple helical domain alone are sufficient to "code" for axially repeating periodicity of fibrils. To our knowledge, Col108 is the first designed triple helix to self-assemble into periodic fibrils and offers a unique opportunity to unravel the specific molecular interactions of collagen fibrillogenesis.

Water distribution in dentin matrices: bound vs. unbound water

OBJECTIVE

This work measured the amount of bound versus unbound water in completely-demineralized dentin.

METHODS

Dentin beams prepared from extracted human teeth were completely demineralized, rinsed and dried to constant mass. They were rehydrated in 41% relative humidity (RH), while gravimetrically measuring their mass increase until the first plateau was reached at 0.064 (vacuum) or 0.116 gH2O/g dry mass (Drierite). The specimens were then exposed to 60% RH until attaining the second plateau at 0.220 (vacuum) or 0.191 gH2O/g dry mass (Drierite), and subsequently exposed to 99% RH until attaining the third plateau at 0.493 (vacuum) or 0.401 gH2O/g dry mass (Drierite).

RESULTS

Exposure of the first layer of bound water to 0% RH for 5 min produced a -0.3% loss of bound water; in the second layer of bound water it caused a -3.3% loss of bound water; in the third layer it caused a -6% loss of bound water. Immersion in 100% ethanol or acetone for 5 min produced a 2.8 and 1.9% loss of bound water from the first layer, respectively; it caused a -4 and -7% loss of bound water in the second layer, respectively; and a -17 and -23% loss of bound water in the third layer. Bound water represented 21-25% of total dentin water. Chemical dehydration of water-saturated dentin with ethanol/acetone for 1 min only removed between 25 and 35% of unbound water, respectively.

SIGNIFICANCE

Attempts to remove bound water by evaporation were not very successful. Chemical dehydration with 100% acetone was more successful than 100% ethanol especially the third layer of bound water. Since unbound water represents between 75 and 79% of total matrix water, the more such water can be removed, the more resin can be infiltrated.

Interaction between extracellular matrix molecules and microbial pathogens: evidence for the missing link in autoimmunity with rheumatoid arthritis as a disease model

Rheumatoid arthritis (RA) is an autoimmune disease characterized by inflammation followed by tissue rebuilding or fibrosis. A failure by the body to regulate inflammation effectively is one of the hallmarks of RA. The interaction between the external environment and the human host plays an important role in the development of autoimmunity. In RA, the observation of anti-cyclic citrullinated peptide antibodies (ACPA) to autoantigens is well recognized. Citrullination is a post-translational modification mediated by peptidyl arginine deiminases, which exist in both mammalian and bacterial forms. Previous studies have shown how proteins expressed in the human extracellular matrix (ECM) acquire properties of damage-associated molecular patterns (DAMPs) in RA and include collagens, tenascin-C, and fibronectin (FN). ECM DAMPs can further potentiate tissue damage in RA. Recent work has shown that citrullination in RA occurs at mucosal sites, including the oral cavity and lung. Mucosal sites have been linked with bacterial infection, e.g., periodontal disease, where exogenous pathogens are implicated in the development of autoimmunity via an infectious trigger. Proteases produced at mucosal sites, both by bacteria and the human host, can induce the release of ECM DAMPs, thereby revealing neoepitopes which can be citrullinated and lead to an autoantibody response with further production of ACPA. In this perspectives article, the evidence for the interplay between the ECM and bacteria at human mucosal surfaces, which can become a focus for citrullination and the development of autoimmunity, is explored. Specific examples, with reference to collagen, fibrinogen, and FN, are discussed.

Triple helical collagen-like peptide interactions with selected polyphenolic compounds

Because collagen is the most abundant component of connective tissue, it is an excellent biomaterial in numerous medical applications.

Morphological diversity and polymorphism of self-assembling collagen peptides controlled by length of hydrophobic domains

Synthetic collagen mimetic peptides are used to probe the role of hydrophobic forces in mediating protein self-assembly. Higher order association is an integral property of natural collagens, which assemble into fibers and meshes that comprise the extracellular matrix of connective tissues. The unique triple-helix fold fully exposes two-thirds of positions in the protein to solvent, providing ample opportunities for engineering interaction sites. Inclusion of just a few hydrophobic groups in a minimal peptide promotes a rich variety of self-assembly behaviors, resulting in hundred-nanometer to micron size nanodiscs and nanofibers. Morphology depends primarily on the length of hydrophobic domains. Peptide discs contain lipophilic domains capable of sequestering small hydrophobic dyes. Combining multiple peptide types result in composite structures of discs and fibers ranging from stars to plates-on-a-string. These systems provide valuable tools to shed insight into the fundamental principles underlying hydrophobicity-driven higher order protein association that will facilitate the design of self-assembling systems in biomaterials and nanomedical applications.

