1
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Gajbhiye S, Wairkar S. Collagen fabricated delivery systems for wound healing: A new roadmap. BIOMATERIALS ADVANCES 2022; 142:213152. [PMID: 36270159 DOI: 10.1016/j.bioadv.2022.213152] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Collagen is a biopolymer found in the animal body. It is one of the most abundant proteins in the extracellular matrix that provides strength to the skin, joints, and bones in the human body. It is an important source of elasticity and strength in the extracellular matrix and contributes to the structural and physiological integrity of tissues. Collagen plays an important role in regulating the wound healing process. It helps in wound healing by attracting fibroblasts and encouraging new collagen formation in the wound bed. Therefore, it can be used as a supplementary aid for wound treatment to accelerate the healing process. A prominent benefit of incorporating collagen in wound dressings is its ability to enhance the healing process for critical wounds. Not only collagen but various collagen-containing systems are being prepared to boost its efficacy in wound healing. Different strategies like nanoscale reductions, biopolymers, and incorporating anti-inflammatory and antimicrobial drugs with collagen have been reported. This review article emphasizes the use of collagen for wound healing and various collagen fabricated delivery systems such as nanofibres, nanoparticles, hydrogels, films, and sponges that aid in the healing of wounds.
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Affiliation(s)
- Shruti Gajbhiye
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKMs NMIMS, V.L. Mehta Road, Vile Parle (W), Mumbai, Maharashtra 400056, India
| | - Sarika Wairkar
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKMs NMIMS, V.L. Mehta Road, Vile Parle (W), Mumbai, Maharashtra 400056, India.
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2
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Molecular Tissue Responses to Mechanical Loading. Int J Mol Sci 2022; 23:ijms23042074. [PMID: 35216192 PMCID: PMC8875388 DOI: 10.3390/ijms23042074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 11/25/2022] Open
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3
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Buss DJ, Kröger R, McKee MD, Reznikov N. Hierarchical organization of bone in three dimensions: A twist of twists. J Struct Biol X 2022; 6:100057. [PMID: 35072054 PMCID: PMC8762463 DOI: 10.1016/j.yjsbx.2021.100057] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 11/15/2022] Open
Abstract
Structural hierarchy of bone - observed across multiple scales and in three dimensions (3D) - is essential to its mechanical performance. While the mineralized extracellular matrix of bone consists predominantly of carbonate-substituted hydroxyapatite, type I collagen fibrils, water, and noncollagenous organic constituents (mainly proteins and small proteoglycans), it is largely the 3D arrangement of these inorganic and organic constituents at each length scale that endow bone with its exceptional mechanical properties. Focusing on recent volumetric imaging studies of bone at each of these scales - from the level of individual mineralized collagen fibrils to that of whole bones - this graphical review builds upon and re-emphasizes the original work of James Bell Pettigrew and D'Arcy Thompson who first described the ubiquity of spiral structure in Nature. Here we illustrate and discuss the omnipresence of twisted, curved, sinusoidal, coiled, spiraling, and braided motifs in bone in at least nine of its twelve hierarchical levels - a visualization undertaking that has not been possible until recently with advances in 3D imaging technologies (previous 2D imaging does not provide this information). From this perspective, we hypothesize that the twisting motif occurring across each hierarchical level of bone is directly linked to enhancement of function, rather than being simply an energetically favorable way to assemble mineralized matrix components. We propose that attentive consideration of twists in bone and the skeleton at different scales will likely develop, and will enhance our understanding of structure-function relationships in bone.
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Affiliation(s)
- Daniel J Buss
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A 0C7, Canada
| | - Roland Kröger
- Department of Physics, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Marc D McKee
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A 0C7, Canada.,Faculty of Dentistry, McGill University, 3640 University Street, Montreal, Quebec H3A 0C7, Canada
| | - Natalie Reznikov
- Department of Bioengineering, McGill University, 3480 University Street, Montreal, Quebec H3A 0E9, Canada
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4
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Khazaei S, Soleimani M, Tafti SHA, Aghdam RM, Hojati Z. Improvement of Heart Function After Transplantation of Encapsulated Stem Cells Induced with miR-1/Myocd in Myocardial Infarction Model of Rat. Cell Transplant 2021; 30:9636897211048786. [PMID: 34606735 PMCID: PMC8493326 DOI: 10.1177/09636897211048786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cardiovascular disease is one of the most common causes of death worldwide. Mesenchymal stem cells (MSCs) are one of the most common sources in cell-based therapies in heart regeneration. There are several methods to differentiate MSCs into cardiac-like cells, such as gene induction. Moreover, using a three-dimensional (3D) culture, such as hydrogels increases efficiency of differentiation. In the current study, mouse adipose-derived MSCs were co-transduced with lentiviruses containing microRNA-1 (miR-1) and Myocardin (Myocd). Then, expression of cardiac markers, such as NK2 homeobox 5(Nkx2-5), GATA binding protein 4 (Gata4), and troponin T type 2 (Tnnt2) was investigated, at both gene and protein levels in two-dimensional (2D) culture and chitosan/collagen hydrogel (CS/CO) as a 3D culture. Additionally, after induction of myocardial infarction (MI) in rats, a patch containing the encapsulated induced cardiomyocytes (iCM/P) was implanted to MI zone. Subsequently, 30 days after MI induction, echocardiography, immunohistochemistry staining, and histological examination were performed to evaluate cardiac function. The results of quantitative real -time polymerase chain reaction (qRT-PCR) and immunocytochemistry showed that co-induction of miR-1 and Myocd in MSCs followed by 3D culture of transduced cells increased expression of cardiac markers. Besides, results of in vivo study implicated that heart function was improved in MI model of rats in iCM/P-treated group. The results suggested that miR-1/Myocd induction combined with encapsulation of transduced cells in CS/CO hydrogel increased efficiency of MSCs differentiation into iCMs and could improve heart function in MI model of rats after implantation.
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Affiliation(s)
- Samaneh Khazaei
- Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, Isfahan University, Isfahan, Iran
| | - Masoud Soleimani
- Tissue Engineering and Hematology Department, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.,Tissue Engineering and Nanomedicine Research Center, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Hossein Ahmadi Tafti
- Research Center for Advanced Technologies in Cardiovascular Medicine, Tehran heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Zohreh Hojati
- Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, Isfahan University, Isfahan, Iran
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5
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Al-Shaer A, Lyons A, Ishikawa Y, Hudson BG, Boudko SP, Forde NR. Sequence-dependent mechanics of collagen reflect its structural and functional organization. Biophys J 2021; 120:4013-4028. [PMID: 34390685 DOI: 10.1016/j.bpj.2021.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/25/2021] [Accepted: 08/06/2021] [Indexed: 01/06/2023] Open
Abstract
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.
