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Genomics May 2020Collagens and collagen-like proteins are found in a wide range of organisms. The common feature of these proteins is a triple helix fold, requiring a characteristic...
Collagens and collagen-like proteins are found in a wide range of organisms. The common feature of these proteins is a triple helix fold, requiring a characteristic pattern of amino acid sequences, composed of Gly-X-Y tripeptide repeats. Collagen-like proteins from bacteria are heterogeneous in terms of length and amino acid composition of their collagenous sequences. However, different bacteria live in different environments, some at extreme temperatures and conditions. This study explores the occurrence of collagen-like sequences in the genomes of different extreme condition-adapted bacteria, and investigates features that could be linked to conditions where they thrive. Our results show that proteins containing collagen-like sequences are encoded by genomes of various extremophiles. Some of these proteins contain conservative domains, characteristic of cell or endospore surface proteins, while most other proteins are unknown. The characteristics of collagenous sequences may depend on both, the phylogenetic relationship and the living conditions of the bacteria.
Topics: Amino Acid Sequence; Amino Acids; Bacterial Proteins; Collagen; Conserved Sequence; Extremophiles; Firmicutes; Genome, Bacterial; Protein Domains
PubMed: 31884159
DOI: 10.1016/j.ygeno.2019.12.023 -
The Journal of Investigative Dermatology Jul 1982Recent biochemical and immunohistochemical studies have described several components of basement membranes including heparan sulfate proteoglycan, 2 high molecular... (Review)
Review
Recent biochemical and immunohistochemical studies have described several components of basement membranes including heparan sulfate proteoglycan, 2 high molecular weight glycoproteins (fibronectin and laminin), and 2 collagen types (IV and V). These collagens have several properties which distinguish them from other types that are located in the interstitium: (a) type IV forms an amorphous, felt-like matrix, and neither IV nor V is found in large, cross-banded fibrils, (b) both have an increased content of hydrophobic amino acids, (c) the precursor (pro) forms are larger than those of interstitial collagens, (d) type IV contains interruptions within the triple helix, and e) both IV and V are resistant to human skin collagenase but are substrates for selected neutral proteases derived from mast cells, macrophages, and granulocytes. By immunofluorescence staining, type IV collagen has been localized to basement membranes at the dermal-epidermal junction, in capillaries, and beneath endothelial cells in larger vessels. Ultrastructurally it has been shown to be a specific component of the lamina densa. Type V collagen has been localized to the pericellular matrices of several cells types and may be specific for extramembranous structures which are closely associated with basal laminae. Other collagenous proteins have been described which may be associated with the extracellular matrix. One of these is secreted by endothelial cells in culture and by peptide mapping represents a novel collagen type. It is secreted under ascorbate-free conditions and is highly sensitive to proteolytic degradation. It has been proposed that a dynamic reciprocity exists between cells and their extracellular matrix which partially determines cell shape, biosynthesis, migration, and attachment. Examples of phenotypic modulation in several of these phenomena have been shown with endothelial cells grown on different substrates and isolated from different vascular environments.
Topics: Basement Membrane; Collagen; Endothelium; Humans; Muscles; Skin
PubMed: 7045245
DOI: 10.1111/1523-1747.ep12545773 -
The Journal of Biological Chemistry Dec 2021Collagens play important roles in development and homeostasis in most higher organisms. In order to function, collagens require the specific chaperone HSP47 for proper...
Collagens play important roles in development and homeostasis in most higher organisms. In order to function, collagens require the specific chaperone HSP47 for proper folding and secretion. HSP47 is known to bind to the collagen triple helix, but the exact positions and numbers of binding sites are not clear. Here, we employed a collagen II peptide library to characterize high-affinity binding sites for HSP47. We show that many previously predicted binding sites have very low affinities due to the presence of a negatively charged amino acid in the binding motif. In contrast, large hydrophobic amino acids such as phenylalanine at certain positions in the collagen sequence increase binding strength. For further characterization, we determined two crystal structures of HSP47 bound to peptides containing phenylalanine or leucine. These structures deviate significantly from previously published ones in which different collagen sequences were used. They reveal local conformational rearrangements of HSP47 at the binding site to accommodate the large hydrophobic side chain from the middle strand of the collagen triple helix and, most surprisingly, possess an altered binding stoichiometry in the form of a 1:1 complex. This altered stoichiometry is explained by steric collisions with the second HSP47 molecule present in all structures determined thus far caused by the newly introduced large hydrophobic residue placed on the trailing strand. This exemplifies the importance of considering all three sites of homotrimeric collagen as independent interaction surfaces and may provide insight into the formation of higher oligomeric complexes at promiscuous collagen-binding sites.