Predominant role of water in native collagen assembly inside the bone matrix

Bone is one of the most intriguing biomaterials found in nature consisting of bundles of collagen helixes, hydroxyapatite, and water, forming an exceptionally tough, yet lightweight material. We present here an experimental tool to map water-dependent subtle changes in triple helical assembly of collagen protein in its absolute native environment. Collagen being the most abundant animal protein has been subject of several structural studies in last few decades, mostly on an extracted, overexpressed, and synthesized form of collagen protein. Our method is based on a (1)H detected solid-state nuclear magnetic resonance (ssNMR) experiment performed on native collagen protein inside intact bone matrix. Recent development in (1)H homonuclear decoupling sequences has made it possible to observe specific atomic resolution in a large complex system. The method consists of observing a natural-abundance two-dimensional (2D) (1)H/(13)C heteronuclear correlation (HETCOR) and(1)H double quantum-single quantum (DQ-SQ) correlation ssNMR experiment. The 2D NMR experiment maps three-dimensional assembly of native collagen protein and shows that extracted form of collagen protein is significantly different from protein in the native state. The method also captures native collagen subtle changes (of the order of ∼1.0 Å) due to dehydration and H/D exchange, giving an experimental tool to map small changes. The method has the potential to be of wide applicability to other collagen containing biomaterials.

Peptide internalization enabled by folding: triple helical cell-penetrating peptides

Cell-penetrating peptides (CPPs) are known as efficient transporters of molecular cargo across cellular membranes. Their properties make them ideal candidates for in vivo applications. However, challenges in the development of effective CPPs still exist: CPPs are often fast degraded by proteases and large concentration of CPPs required for cargo transporting can cause cytotoxicity. It was previously shown that restricting peptide flexibility can improve peptide stability against enzymatic degradation and limiting length of CPP peptide can lower cytotoxic effects. Here, we present peptides (30-mers) that efficiently penetrate cellular membranes by combining very short CPP sequences and collagen-like folding domains. The CPP domains are hexa-arginine (R6) or arginine/glycine (RRGRRG). Folding is achieved through multiple proline-hydroxyproline-glycine (POG [proline-hydroxyproline-glycine])n repeats that form a collagen-like triple helical conformation. The folded peptides with CPP domains are efficiently internalized, show stability against enzymatic degradation in human serum and have minimal toxicity. Peptides lacking correct folding (random coil) or CPP domains are unable to cross cellular membranes. These features make triple helical cell-penetrating peptides promising candidates for efficient transporters of molecular cargo across cellular membranes.

Extracellular matrix assembly: a multiscale deconstruction

The biochemical and biophysical properties of the extracellular matrix (ECM) dictate tissue-specific cell behaviour. The molecules that are associated with the ECM of each tissue, including collagens, proteoglycans, laminins and fibronectin, and the manner in which they are assembled determine the structure and the organization of the resultant ECM. The product is a specific ECM signature that is comprised of unique compositional and topographical features that both reflect and facilitate the functional requirements of the tissue.

Direct Evidence of Imino Acid-Aromatic Interactions in Native Collagen Protein by DNP-Enhanced Solid-State NMR Spectroscopy

Aromatic amino acids (AAAs) have rare presence (∼1.4% abundance of Phe) inside of collagen protein, which is the most abundant animal protein playing a functional role in skin, bone, and connective tissues. The role of AAAs is very crucial and has been debated. We present here experimental results depicting interaction of AAAs with imino acids in a native collagen protein sample. The interaction is probed by solid-state NMR (ssNMR) spectroscopy experiments such as (1)H-(13)C heteronuclear correlation (HETCOR) performed on a native collagen sample. The natural abundance (13)C spectrum was obtained by dynamic nuclear polarization (DNP) sensitivity enhancement coupled with ssNMR, providing ∼30-fold signal enhancement. Our results also open up new avenues of probing collagen structure/dynamics closest to the native state by ssNMR experiments coupled with DNP.

Extracellular matrix assembly: a multiscale deconstruction

The biochemical and biophysical properties of the extracellular matrix (ECM) dictate tissue-specific cell behaviour. The molecules that are associated with the ECM of each tissue, including collagens, proteoglycans, laminins and fibronectin, and the manner in which they are assembled determine the structure and the organization of the resultant ECM. The product is a specific ECM signature that is comprised of unique compositional and topographical features that both reflect and facilitate the functional requirements of the tissue.