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Affiliation(s)
- Alaa Al-Shaer
- Department of Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada
| | - Aaron Lyons
- Department of Physics, Burnaby, British Columbia, Canada
| | - Yoshihiro Ishikawa
- Department of Ophthalmology, University of California San Francisco, School of Medicine, San Francisco, California
| | - Billy G Hudson
- Department of Medicine, Division of Nephrology and Hypertension, Nashville, Tennessee; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biochemistry, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Nashville, Tennessee; Department of Cell and Developmental Biology, Nashville, Tennessee; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee
| | - Sergei P Boudko
- Department of Medicine, Division of Nephrology and Hypertension, Nashville, Tennessee; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biochemistry, Nashville, Tennessee
| | - Nancy R Forde
- Department of Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada; Department of Physics, Burnaby, British Columbia, Canada; Department of Chemistry, Burnaby, British Columbia, Canada; Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada.
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6
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Salvatore L, Gallo N, Natali ML, Terzi A, Sannino A, Madaghiele M. Mimicking the Hierarchical Organization of Natural Collagen: Toward the Development of Ideal Scaffolding Material for Tissue Regeneration. Front Bioeng Biotechnol 2021; 9:644595. [PMID: 33987173 PMCID: PMC8112590 DOI: 10.3389/fbioe.2021.644595] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/15/2021] [Indexed: 12/11/2022] Open
Abstract
Biological materials found in living organisms, many of which are proteins, feature a complex hierarchical organization. Type I collagen, a fibrous structural protein ubiquitous in the mammalian body, provides a striking example of such a hierarchical material, with peculiar architectural features ranging from the amino acid sequence at the nanoscale (primary structure) up to the assembly of fibrils (quaternary structure) and fibers, with lengths of the order of microns. Collagen plays a dominant role in maintaining the biological and structural integrity of various tissues and organs, such as bone, skin, tendons, blood vessels, and cartilage. Thus, "artificial" collagen-based fibrous assemblies, endowed with appropriate structural properties, represent ideal substrates for the development of devices for tissue engineering applications. In recent years, with the ultimate goal of developing three-dimensional scaffolds with optimal bioactivity able to promote both regeneration and functional recovery of a damaged tissue, numerous studies focused on the capability to finely modulate the scaffold architecture at the microscale and the nanoscale in order to closely mimic the hierarchical features of the extracellular matrix and, in particular, the natural patterning of collagen. All of these studies clearly show that the accurate characterization of the collagen structure at the submolecular and supramolecular levels is pivotal to the understanding of the relationships between the nanostructural/microstructural properties of the fabricated scaffold and its macroscopic performance. Several studies also demonstrate that the selected processing, including any crosslinking and/or sterilization treatments, can strongly affect the architecture of collagen at various length scales. The aim of this review is to highlight the most recent findings on the development of collagen-based scaffolds with optimized properties for tissue engineering. The optimization of the scaffolds is particularly related to the modulation of the collagen architecture, which, in turn, impacts on the achieved bioactivity.
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Affiliation(s)
- Luca Salvatore
- Department of Engineering for Innovation, University of Salento, Lecce, Italy
| | - Nunzia Gallo
- Department of Engineering for Innovation, University of Salento, Lecce, Italy
| | - Maria Lucia Natali
- Department of Engineering for Innovation, University of Salento, Lecce, Italy
| | - Alberta Terzi
- Institute of Crystallography, National Research Council, Bari, Italy
| | - Alessandro Sannino
- Department of Engineering for Innovation, University of Salento, Lecce, Italy
| | - Marta Madaghiele
- Department of Engineering for Innovation, University of Salento, Lecce, Italy
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7
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Cutini M, Bechis I, Corno M, Ugliengo P. Balancing Cost and Accuracy in Quantum Mechanical Simulations on Collagen Protein Models. J Chem Theory Comput 2021; 17:2566-2574. [PMID: 33754704 DOI: 10.1021/acs.jctc.1c00015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Collagen proteins are spread in almost every vertebrate's tissue with mechanical function. The defining feature of this fundamental family of proteins is its well-known collagen triple-helical domain. This helical domain can have different geometries, varying in helical elongation and interstrands contact, as a function of the amino acidic composition. The helical geometrical features play an important role in the interaction of the collagen protein with cell receptors, but for the vast majority of collagen compositions, these geometrical features are unknown. Quantum mechanical (QM) simulations based on the density functional theory (DFT) provide a robust approach to characterize the scenario on the collagen composition-structure relationships. In this work, we analyze the role of the adopted computational method in predicting the collagen structure for two purposes. First, we look for a cost-effective computational approach to apply to a large-scale composition-structure analysis. Second, we attempt to assess the robustness of the predictions by varying the QM methods. Therefore, we have run geometry optimization on periodic models of the collagen protein using a variety of approaches based on the most commonly used DFT functionals (PBE, HSE06, and B3LYP) with and without dispersion correction (D3ABC). We have coupled these methods with several different basis sets, looking for the highest accuracy/cost ratio. Furthermore, we have studied the performance of the composite HF-3c method and the semiempirical GFN1-xTB method. Our results identify a computational recipe that is potentially capable of predicting collagen structural features in line with DFT simulations, with orders of magnitude reduced computational cost, encouraging further investigations on the topic.
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Affiliation(s)
- Michele Cutini
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Centre, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
| | - Irene Bechis
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Centre, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
| | - Marta Corno
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Centre, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
| | - Piero Ugliengo
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Centre, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
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8
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Xu Y, Kirchner M. Collagen Mimetic Peptides. Bioengineering (Basel) 2021; 8:5. [PMID: 33466358 PMCID: PMC7824840 DOI: 10.3390/bioengineering8010005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022] Open
Abstract
Since their first synthesis in the late 1960s, collagen mimetic peptides (CMPs) have been used as a molecular tool to study collagen, and as an approach to develop novel collagen mimetic biomaterials. Collagen, a major extracellular matrix (ECM) protein, plays vital roles in many physiological and pathogenic processes. Applications of CMPs have advanced our understanding of the structure and molecular properties of a collagen triple helix-the building block of collagen-and the interactions of collagen with important molecular ligands. The accumulating knowledge is also paving the way for developing novel CMPs for biomedical applications. Indeed, for the past 50 years, CMP research has been a fast-growing, far-reaching interdisciplinary field. The major development and achievement of CMPs were documented in a few detailed reviews around 2010. Here, we provided a brief overview of what we have learned about CMPs-their potential and their limitations. We focused on more recent developments in producing heterotrimeric CMPs, and CMPs that can form collagen-like higher order molecular assemblies. We also expanded the traditional view of CMPs to include larger designed peptides produced using recombinant systems. Studies using recombinant peptides have provided new insights on collagens and promoted progress in the development of collagen mimetic fibrillar self-assemblies.
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Affiliation(s)
- Yujia Xu
- Department of Chemistry, Hunter College of the City University of New York, 695 Park Ave., New York, NY 10065, USA;
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9
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Xu Y, Nudelman F, Eren ED, Wirix MJM, Cantaert B, Nijhuis WH, Hermida-Merino D, Portale G, Bomans PHH, Ottmann C, Friedrich H, Bras W, Akiva A, Orgel JPRO, Meldrum FC, Sommerdijk N. Intermolecular channels direct crystal orientation in mineralized collagen. Nat Commun 2020; 11:5068. [PMID: 33033251 PMCID: PMC7545172 DOI: 10.1038/s41467-020-18846-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/27/2020] [Indexed: 12/27/2022] Open
Abstract
The mineralized collagen fibril is the basic building block of bone, and is commonly pictured as a parallel array of ultrathin carbonated hydroxyapatite (HAp) platelets distributed throughout the collagen. This orientation is often attributed to an epitaxial relationship between the HAp and collagen molecules inside 2D voids within the fibril. Although recent studies have questioned this model, the structural relationship between the collagen matrix and HAp, and the mechanisms by which collagen directs mineralization remain unclear. Here, we use XRD to reveal that the voids in the collagen are in fact cylindrical pores with diameters of ~2 nm, while electron microscopy shows that the HAp crystals in bone are only uniaxially oriented with respect to the collagen. From in vitro mineralization studies with HAp, CaCO3 and γ-FeOOH we conclude that confinement within these pores, together with the anisotropic growth of HAp, dictates the orientation of HAp crystals within the collagen fibril.