Topics: Amino Acid Sequence; Animals; Binding Sites; Collagen; Crystallography, X-Ray; Dogs; HSP47 Heat-Shock Proteins; Models, Molecular; Peptides; Protein Binding; Protein Conformation
PubMed: 34487762
DOI: 10.1016/j.jbc.2021.101169 -
Marine Drugs Feb 2019The extraction and purification of collagen are of great interest due to its biological function and medicinal applications. Although marine invertebrates are abundant... (Review)
Review
The extraction and purification of collagen are of great interest due to its biological function and medicinal applications. Although marine invertebrates are abundant in the animal kingdom, our knowledge of their extracellular matrix (ECM), which mainly contains collagen, is lacking. The functions of collagen isolated from marine invertebrates remain an untouched source of the proteinaceous component in the development of groundbreaking pharmaceuticals. This review will give an overview of currently used collagens and their future applications, as well as the methodological issues of collagens from marine invertebrates for potential drug discovery.
Topics: Animals; Aquatic Organisms; Collagen; Drug Discovery; Extracellular Matrix; Humans; Invertebrates
PubMed: 30769916
DOI: 10.3390/md17020118 -
International Journal of Molecular... Jun 2022Epithelial cells of multiple types produce and interact with the extracellular matrix to maintain structural integrity and promote healthy function within diverse...
Epithelial cells of multiple types produce and interact with the extracellular matrix to maintain structural integrity and promote healthy function within diverse endogenous tissues. Collagen is a critical component of the matrix, and challenges to collagen's stability in aging, disease, and injury influence survival of adherent epithelial cells. The retinal pigment epithelium (RPE) is important for maintaining proper function of the light-sensitive photoreceptors in the neural retina, in part through synergy with the collagen-rich Bruch's membrane that promotes RPE adherence. Degradation of Bruch's is associated with RPE degeneration, which is implicated early in age-related macular degeneration, a leading cause of irreversible vision loss worldwide. Collagen mimetic peptides (CMPs) effectively repair damage to collagen helices, which are present in all collagens. Our previous work indicates that in doing so, CMPs promote survival and integrity of affected cells and tissues in models of ocular injury and disease, including wounding of corneal epithelial cells. Here, we show that CMPs increase adherence and migration of the ARPE-19 line of human RPE cells challenged by digestion of their collagen substrate. Application of CMPs also reduced both ARPE-19 secretion of pro-inflammatory cytokines (interleukins 6 and 8) and production of reactive oxygen species. Taken together, these results suggest that repairing collagen damaged by aging or other pathogenic processes in the posterior eye could improve RPE adherence and survival and, in doing so, reduce the inflammatory and oxidative stress that perpetuates the cycle of destruction at the root of age-related diseases of the outer retina.
Topics: Bruch Membrane; Collagen; Humans; Oxidative Stress; Peptides; Retinal Pigment Epithelium
PubMed: 35806007
DOI: 10.3390/ijms23137004 -
Journal of Biomedical Materials... Jan 2022This article describes the compositional, mechanical, and structural differences between collagen gels fabricated from different sources and processing methods. Despite...
This article describes the compositional, mechanical, and structural differences between collagen gels fabricated from different sources and processing methods. Despite extensive use of collagen in the manufacturing of biomaterials and implants, there is little information as to the variation in properties based on collagen source or processing methods. As such, differences in purity and composition may affect gel structure and mechanical performance. Using mass spectrometry, we assessed protein composition of collagen from seven different sources. The mechanics and gelation kinetics of each gel were assessed through oscillatory shear rheology. Scanning electron microscopy enabled visualization of distinct differences in fiber morphology. Mechanics and gelation kinetics differed with source and processing method and were found to correlate with differences in composition. Gels fabricated from telopeptide-containing collagens had higher storage modulus (144 vs. 54 Pa) and faster gelation (251 vs. 734 s) compared to atelocollagens, despite having lower purity (93.4 vs. 99.8%). For telopeptide-containing collagens, as collagen purity increased, storage modulus increased and fiber diameter decreased. As α1/α2 chain ratio increased, fiber diameter increased and gelation slowed. As such, this study provides an examination of the effects of collagen processing on key quality attributes for use of collagen gels in biomedical contexts.
Topics: Collagen; Gels; Kinetics; Microscopy, Electron, Scanning; Rheology
PubMed: 34236763
DOI: 10.1002/jbm.a.37261 -
International Journal of Molecular... Jan 2010Collagens, or more precisely collagen-based extracellular matrices, are often considered as a metazoan hallmark. Among the collagens, fibrillar collagens are present... (Review)
Review
Collagens, or more precisely collagen-based extracellular matrices, are often considered as a metazoan hallmark. Among the collagens, fibrillar collagens are present from sponges to humans, and are involved in the formation of the well-known striated fibrils. In this review we discuss the different steps in the evolution of this protein family, from the formation of an ancestral fibrillar collagen gene to the formation of different clades. Genomic data from the choanoflagellate (sister group of Metazoa) Monosiga brevicollis, and from diploblast animals, have suggested that the formation of an ancestral alpha chain occurred before the metazoan radiation. Phylogenetic studies have suggested an early emergence of the three clades that were first described in mammals. Hence the duplication events leading to the formation of the A, B and C clades occurred before the eumetazoan radiation. Another important event has been the two rounds of "whole genome duplication" leading to the amplification of fibrillar collagen gene numbers, and the importance of this diversification in developmental processes. We will also discuss some other aspects of fibrillar collagen evolution such as the development of the molecular mechanisms involved in the formation of procollagen molecules and of striated fibrils.