Extracellular matrix assembly: a multiscale deconstruction

The biochemical and biophysical properties of the extracellular matrix (ECM) dictate tissue-specific cell behaviour. The molecules that are associated with the ECM of each tissue, including collagens, proteoglycans, laminins and fibronectin, and the manner in which they are assembled determine the structure and the organization of the resultant ECM. The product is a specific ECM signature that is comprised of unique compositional and topographical features that both reflect and facilitate the functional requirements of the tissue.

Vibrational sum-frequency scattering for detailed studies of collagen fibers in aqueous environments

Protein fibers play a crucial role in many disease related phenomena and biological systems. A structural analysis of fibrous proteins often requires labeling approaches or disruptive sample preparation while it lacks chemical specificity. Here we demonstrate that the technique of vibrational sum-frequency scattering (SFS) provides a label-free pathway for the chemical and structural analysis of protein fibers in solution. By examining collagen, the most abundant protein in mammals, we demonstrate that the SFS signal of fibers can be detected in the NH, CH stretching and bending, and amide I regions. SFS spectra were found to depend on the scattering angle, which implies the possibility to selectively probe various features of the fibers. The fitting of the data and maximum entropy method analysis revealed a different phase for side-chains and carbonyl contributions, which helps to identify these otherwise overlapping spectral peaks and provides the possibility to perform orientational analysis. Our findings suggest that SFS allows for the greater understanding of protein fibers in solution, which is important when, for example, designing scaffolds in tissue engineering or developing cures for diseases associated with protein fibers.

Biophysical highlights from 54 years of macromolecular crystallography

The United Nations has declared 2014 the International Year of Crystallography, and in commemoration, this review features a selection of 54 notable macromolecular crystal structures that have illuminated the field of biophysics in the 54 years since the first excitement of the myoglobin and hemoglobin structures in 1960. Chronological by publication of the earliest solved structure, each illustrated entry briefly describes key concepts or methods new at the time and key later work leveraged by knowledge of the three-dimensional atomic structure.

X-ray micro-diffraction studies on biological samples at the BioCAT Beamline 18-ID at the Advanced Photon Source

The small source sizes of third-generation synchrotron sources are ideal for the production of microbeams for diffraction studies of crystalline and non-crystalline materials. While several such facilities have been available around the world for some time now, few have been optimized for the handling of delicate soft-tissue specimens under cryogenic conditions. Here the development of a new X-ray micro-diffraction instrument at the Biophysics Collaborative Access Team beamline 18-ID at the Advanced Photon Source, and its use with newly developed cryo-diffraction techniques for soft-tissue studies, are described. The combination of the small beam sizes delivered by this instrument, the high delivered flux and successful cryo-freezing of rat-tail tendon has enabled us to record data to better than 4 Å resolution. The ability to quickly raster scan samples in the beam allows selection of ordered regions in fibrous samples for markedly improved data quality. Examples of results of experiments obtainable using this instrument are presented.

Correlation of discoloration and biomechanical properties in porcine sclera induced by genipin

AIM

To study the feasibility of using the discoloration to evaluate the biomechanical properties after treating with genipin.

METHODS

Porcine cadaver eyes were treated for 30min with 1.0% (by w/v) genipin. Untreated samples were used as controls. After treatment, scleral strips of 4.0×10.0-mm(2) were cut. The denaturation temperature (Td) measurement and stress-strain test were performed after taking photograph to analyze the color.

RESULTS

Within 24h after treating with genipin, the sclera exhibited a bluish color which became deeper with time. And the denaturation temperature also was increased gradually. Compared with untreated groups, at 1, 6, 12, 24 and 36h after treatment, the ultimate stress were increased by 56%, 153%, 173%, 225% and 211% respectively. The Young's modulus at 10% strain also increased by 170%, 246%, 264%, 389% and 288% respectively. There were strong correlation between the discoloration and the biomechanical properties (ΔE-Ultimate stress: R(2)=0.892, P=0.00; ΔE-Young's modulus: R(2)=0.602, P=0.00).

CONCLUSION

Genipin could be used to strengthen collagen gradually in a relatively short time span. And the biomechanical properties could be reliably evaluated via simple visible discoloration.