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Affiliation(s)
- YiFei Xu
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Fabio Nudelman
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,School of Chemistry, University of Edinburgh, Joseph Black Building, The King's Buildings, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - E Deniz Eren
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Chemical Engineering and Chemistry, Laboratory of Physical Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Maarten J M Wirix
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Bram Cantaert
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Wouter H Nijhuis
- Department of Orthopaedic Surgery, University Medical Centre Utrecht, Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - Daniel Hermida-Merino
- Netherlands Organization for Scientific Research (NWO), DUBBLE@ESRF, BP220, F38043, Grenoble, France
| | - Giuseppe Portale
- Netherlands Organization for Scientific Research (NWO), DUBBLE@ESRF, BP220, F38043, Grenoble, France.,Macromolecular Science and New Polymeric Materials, Zernike Institute for Advanced Materials, University of Groningen, Nijemborg 4, 9747, Groningen, The Netherlands
| | - Paul H H Bomans
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Christian Ottmann
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Heiner Friedrich
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Chemical Engineering and Chemistry, Laboratory of Physical Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Wim Bras
- Netherlands Organization for Scientific Research (NWO), DUBBLE@ESRF, BP220, F38043, Grenoble, France.,Chemical Sciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Anat Akiva
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Cell Biology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein, 6525 GA, Nijmegen, The Netherlands
| | - Joseph P R O Orgel
- Departments of Biology, Physics and Biomedical Engineering, Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA.
| | - Fiona C Meldrum
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Nico Sommerdijk
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands. .,Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands. .,Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein, 6525 GA, Nijmegen, The Netherlands.
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10
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Tang M, Wang X, Gandhi NS, Foley BL, Burrage K, Woods RJ, Gu Y. Effect of hydroxylysine-O-glycosylation on the structure of type I collagen molecule: A computational study. Glycobiology 2020; 30:830-843. [PMID: 32188979 PMCID: PMC7526737 DOI: 10.1093/glycob/cwaa026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/07/2020] [Accepted: 03/16/2020] [Indexed: 12/25/2022] Open
Abstract
Collagen undergoes many types of post-translational modifications (PTMs), including intracellular modifications and extracellular modifications. Among these PTMs, glycosylation of hydroxylysine (Hyl) is the most complicated. Experimental studies demonstrated that this PTM ceases once the collagen triple helix is formed and that Hyl-O-glycosylation modulates collagen fibrillogenesis. However, the underlying atomic-level mechanisms of these phenomena remain unclear. In this study, we first adapted the force field parameters for O-linkages between Hyl and carbohydrates and then investigated the influence of Hyl-O-glycosylation on the structure of type I collagen molecule, by performing comprehensive molecular dynamic simulations in explicit solvent of collagen molecule segment with and without the glycosylation of Hyl. Data analysis demonstrated that (i) collagen triple helices remain in a triple-helical structure upon glycosylation of Hyl; (ii) glycosylation of Hyl modulates the peptide backbone conformation and their solvation environment in the vicinity and (iii) the attached sugars are arranged such that their hydrophilic faces are well exposed to the solvent, while their hydrophobic faces point towards the hydrophobic portions of collagen. The adapted force field parameters for O-linkages between Hyl and carbohydrates will aid future computational studies on proteins with Hyl-O-glycosylation. In addition, this work, for the first time, presents the detailed effect of Hyl-O-glycosylation on the structure of human type I collagen at the atomic level, which may provide insights into the design and manufacture of collagenous biomaterials and the development of biomedical therapies for collagen-related diseases.
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Affiliation(s)
- Ming Tang
- School of Chemistry Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, 4001 Australia
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Neha S Gandhi
- School of Mathematical Sciences, Queensland University of Technology, Brisbane 4001, Australia
| | | | - Kevin Burrage
- School of Mathematical Sciences, Queensland University of Technology, Brisbane 4001, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane 4001, Australia
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - YuanTong Gu
- School of Chemistry Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, 4001 Australia
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11
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Zhu J, Madhurapantula RS, Kalyanasundaram A, Sabharwal T, Antipova O, Bishnoi SW, Orgel JPRO. Ultrastructural Location and Interactions of the Immunoglobulin Receptor Binding Sequence within Fibrillar Type I Collagen. Int J Mol Sci 2020; 21:ijms21114166. [PMID: 32545195 PMCID: PMC7312686 DOI: 10.3390/ijms21114166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
Collagen type I is a major constituent of animal bodies. It is found in large quantities in tendon, bone, skin, cartilage, blood vessels, bronchi, and the lung interstitium. It is also produced and accumulates in large amounts in response to certain inflammations such as lung fibrosis. Our understanding of the molecular organization of fibrillar collagen and cellular interaction motifs, such as those involved with immune-associated molecules, continues to be refined. In this study, antibodies raised against type I collagen were used to label intact D-periodic type I collagen fibrils and observed with atomic force microscopy (AFM), and X-ray diffraction (XRD) and immunolabeling positions were observed with both methods. The antibodies bind close to the C-terminal telopeptide which verifies the location and accessibility of both the major histocompatibility complex (MHC) class I (MHCI) binding domain and C-terminal telopeptide on the outside of the collagen fibril. The close proximity of the C-telopeptide and the MHC1 domain of type I collagen to fibronectin, discoidin domain receptor (DDR), and collagenase cleavage domains likely facilitate the interaction of ligands and receptors related to cellular immunity and the collagen-based Extracellular Matrix.
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Affiliation(s)
- Jie Zhu
- Institute of Biophysics, College of science, Northwest A&F University, Yangling 712100, China
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA; (R.S.M.); (A.K.); (T.S.); (O.A.)
- Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
- Correspondence: (J.Z.); (J.P.R.O.O.)
| | - Rama S. Madhurapantula
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA; (R.S.M.); (A.K.); (T.S.); (O.A.)
- Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Aruna Kalyanasundaram
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA; (R.S.M.); (A.K.); (T.S.); (O.A.)
| | - Tanya Sabharwal
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA; (R.S.M.); (A.K.); (T.S.); (O.A.)
| | - Olga Antipova
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA; (R.S.M.); (A.K.); (T.S.); (O.A.)
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sandra W. Bishnoi
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Joseph P. R. O. Orgel
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA; (R.S.M.); (A.K.); (T.S.); (O.A.)
- Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
- Correspondence: (J.Z.); (J.P.R.O.O.)