Topics: Animals; Choanoflagellata; Evolution, Molecular; Fibrillar Collagens; Humans; Protein Structure, Secondary; Protein Structure, Tertiary; Sea Urchins
PubMed: 20386646
DOI: 10.3390/ijms11020407 -
Journal of Cell Science Apr 2005Collagen fibrils in the extracellular matrix allow connective tissues such as tendon, skin and bone to withstand tensile forces. The fibrils are indeterminate in length,... (Review)
Review
Collagen fibrils in the extracellular matrix allow connective tissues such as tendon, skin and bone to withstand tensile forces. The fibrils are indeterminate in length, insoluble and form elaborate three-dimensional arrays that extend over numerous cell lengths. Studies of the molecular basis of collagen fibrillogenesis have provided insight into the trafficking of procollagen (the precursor of collagen) through the cellular secretory pathway, the conversion of procollagen to collagen by the procollagen metalloproteinases, and the directional deposition of fibrils involving the plasma membrane and late secretory pathway. Fibril-associated molecules are targeted to the surface of collagen fibrils, and these molecules play an important role in regulating the diameter and interactions between the fibrils.
Topics: Animals; Extracellular Matrix; Fibrillar Collagens; Humans; Procollagen; Protein Transport
PubMed: 15788652
DOI: 10.1242/jcs.01731 -
Biophysical Journal Sep 2021Extracellular matrix mechanics influence diverse cellular functions, yet surprisingly little is known about the mechanical properties of their constituent collagen...
Extracellular matrix mechanics influence diverse cellular functions, yet surprisingly little is known about the mechanical properties of their constituent collagen proteins. In particular, network-forming collagen IV, an integral component of basement membranes, has been far less studied than fibril-forming collagens. A key feature of collagen IV is the presence of interruptions in the triple-helix-defining (Gly-X-Y) sequence along its collagenous domain. Here, we used atomic force microscopy to determine the impact of sequence heterogeneity on the local flexibility of collagen IV and of the fibril-forming collagen III. Our extracted flexibility profile of collagen IV reveals that it possesses highly heterogeneous mechanics, ranging from semiflexible regions as found for fibril-forming collagens to a lengthy region of high flexibility toward its N-terminus. A simple model in which flexibility is dictated only by the presence of interruptions fit the extracted profile reasonably well, providing insight into the alignment of chains and demonstrating that interruptions, particularly when coinciding in multiple chains, significantly enhance local flexibility. To a lesser extent, sequence variations within the triple helix lead to variable flexibility, as seen along the continuously triple-helical collagen III. We found this fibril-forming collagen to possess a high-flexibility region around its matrix-metalloprotease binding site, suggesting a unique mechanical fingerprint of this region that is key for matrix remodeling. Surprisingly, proline content did not correlate with local flexibility in either collagen type. We also found that physiologically relevant changes in pH and chloride concentration did not alter the flexibility of collagen IV, indicating such environmental changes are unlikely to control its compaction during secretion. Although extracellular chloride ions play a role in triggering collagen IV network formation, they do not appear to modulate the structure of its collagenous domain.
Topics: Basement Membrane; Collagen; Extracellular Matrix; Fibrillar Collagens; Protein Conformation
PubMed: 34390685
DOI: 10.1016/j.bpj.2021.08.013 -
Matrix Biology : Journal of the... Aug 2018The collagen network is altered in fibrotic diseases associated with extracellular matrix (ECM) biosynthesis and remodeling. This mini-review focuses on the quantitative... (Review)
Review
The collagen network is altered in fibrotic diseases associated with extracellular matrix (ECM) biosynthesis and remodeling. This mini-review focuses on the quantitative and qualitative modifications of collagens occurring at the molecular and tissue levels in fibrosis. They result from changes in collagen expression, biosynthesis, enzymatic cross-linking and degradation by several protease families. These molecular modifications, which are mostly regulated by TGF-β, are associated with altered collagen organization at the tissue level, leading to a fibrotic signature that can be analyzed by Second Harmonic Generation (SHG) microscopy.
Topics: Collagen; Extracellular Matrix; Fibrosis; Humans; Second Harmonic Generation Microscopy; Transforming Growth Factor beta
PubMed: 29458139
DOI: 10.1016/j.matbio.2018.02.004