The collagen-like protein gp12 is a temperature-dependent reversible binder of SPP1 viral capsids

Icosahedral capsids of viruses are lattices of defined geometry and homogeneous size. The (quasi-)equivalent organization of their protein building blocks provides, in numerous systems, the binding sites to assemble arrays of viral polypeptides organized with nanometer precision that protrude from the capsid surface. The capsid of bacterial virus (bacteriophage) SPP1 exposes, at its surface, the 6.6-kDa viral polypeptide gp12 that binds to the center of hexamers of the major capsid protein. Gp12 forms an elongated trimer with collagen-like properties. This is consistent with the fold of eight internal GXY repeats of gp12 to build a stable intersubunit triple helix in a prokaryotic setting. The trimer dissociates and unfolds at near physiological temperatures, as reported for eukaryotic collagen. Its structural organization is reacquired within seconds upon cooling. Interaction with the SPP1 capsid hexamers strongly stabilizes gp12, increasing its Tm to 54 °C. Above this temperature, gp12 dissociates from its binding sites and unfolds reversibly. Multivalent binding of gp12 trimers to the capsid is highly cooperative. The capsid lattice also provides a platform to assist folding and association of unfolded gp12 polypeptides. The original physicochemical properties of gp12 offer a thermoswitchable system for multivalent binding of the polypeptide to the SPP1 capsid surface.

Sources of superoxide/H2O2 during mitochondrial proline oxidation

p53 Inducible gene 6 (PIG6) encodes mitochondrial proline dehydrogenase (PRODH) and is up-regulated several fold upon p53 activation. Proline dehydrogenase is proposed to generate radicals that contribute to cancer cell apoptosis. However, there are at least 10 mitochondrial sites that can produce superoxide and/or H₂O₂, and it is unclear whether proline dehydrogenase generates these species directly, or instead drives production by other sites. Amongst six cancer cell lines, ZR75-30 human breast cancer cells had the highest basal proline dehydrogenase levels, and mitochondria isolated from ZR75-30 cells consumed oxygen and produced H₂O₂ with proline as sole substrate. Insects use proline oxidation to fuel flight, and mitochondria isolated from Drosophila melanogaster were even more active with proline as sole substrate than ZR75-30 mitochondria. Using mitochondria from these two models we identified the sites involved in formation of superoxide/H₂O₂ during proline oxidation. In mitochondria from Drosophila the main sites were respiratory complexes I and II. In mitochondria from ZR75-30 breast cancer cells the main sites were complex I and the oxoglutarate dehydrogenase complex. Even with combinations of substrates and respiratory chain inhibitors designed to minimize the contributions of other sites and maximize any superoxide/H₂O₂ production from proline dehydrogenase itself, there was no significant direct contribution of proline dehydrogenase to the observed H₂O₂ production. Thus proline oxidation by proline dehydrogenase drives superoxide/H₂O₂ production, but it does so mainly or exclusively by providing anaplerotic carbon for other mitochondrial dehydrogenases and not by producing superoxide/H₂O₂ directly.

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Proline dehydrogenase is thought to produce reactive oxygen species (ROS) in cancer cells and to promote apoptosis.

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Isolated mitochondria from Drosophila melanogaster and from a human breast cancer cell line oxidize proline producing superoxide/H₂O₂ at measurable rates.

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Proline oxidation drives superoxide/H₂O₂ production indirectly at other sites and it is unlikely that proline dehydrogenase produces superoxide/H₂O₂ itself.

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In Drosophila, superoxide/H₂O₂ arises from sites I_F and II_F (the flavin sites from complexes I and II, respectively).

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In the breast cancer cell line the main sites are I_F and O_F (from the oxoglutarate dehydrogenase complex).

Chain registry and load-dependent conformational dynamics of collagen

Degradation of fibrillar collagen is critical for tissue maintenance. Yet, understanding collagen catabolism has been challenging partly due to a lack of atomistic picture for its load-dependent conformational dynamics, as both mechanical load and local unfolding of collagen affect its cleavage by matrix metalloproteinase (MMP). We use molecular dynamics simulation to find the most cleavage-prone arrangement of α chains in a collagen triple helix and find amino acids that modulate stability of the MMP cleavage domain depending on the chain registry within the molecule. The native-like state is mechanically inhomogeneous, where the cleavage site interfaces a stiff region and a locally unfolded and flexible region along the molecule. In contrast, a triple helix made of the stable glycine-proline-hydroxyproline motif is uniformly flexible and is dynamically stabilized by short-lived, low-occupancy hydrogen bonds. These results provide an atomistic basis for the mechanics, conformation, and stability of collagen that affect catabolism.