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12
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Madhurapantula RS, Krell G, Morfin B, Roy R, Lister K, Orgel JP. Advanced Methodology and Preliminary Measurements of Molecular and Mechanical Properties of Heart Valves under Dynamic Strain. Int J Mol Sci 2020; 21:E763. [PMID: 31991583 PMCID: PMC7037596 DOI: 10.3390/ijms21030763] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 11/16/2022] Open
Abstract
Mammalian heart valves are soft tissue assemblies with multi-scale material properties. This is because they are constructs comprising both muscle and non-contractile extracellular matrix proteins (such as collagens and proteoglycans) and transition regions where one form of tissue structure becomes another, significantly different form. The leaflets of the mitral and tricuspid valves are connected to chordae tendinae which, in turn, bind through papillary muscles to the cardiac wall of the ventricle. The transition regions between these tissue subsets are complex and diffuse. Their material composition and mechanical properties have not been previously described with both micro and nanoscopic data recorded simultaneously, as reported here. Annotating the mechanical characteristics of these tissue transitions will be of great value in developing novel implants, improving the state of the surgical simulators and advancing robot-assisted surgery. We present here developments in multi-scale methodology that produce data that can relate mechanical properties to molecular structure using scanning X-ray diffraction. We correlate these data to corresponding tissue level (macro and microscopic) stress and strain, with particular emphasis on the transition regions and present analyses to indicate points of possible failure in these tissues.
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Affiliation(s)
- Rama S. Madhurapantula
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA;
- Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA;
| | - Gabriel Krell
- Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA;
| | - Berenice Morfin
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA;
| | - Rajarshi Roy
- Corvid Technologies, Mooresville, NC 28117, USA; (R.R.); (K.L.)
| | - Kevin Lister
- Corvid Technologies, Mooresville, NC 28117, USA; (R.R.); (K.L.)
| | - Joseph P.R.O. Orgel
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA;
- Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA;
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
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13
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Kirkness MWH, Lehmann K, Forde NR. Mechanics and structural stability of the collagen triple helix. Curr Opin Chem Biol 2019; 53:98-105. [DOI: 10.1016/j.cbpa.2019.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/24/2019] [Accepted: 08/12/2019] [Indexed: 01/18/2023]
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14
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Giannini C, Terzi A, Fusaro L, Sibillano T, Diaz A, Ramella M, Lutz‐Bueno V, Boccafoschi F, Bunk O. Scanning X-ray microdiffraction of decellularized pericardium tissue at increasing glucose concentration. JOURNAL OF BIOPHOTONICS 2019; 12:e201900106. [PMID: 31211508 PMCID: PMC7065647 DOI: 10.1002/jbio.201900106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/20/2019] [Accepted: 06/14/2019] [Indexed: 05/27/2023]
Abstract
Blood glucose supplies energy to cells and is critical for the human brain. Glycation of collagen, the nonenzymatic formation of glucose-bridges, relates to diseases of aging populations and diabetics. This chemical reaction, together with its biomechanical effects, has been well studied employing animal models. However, the direct impact of glycation on collagen nano-structure is largely overlooked, and there is a lack of ex vivo model systems. Here, we present the impact of glucose on collagen nanostructure in a model system based on abundantly available connective tissue of farm animals. By combining ex vivo small and wide-angle X-ray scattering (SAXS/WAXS) imaging, we characterize intra- and inter-molecular parameters of collagen in decellularized bovine pericardium with picometer precision. We observe three distinct regimes according to glucose concentration. Such a study opens new avenues for inspecting the effects of diabetes mellitus on connective tissues and the influence of therapies on the resulting secondary disorders.
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Affiliation(s)
- Cinzia Giannini
- Institute of CrystallographyNational Research CouncilBariItaly
| | - Alberta Terzi
- Institute of CrystallographyNational Research CouncilBariItaly
| | - Luca Fusaro
- Department of Health SciencesUniversity of Piemonte OrientaleNovaraItaly
- Tissuegraft srl.NovaraItaly
| | | | - Ana Diaz
- Paul Scherrer InstitutVilligenSwitzerland
| | - Martina Ramella
- Department of Health SciencesUniversity of Piemonte OrientaleNovaraItaly
- Tissuegraft srl.NovaraItaly
| | | | - Francesca Boccafoschi
- Institute of CrystallographyNational Research CouncilBariItaly
- Department of Health SciencesUniversity of Piemonte OrientaleNovaraItaly
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15
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Orgel JPRO, Madhurapantula RS. A structural prospective for collagen receptors such as DDR and their binding of the collagen fibril. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118478. [PMID: 31004686 DOI: 10.1016/j.bbamcr.2019.04.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/13/2022]
Abstract
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.
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Affiliation(s)
- Joseph P R O Orgel
- Departments of Biology and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA.
| | - Rama S Madhurapantula
- Departments of Biology and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
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16
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Simon P, Grüner D, Worch H, Pompe W, Lichte H, El Khassawna T, Heiss C, Wenisch S, Kniep R. First evidence of octacalcium phosphate@osteocalcin nanocomplex as skeletal bone component directing collagen triple-helix nanofibril mineralization. Sci Rep 2018; 8:13696. [PMID: 30209287 PMCID: PMC6135843 DOI: 10.1038/s41598-018-31983-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/29/2018] [Indexed: 01/27/2023] Open
Abstract
Tibia trabeculae and vertebrae of rats as well as human femur were investigated by high-resolution TEM at the atomic scale in order to reveal snapshots of the morphogenetic processes of local bone ultrastructure formation. By taking into account reflections of hydroxyapatite for Fourier filtering the appearance of individual alpha-chains within the triple-helix clearly shows that bone bears the feature of an intergrowth composite structure extending from the atomic to the nanoscale, thus representing a molecular composite of collagen and apatite. Careful Fourier analysis reveals that the non-collagenous protein osteocalcin is present directly combined with octacalcium phosphate. Besides single spherical specimen of about 2 nm in diameter, osteocalcin is spread between and over collagen fibrils and is often observed as pearl necklace strings. In high-resolution TEM, the three binding sites of the γ-carboxylated glutamic acid groups of the mineralized osteocalcin were successfully imaged, which provide the chemical binding to octacalcium phosphate. Osteocalcin is attached to the collagen structure and interacts with the Ca-sites on the (100) dominated hydroxyapatite platelets with Ca-Ca distances of about 9.5 Å. Thus, osteocalcin takes on the functions of Ca-ion transport and suppression of hydroxyapatite expansion.
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Affiliation(s)
- Paul Simon
- Max-Planck-Institut für Chemische Physik fester Stoffe, Nöthnitzer Str. 40, 01187, Dresden, Germany.
| | - Daniel Grüner
- Forschungszentrum Jülich GmbH, Institute of Energy and Climate Research, IEK-2, 52425, Jülich, Germany
| | - Hartmut Worch
- Institute of Materials Science, Technical University of Dresden, Helmholtzstr. 7, 01069, Dresden, Germany
| | - Wolfgang Pompe
- Institute of Materials Science, Technical University of Dresden, Helmholtzstr. 7, 01069, Dresden, Germany
| | - Hannes Lichte
- Institute of Structure Physics, Technical University of Dresden, Zum Triebenberg 50, 01328, Dresden Zaschendorf, Germany
| | - Thaqif El Khassawna
- Experimental Trauma Surgery, Faculty of Medicine, Justus-Liebig University of Giessen, Aulweg 128, Giessen, 35392, Germany
| | - Christian Heiss
- Experimental Trauma Surgery, Faculty of Medicine, Justus-Liebig University of Giessen, Aulweg 128, Giessen, 35392, Germany
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital of Giessen-Marburg, Giessen, Germany
| | - Sabine Wenisch
- Clinic of Small animals, c/o Institute of Veterinary Anatomy, Justus-Liebig University of Giessen, Giessen, Germany
| | - Rüdiger Kniep
- Max-Planck-Institut für Chemische Physik fester Stoffe, Nöthnitzer Str. 40, 01187, Dresden, Germany
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17
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Reznikov N, Bilton M, Lari L, Stevens MM, Kröger R. Fractal-like hierarchical organization of bone begins at the nanoscale. Science 2018; 360:360/6388/eaao2189. [PMID: 29724924 DOI: 10.1126/science.aao2189] [Citation(s) in RCA: 259] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 03/08/2018] [Indexed: 01/01/2023]
Abstract
The components of bone assemble hierarchically to provide stiffness and toughness. However, the organization and relationship between bone's principal components-mineral and collagen-has not been clearly elucidated. Using three-dimensional electron tomography imaging and high-resolution two-dimensional electron microscopy, we demonstrate that bone mineral is hierarchically assembled beginning at the nanoscale: Needle-shaped mineral units merge laterally to form platelets, and these are further organized into stacks of roughly parallel platelets. These stacks coalesce into aggregates that exceed the lateral dimensions of the collagen fibrils and span adjacent fibrils as continuous, cross-fibrillar mineralization. On the basis of these observations, we present a structural model of hierarchy and continuity for the mineral phase, which contributes to the structural integrity of bone.
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Affiliation(s)
- Natalie Reznikov
- Department of Materials, Department of Bioengineering and Institute for Biomedical Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Matthew Bilton
- Department of Physics, University of York, Heslington, York, UK.,4D LABS, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Leonardo Lari
- Department of Physics, University of York, Heslington, York, UK.,York JEOL Nanocentre, Science Park, York, UK
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering and Institute for Biomedical Engineering, Faculty of Engineering, Imperial College London, London, UK.
| | - Roland Kröger
- Department of Physics, University of York, Heslington, York, UK.
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18
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Li X, Buda F, de Groot HJ, Sevink GJA. Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2018; 122:14877-14888. [PMID: 30258522 PMCID: PMC6150686 DOI: 10.1021/acs.jpcc.8b01790] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/30/2018] [Indexed: 06/08/2023]
Abstract
Chlorosome antennae form an interesting class of materials for studying the role of structural motifs and dynamics in nonadiabatic energy transfer. They perform robust and highly quantum-efficient transfer of excitonic energy while allowing for compositional variation and completely lacking the usual regulatory proteins. Here, we first cast the geometrical analysis for ideal tubular scaffolding models into a formal framework, to relate effective helical properties of the assembly structures to established characterization data for various types of chlorosomes. This analysis shows that helicity is uniquely defined for chlorosomes composed of bacteriochlorophyll (BChl) d and that three chiral angles are consistent with the nuclear magnetic resonance (NMR) and electron microscope data for BChl c, including two novel ones that are at variance with current interpretations of optical data based on perfect cylindrical symmetry. We use this information as a starting point for investigating dynamic and static heterogeneity at the molecular level by unconstrained molecular dynamics. We first identify a rotational degree of freedom, along the Mg-OH coordination bond, that alternates along the syn-anti stacks and underlies the (flexible) curvature on a larger scale. Because rotation directly relates to the formation or breaking of interstack hydrogen bonds of the O-H···O=C structural motif along the syn-anti stacks, we analyzed the relative fractions of hydrogen-bonded and the nonbonded regions, forming stripe domains in otherwise spectroscopically homogeneous curved slabs. The ratios 7:3 for BChl c and 9:1 for BChl d for the two distinct structural components agree well with the signal intensities determined by NMR. In addition, rotation with curvature-independent formation of stripe domains offers a viable explanation for the localization and dispersion of exciton states over two fractions, as observed in single chlorosome fluorescence decay studies.
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19
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Ganesan VV, Dhanasekaran M, Thangavel N, Dhathathreyan A. Elastic compliance of fibrillar assemblies in type I collagen. Biophys Chem 2018; 240:15-24. [PMID: 29857170 DOI: 10.1016/j.bpc.2018.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/17/2018] [Accepted: 05/22/2018] [Indexed: 11/17/2022]
Abstract
Fibrillary assemblies of Type I collagen find important applications in tissue engineering and as matrices for biophysical studies. The mechanical and structural properties of these structures are governed by factors such as protein concentration, temperature, pH and ionic strength. This study reports on an impedance based analysis of the elastic compliance of fibrillary assemblies of Type I collagen using quartz crystal microbalance with dissipation (QCM-D) at a fundamental frequency of 5 MHz and overtones (n = 3,5,7,9,11). Here, In situ partial fibrillation of the adsorbing collagen followed by its fibrillary assemblies on hydrophilic gold coated quartz surface have been crosslinked using Gallic acid (GA), Chromium (III) gallate (Cr-GA), Catechin (Cat), Tetrakis(hydroxymethyl)phosphonium sulfate (THPS) and Oxazolidine (Ox). This approach allows direct comparison of how viscoelastic properties track the structural evolution of the fiber and network length scales. The collagen crosslinking shows significant positive impact on the protein's mechanical behaviour and on the type of crosslinking agents used. The elastic modulus increases as collagen <GA < THPS < Cr-GA < Cat < Ox. Atomic force microscopic studies on the adsorbed collagen after cross linking confirmed the presence of fibrous assemblies. The results indicate stabilization and reinforcement through strong physical entanglement between the molecules of collagen as well as chemical interaction between collagen matrix and fibrils during cross linking. The elastic compliance evaluated from ΔDissipation/Δfreq. from QCM-D showed that cross linking with GA, Cr-GA and Ox resulted in flexible fibrillary network while agents like THPS and Cat showed elastic moduli similar to that of pure collagen. Results suggest that optimal collagen-crosslinking agent ratio and degree of crosslinking of collagen can help tailor the mechanical properties for specific applications in design of bio-materials of these composites.
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20
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Langhans SA. Three-Dimensional in Vitro Cell Culture Models in Drug Discovery and Drug Repositioning. Front Pharmacol 2018; 9:6. [PMID: 29410625 PMCID: PMC5787088 DOI: 10.3389/fphar.2018.00006] [Citation(s) in RCA: 875] [Impact Index Per Article: 145.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/03/2018] [Indexed: 02/06/2023] Open
Abstract
Drug development is a lengthy and costly process that proceeds through several stages from target identification to lead discovery and optimization, preclinical validation and clinical trials culminating in approval for clinical use. An important step in this process is high-throughput screening (HTS) of small compound libraries for lead identification. Currently, the majority of cell-based HTS is being carried out on cultured cells propagated in two-dimensions (2D) on plastic surfaces optimized for tissue culture. At the same time, compelling evidence suggests that cells cultured in these non-physiological conditions are not representative of cells residing in the complex microenvironment of a tissue. This discrepancy is thought to be a significant contributor to the high failure rate in drug discovery, where only a low percentage of drugs investigated ever make it through the gamut of testing and approval to the market. Thus, three-dimensional (3D) cell culture technologies that more closely resemble in vivo cell environments are now being pursued with intensity as they are expected to accommodate better precision in drug discovery. Here we will review common approaches to 3D culture, discuss the significance of 3D cultures in drug resistance and drug repositioning and address some of the challenges of applying 3D cell cultures to high-throughput drug discovery.
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Affiliation(s)
- Sigrid A. Langhans
- Nemours Center for Childhood Cancer Research and Nemours Center for Neuroscience Research, Alfred I. duPont Hospital for Children, Wilmington, DE, United States
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21
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Patel S, Rauf A, Meher BR. In silico analysis of ChtBD3 domain to find its role in bacterial pathogenesis and beyond. Microb Pathog 2017; 110:519-526. [PMID: 28760454 DOI: 10.1016/j.micpath.2017.07.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 12/12/2022]
Abstract
Chitin binding domain 3, known by the acronym ChtBD3, is a domain in the enzymes and proteins of several pathogenic virus, bacteria and fungi. As this domain is evolutionarily-conserved in virulence factors of these infectious agents, its detailed investigation is of clinical interest. In this regard, the current in silico study analyzed ChtBD3 domain distribution in bacterial proteins present in publicly-available SMART (simple modular architecture research tool) database. Also, the co-occurring domains of ChtBD3 in the studied proteins were mapped to understand positional rearrangement of the domain and consequent functional diversity. Custom-made scripts were used to interpret the data and to derive patterns. As expected, interesting results were obtained. ChtBD3 domain co-occurred with other critical domains like peptidase, glycol_hydrolase, kinase, hemagglutinin-acting, collagen-binding, among others. The findings are expected to be of clinical relevance.
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, 92182, USA.
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar, 23561, Khyber Pakhtunkhwa, Pakistan.
| | - Biswa Ranjan Meher
- Centre for Life Sciences, Central University of Jharkhand, Brambe, Ranchi, 835205, Jharkhand, India
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22
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Dong S, Huang Z, Tang L, Zhang X, Zhang Y, Jiang Y. A three-dimensional collagen-fiber network model of the extracellular matrix for the simulation of the mechanical behaviors and micro structures. Comput Methods Biomech Biomed Engin 2017; 20:991-1003. [DOI: 10.1080/10255842.2017.1321113] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Shoubin Dong
- School of Computer Science & Engineering, South China University of Technology, Guangzhou, China
| | - Zetao Huang
- School of Computer Science & Engineering, South China University of Technology, Guangzhou, China
| | - Liqun Tang
- School of Civil Engineering & Transportation, South China University of Technology, Guangzhou, China
| | - Xiaoyang Zhang
- School of Civil Engineering & Transportation, South China University of Technology, Guangzhou, China
| | - Yongrou Zhang
- School of Civil Engineering & Transportation, South China University of Technology, Guangzhou, China
| | - Yi Jiang
- Department of Mathematics & Statistics, Georgia State University, Atlanta, Georgia, USA
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23
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Esipova NG, Tumanyan VG. Omnipresence of the polyproline II helix in fibrous and globular proteins. Curr Opin Struct Biol 2017; 42:41-49. [DOI: 10.1016/j.sbi.2016.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/10/2016] [Accepted: 10/14/2016] [Indexed: 10/20/2022]
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24
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Patel S, Goyal A. Chitin and chitinase: Role in pathogenicity, allergenicity and health. Int J Biol Macromol 2017; 97:331-338. [PMID: 28093332 DOI: 10.1016/j.ijbiomac.2017.01.042] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/05/2017] [Accepted: 01/10/2017] [Indexed: 01/09/2023]
Abstract
Chitin, a polysaccharide with particular abundance in fungi, nematodes and arthropods is immunogenic. It acts as a threat to other organisms, to tackle which they have been endowed with chitinase enzyme. Even if this enzyme is not present in all organisms, they possess proteins having chitin-binding domain(s) (ChtBD). Many lethal viruses like Ebola, and HCV (Hepatitis C virus) have these domains to manipulate their carriers and target organisms. In keeping with the basic rule of survival, the self-origin (own body component) chitins and chitinases are protective, but that of non-self origin (from other organisms) are detrimental to health. The exogenous chitins and chitinases provoke human innate immunity to generate a deluge of inflammatory cytokines, which injure organs (leading to asthma, atopic dermatitis etc.), and in persistent situations lead to death (multiple sclerosis, systemic lupus erythromatosus (SLE), cancer, etc.). Unfortunately, chitin-chitinase-stimulated hypersensitivity is a common cause of occupational allergy. On the other hand, chitin, and its deacetylated derivative chitosan are increasingly proving useful in pharmaceutical, agriculture, and biocontrol applications. This critical review discusses the complex nexus of chitin and chitinase and assesses both their pathogenic as well as utilitarian aspects.
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182, USA.
| | - Arun Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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25
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Heterogeneous nanomechanical properties of type I collagen in longitudinal direction. Biomech Model Mechanobiol 2017; 16:1023-1033. [DOI: 10.1007/s10237-016-0870-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 12/24/2016] [Indexed: 01/28/2023]
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Abstract
Fibrillar collagens (types I, II, III, V, XI, XXIV and XXVII) constitute a sub-group within the collagen family (of which there are 28 types in humans) whose functions are to provide three-dimensional frameworks for tissues and organs. These networks confer mechanical strength as well as signalling and organizing functions through binding to cellular receptors and other components of the extracellular matrix (ECM). Here we describe the structure and assembly of fibrillar collagens, and their procollagen precursors, from the molecular to the tissue level. We show how the structure of the collagen triple-helix is influenced by the amino acid sequence, hydrogen bonding and post-translational modifications, such as prolyl 4-hydroxylation. The numerous steps in the biosynthesis of the fibrillar collagens are reviewed with particular attention to the role of prolyl 3-hydroxylation, collagen chaperones, trimerization of procollagen chains and proteolytic maturation. The multiple steps controlling fibril assembly are then discussed with a focus on the cellular control of this process in vivo. Our current understanding of the molecular packing in collagen fibrils, from different tissues, is then summarized on the basis of data from X-ray diffraction and electron microscopy. These results provide structural insights into how collagen fibrils interact with cell receptors, other fibrillar and non-fibrillar collagens and other ECM components, as well as enzymes involved in cross-linking and degradation.
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Affiliation(s)
- Jordi Bella
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - David J S Hulmes
- Tissue Biology and Therapeutic Engineering Unit (UMR5305), CNRS/Université Claude Bernard Lyon 1, Lyon, France
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27
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Abstract
During the 1930s and 1940s the technique of X-ray diffraction was applied widely by William Astbury and his colleagues to a number of naturally-occurring fibrous materials. On the basis of the diffraction patterns obtained, he observed that the structure of each of the fibres was dominated by one of a small number of different types of molecular conformation. One group of fibres, known as the k-m-e-f group of proteins (keratin - myosin - epidermin - fibrinogen), gave rise to diffraction characteristics that became known as the α-pattern. Others, such as those from a number of silks, gave rise to a different pattern - the β-pattern, while connective tissues yielded a third unique set of diffraction characteristics. At the time of Astbury's work, the structures of these materials were unknown, though the spacings of the main X-ray reflections gave an idea of the axial repeats and the lateral packing distances. In a breakthrough in the early 1950s, the basic structures of all of these fibrous proteins were determined. It was found that the long protein chains, composed of strings of amino acids, could be folded up in a systematic manner to generate a limited number of structures that were consistent with the X-ray data. The most important of these were known as the α-helix, the β-sheet, and the collagen triple helix. These studies provided information about the basic building blocks of all proteins, both fibrous and globular. They did not, however, provide detailed information about how these molecules packed together in three-dimensions to generate the fibres found in vivo. A number of possible packing arrangements were subsequently deduced from the X-ray diffraction and other data, but it is only in the last few years, through the continued improvements of electron microscopy, that the packing details within some fibrous proteins can now be seen directly. Here we outline briefly some of the milestones in fibrous protein structure determination, the role of the amino acid sequences and how new techniques, including electron microscopy, are helping to define fibrous protein structures in three-dimensions. We also introduce the idea that, from the known sequence characteristics of different fibrous proteins, new molecules can be designed and synthesized, thereby generating new biological materials with specific structural properties. Some of these, for example, are planned for use in drug delivery systems. Along the way we also introduce the various Chapters of the book, where individual fibrous proteins are discussed in detail.
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Solomonov I, Zehorai E, Talmi-Frank D, Wolf SG, Shainskaya A, Zhuravlev A, Kartvelishvily E, Visse R, Levin Y, Kampf N, Jaitin DA, David E, Amit I, Nagase H, Sagi I. Distinct biological events generated by ECM proteolysis by two homologous collagenases. Proc Natl Acad Sci U S A 2016; 113:10884-9. [PMID: 27630193 PMCID: PMC5047162 DOI: 10.1073/pnas.1519676113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
It is well established that the expression profiles of multiple and possibly redundant matrix-remodeling proteases (e.g., collagenases) differ strongly in health, disease, and development. Although enzymatic redundancy might be inferred from their close similarity in structure, their in vivo activity can lead to extremely diverse tissue-remodeling outcomes. We observed that proteolysis of collagen-rich natural extracellular matrix (ECM), performed uniquely by individual homologous proteases, leads to distinct events that eventually affect overall ECM morphology, viscoelastic properties, and molecular composition. We revealed striking differences in the motility and signaling patterns, morphology, and gene-expression profiles of cells interacting with natural collagen-rich ECM degraded by different collagenases. Thus, in contrast to previous notions, matrix-remodeling systems are not redundant and give rise to precise ECM-cell crosstalk. Because ECM proteolysis is an abundant biochemical process that is critical for tissue homoeostasis, these results improve our fundamental understanding its complexity and its impact on cell behavior.
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Affiliation(s)
- Inna Solomonov
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eldar Zehorai
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dalit Talmi-Frank
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sharon G Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alla Shainskaya
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alina Zhuravlev
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elena Kartvelishvily
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Robert Visse
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, United Kingdom
| | - Yishai Levin
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nir Kampf
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hideaki Nagase
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, United Kingdom
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel;
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29
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Collagen structure: new tricks from a very old dog. Biochem J 2016; 473:1001-25. [PMID: 27060106 DOI: 10.1042/bj20151169] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/01/2016] [Indexed: 12/22/2022]
Abstract
The main features of the triple helical structure of collagen were deduced in the mid-1950s from fibre X-ray diffraction of tendons. Yet, the resulting models only could offer an average description of the molecular conformation. A critical advance came about 20 years later with the chemical synthesis of sufficiently long and homogeneous peptides with collagen-like sequences. The availability of these collagen model peptides resulted in a large number of biochemical, crystallographic and NMR studies that have revolutionized our understanding of collagen structure. High-resolution crystal structures from collagen model peptides have provided a wealth of data on collagen conformational variability, interaction with water, collagen stability or the effects of interruptions. Furthermore, a large increase in the number of structures of collagen model peptides in complex with domains from receptors or collagen-binding proteins has shed light on the mechanisms of collagen recognition. In recent years, collagen biochemistry has escaped the boundaries of natural collagen sequences. Detailed knowledge of collagen structure has opened the field for protein engineers who have used chemical biology approaches to produce hyperstable collagens with unnatural residues, rationally designed collagen heterotrimers, self-assembling collagen peptides, etc. This review summarizes our current understanding of the structure of the collagen triple helical domain (COL×3) and gives an overview of some of the new developments in collagen molecular engineering aiming to produce novel collagen-based materials with superior properties.
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30
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Zhang R, Chen J, Jiang X, Yin L, Zhang X. Antioxidant and hypoglycaemic effects of tilapia skin collagen peptide in mice. Int J Food Sci Technol 2016. [DOI: 10.1111/ijfs.13193] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ruilin Zhang
- College of Food Science and Engineering; South China University of Technology; Guangzhou China
- Era (China) Company Ltd; Shenzhen China
| | - Jian Chen
- College of Food Science and Engineering; South China University of Technology; Guangzhou China
| | | | | | - Xuewu Zhang
- College of Food Science and Engineering; South China University of Technology; Guangzhou China
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31
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Abstract
A brief overview of isolated collagen fibril mechanics testing is followed by presentation of the first results testing fibrils isolated from load-bearing mammalian tendons using a microelectromechanical systems platform. The in vitro modulus (326 ± 112 MPa) and fracture stress (71 ± 23 MPa) are shown to be lower than previously measured on fibrils extracted from sea cucumber dermis and tested with the same technique. Scanning electron microscope images show the fibrils can fail with a mechanism that involves circumferential rupture, whereas the core of the fibril stays at least partially intact.
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Affiliation(s)
- Yehe Liu
- Department of Biomedical Engineering , Case Western Reserve University , Cleveland, OH , USA
| | - Roberto Ballarini
- Department of Civil and Environmental Engineering , University of Houston , Houston, TX , USA
| | - Steven J Eppell
- Department of Biomedical Engineering , Case Western Reserve University , Cleveland, OH , USA
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32
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Dutov P, Antipova O, Varma S, Orgel JPRO, Schieber JD. Measurement of Elastic Modulus of Collagen Type I Single Fiber. PLoS One 2016; 11:e0145711. [PMID: 26800120 PMCID: PMC4723153 DOI: 10.1371/journal.pone.0145711] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 12/08/2015] [Indexed: 12/16/2022] Open
Abstract
Collagen fibers are the main components of the extra cellular matrix and the primary contributors to the mechanical properties of tissues. Here we report a novel approach to measure the longitudinal component of the elastic moduli of biological fibers under conditions close to those found in vivo and apply it to type I collagen from rat tail tendon. This approach combines optical tweezers, atomic force microscopy, and exploits Euler-Bernoulli elasticity theory for data analysis. This approach also avoids drying for measurements or visualization, since samples are freshly extracted. Importantly, strains are kept below 0.5%, which appear consistent with the linear elastic regime. We find, surprisingly, that the longitudinal elastic modulus of type I collagen cannot be represented by a single quantity but rather is a distribution that is broader than the uncertainty of our experimental technique. The longitudinal component of the single-fiber elastic modulus is between 100 MPa and 360 MPa for samples extracted from different rats and/or different parts of a single tail. Variations are also observed in the fibril-bundle/fibril diameter with an average of 325±40 nm. Since bending forces depend on the diameter to the fourth power, this variation in diameter is important for estimating the range of elastic moduli. The remaining variations in the modulus may be due to differences in composition of the fibril-bundles, or the extent of the proteoglycans constituting fibril-bundles, or that some single fibrils may be of fibril-bundle size.
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Affiliation(s)
- Pavel Dutov
- Center For Molecular Study Of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States of America.,Chemical and Biological Engineering Department, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Olga Antipova
- Center For Molecular Study Of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States of America.,Departments of, Biology, Physics and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, United States of America.,BioCAT, Sector 18, APS/Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL, United States of America
| | - Sameer Varma
- Department of Cell Biology, Microbiology and Molecular Biology, Department of Physics, University of South Florida, Tampa, FL, United States of America
| | - Joseph P R O Orgel
- Center For Molecular Study Of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States of America.,Departments of, Biology, Physics and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, United States of America.,BioCAT, Sector 18, APS/Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL, United States of America
| | - Jay D Schieber
- Center For Molecular Study Of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States of America.,Chemical and Biological Engineering Department, Illinois Institute of Technology, Chicago, IL, United States of America.,Department of Physics, Illinois Institute of Technology, Chicago, IL, United States of America
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33
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Varma S, Botlani M, Hammond JR, Scott HL, Orgel JPRO, Schieber JD. Effect of intrinsic and extrinsic factors on the simulated D-band length of type I collagen. Proteins 2015. [PMID: 26214145 DOI: 10.1002/prot.24864] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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.
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Affiliation(s)
- Sameer Varma
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, 33620
| | - Mohsen Botlani
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, 33620
| | | | - H Larry Scott
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois, 60616
| | - Joseph P R O Orgel
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois, 60616.,Department of Biology, Illinois Institute of Technology, Chicago, Illinois, 60616.,Department of Bioengineering, Illinois Institute of Technology, Chicago, Illinois, 60616
| | - Jay D Schieber
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois, 60616.,Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, Ilinois, 60616
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34
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Hill RC, Wither MJ, Nemkov T, Barrett A, D'Alessandro A, Dzieciatkowska M, Hansen KC. Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen. Mol Cell Proteomics 2015; 14:1946-58. [PMID: 25948757 DOI: 10.1074/mcp.m114.047787] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 11/06/2022] Open
Abstract
Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado, and processed for proteomics analysis. The specimens come from Pleistocene megafauna Bison latifrons, dating back ∼ 120,000 years. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS/MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to type I collagen. In addition, we analyzed a specimen from the extinct B. latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of posttranslational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified for the first time in an ancient protein dataset. Meta-analysis of data from other studies indicates that this modification may be common in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified for the first time in ancient tissue samples. These data provide a framework for analyzing ancient protein signatures in well-preserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation. As such, this analysis has unearthed common posttranslational modifications of collagen that may assist in its preservation over time. The data are available via ProteomeXchange with identifier PXD001827.
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Affiliation(s)
- Ryan C Hill
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Matthew J Wither
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Travis Nemkov
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Alexander Barrett
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Angelo D'Alessandro
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Monika Dzieciatkowska
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Kirk C Hansen
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
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35
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Worthington P, Pochan DJ, Langhans SA. Peptide Hydrogels - Versatile Matrices for 3D Cell Culture in Cancer Medicine. Front Oncol 2015; 5:92. [PMID: 25941663 PMCID: PMC4403249 DOI: 10.3389/fonc.2015.00092] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/30/2015] [Indexed: 12/31/2022] Open
Abstract
Traditional two-dimensional (2D) cell culture systems have contributed tremendously to our understanding of cancer biology but have significant limitations in mimicking in vivo conditions such as the tumor microenvironment. In vitro, three-dimensional (3D) cell culture models represent a more accurate, intermediate platform between simplified 2D culture models and complex and expensive in vivo models. 3D in vitro models can overcome 2D in vitro limitations caused by the oversupply of nutrients, and unphysiological cell-cell and cell-material interactions, and allow for dynamic interactions between cells, stroma, and extracellular matrix. In addition, 3D cultures allow for the development of concentration gradients, including oxygen, metabolites, and growth factors, with chemical gradients playing an integral role in many cellular functions ranging from development to signaling in normal epithelia and cancer environments in vivo. Currently, the most common matrices used for 3D culture are biologically derived materials such as matrigel and collagen. However, in recent years, more defined, synthetic materials have become available as scaffolds for 3D culture with the advantage of forming well-defined, designed, tunable materials to control matrix charge, stiffness, porosity, nanostructure, degradability, and adhesion properties, in addition to other material and biological properties. One important area of synthetic materials currently available for 3D cell culture is short sequence, self-assembling peptide hydrogels. In addition to the review of recent work toward the control of material, structure, and mechanical properties, we will also discuss the biochemical functionalization of peptide hydrogels and how this functionalization, coupled with desired hydrogel material characteristics, affects tumor cell behavior in 3D culture.
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Affiliation(s)
- Peter Worthington
- Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, DE, USA
- Department of Biomedical Engineering, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Darrin J. Pochan
- Department of Materials Science and Engineering, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Sigrid A. Langhans
- Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, DE, USA
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36
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Barrea RA, Antipova O, Gore D, Heurich R, Vukonich M, Kujala NG, Irving TC, Orgel JPRO. X-ray micro-diffraction studies on biological samples at the BioCAT Beamline 18-ID at the Advanced Photon Source. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:1200-1205. [PMID: 25178013 PMCID: PMC4151685 DOI: 10.1107/s1600577514012259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/27/2014] [Indexed: 06/03/2023]
Abstract
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.
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Affiliation(s)
- R. A. Barrea
- The Biophysics Collaborative Access Team (BioCAT), CSRRI and Departments of Biology, Physics and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - O. Antipova
- The Biophysics Collaborative Access Team (BioCAT), CSRRI and Departments of Biology, Physics and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - D. Gore
- The Biophysics Collaborative Access Team (BioCAT), CSRRI and Departments of Biology, Physics and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - R. Heurich
- The Biophysics Collaborative Access Team (BioCAT), CSRRI and Departments of Biology, Physics and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - M. Vukonich
- The Biophysics Collaborative Access Team (BioCAT), CSRRI and Departments of Biology, Physics and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - N. G. Kujala
- The Biophysics Collaborative Access Team (BioCAT), CSRRI and Departments of Biology, Physics and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - T. C. Irving
- The Biophysics Collaborative Access Team (BioCAT), CSRRI and Departments of Biology, Physics and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - J. P. R. O. Orgel
- The Biophysics Collaborative Access Team (BioCAT), CSRRI and Departments of Biology, Physics and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
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