1
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Wong H, Crowet JM, Dauchez M, Ricard-Blum S, Baud S, Belloy N. Multiscale modelling of the extracellular matrix. Matrix Biol Plus 2022; 13:100096. [PMID: 35072037 PMCID: PMC8763633 DOI: 10.1016/j.mbplus.2021.100096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/29/2022] Open
Abstract
The extracellular matrix is a complex three-dimensional network of molecules that provides cells with a complex microenvironment. The major constituents of the extracellular matrix such as collagen, elastin and associated proteins form supramolecular assemblies contributing to its physicochemical properties and organization. The structure of proteins and their supramolecular assemblies such as fibrils have been studied at the atomic level (e.g., by X-ray crystallography, Nuclear Magnetic Resonance and cryo-Electron Microscopy) or at the microscopic scale. However, many protein complexes are too large to be studied at the atomic level and too small to be studied by microscopy. Most extracellular matrix components fall into this intermediate scale, so-called the mesoscopic scale, preventing their detailed characterization. Simulation and modelling are some of the few powerful and promising approaches that can deepen our understanding of mesoscale systems. We have developed a set of modelling tools to study the self-organization of the extracellular matrix and large motion of macromolecules at the mesoscale level by taking advantage of the dynamics of articulated rigid bodies as a mean to study a larger range of motions at the cost of atomic resolution.
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Key Words
- Basement membrane
- CG, coarse-grained
- Cryo-EM, cryogenic electron microscopy
- DOF, degrees of freedom
- ECM, extracellular matrix
- EGF, epidermal growth factor
- Extracellular matrix
- FEM, finite element method
- MD, molecular dynamics
- Mesoscopic scale
- Modelling
- NC, non-collagenous
- NMR, nuclear magnetic resonance
- Rigid bodies
- SAXS, small-angle X-ray scattering
- Simulation
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Affiliation(s)
- Hua Wong
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
| | - Jean-Marc Crowet
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
| | - Manuel Dauchez
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
| | - Sylvie Ricard-Blum
- Univ. Lyon, University Claude Bernard Lyon 1, ICBMS, UMR 5246 CNRS, 69622 Villeurbanne Cedex, France
| | - Stéphanie Baud
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
- Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la Simulation de Champagne-Ardenne (MaSCA), 51097 Reims, France
| | - Nicolas Belloy
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
- Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la Simulation de Champagne-Ardenne (MaSCA), 51097 Reims, France
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2
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Reichheld SE, Muiznieks LD, Huynh Q, Wang N, Ing C, Miao M, Sitarz EE, Pomès R, Sharpe S, Keeley FW. The evolutionary background and functional consequences of the rs2071307 polymorphism in human tropoelastin. Biopolymers 2020; 112:e23414. [PMID: 33351193 DOI: 10.1002/bip.23414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 01/01/2023]
Abstract
Elastin is a major polymeric protein of the extracellular matrix, providing critical properties of extensibility and elastic recoil. The rs2071307 genomic polymorphism, resulting in the substitution of a serine for a glycine residue in a VPG motif in tropoelastin, has an unusually high minor allele frequency in humans. A consequence of such allelic heterozygosity would be the presence of a heterogeneous elastin polymer in up to 50% of the population, a situation which appears to be unique to Homo sapiens. VPG motifs are extremely common in hydrophobic domains of tropoelastins and are the sites of transient β-turns that are essential for maintaining the conformational flexibility required for its function as an entropic elastomer. Earlier data demonstrated that single amino acid substitutions in tropoelastin can have functional consequences for polymeric elastin, particularly when present in mixed polymers. Here, using NMR and molecular dynamics approaches, we show the rs2071307 polymorphism reduces local propensity for β-turn formation, with a consequent increase in polypeptide hydration and an expansion of the conformational ensemble manifested as an increased hydrodynamic radius, radius of gyration and asphericity. Furthermore, this substitution affects functional properties of polymeric elastin, particularly in heterogeneous polymers mimicking allelic heterozygosity. We discuss whether such effects, together with the unusually high minor allele frequency of the polymorphism, could imply some some evolutionary advantage for the heterozygous state.
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Affiliation(s)
- Sean E Reichheld
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA
| | - Lisa D Muiznieks
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,Elvesys Microfluidics Innovation Center, 172 rue de Charonne, 75011, Paris, France
| | - Quang Huynh
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA
| | - Nick Wang
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,135 W 52nd St. Apt 20A, 10019-7691, New York, New York, USA
| | - Christopher Ing
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,ProteinQure, Suite 304, 119 Spadina Avenue, M5V2L1, Toronto, Ontario, Canada
| | - Ming Miao
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA
| | - Eva E Sitarz
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA
| | - Régis Pomès
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Simon Sharpe
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Fred W Keeley
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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3
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Djajamuliadi J, Ohgo K, Kumashiro KK. A Two-State Model Describes the Temperature-Dependent Conformational Equilibrium in the Alanine-Rich Domains in Elastin. J Phys Chem B 2020; 124:9017-9028. [PMID: 32936634 DOI: 10.1021/acs.jpcb.0c06811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Elastin is the insoluble elastomeric protein that provides extensibility and resilience to vertebrate tissues. Limited high-resolution structural data for elastin are notably complex. To access this information, this protein is considered in the simplified context of its two general domain types, that is, hydrophobic (HP) and crosslinking (CL). The question of elastin's structure-function has directed the focus of nearly all previous studies in the literature to the unique repeating sequences characteristic of this protein, found primarily in the HP domains. The CL domains were assumed to play a very limited role in biological elasticity due in part to the significant α-helical character that was (incorrectly) predicted for these regions. In this study, the conformational heterogeneity of alanines in native elastin's CL domains is examined in the context of helix-coil transition theory (HCTT) using solid-state nuclear magnetic resonance (SSNMR) spectroscopy in tandem with strategic isotopic labeling. Helix and coil populations are observed at all temperatures, but the former increases significantly at lower temperatures. Below the glass transition temperature (Tg), two major populations of alanines in the CL regions are resolved by two-dimensional SSNMR; one-dimensional methods are used for characterization in nativelike conditions. The spectra of 13CO-Ala in the CL regions are simulated using an HCTT-based statistical mechanical representation. Below Tg, longer segments with significant helical probabilities are consistent with the experimental data. At higher temperatures, the SSNMR lineshapes are best fit with a distribution of shorter (Ala)n segments, most in random coil. These results are used to refine a structure-function model for elastin in the context of HCTT, redirecting attention to the CL domains and their role in elasticity.
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Affiliation(s)
- Jhonsen Djajamuliadi
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kosuke Ohgo
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kristin K Kumashiro
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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4
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Vindin H, Mithieux SM, Weiss AS. Elastin architecture. Matrix Biol 2019; 84:4-16. [DOI: 10.1016/j.matbio.2019.07.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 11/15/2022]
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5
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Tarakanova A, Yeo GC, Baldock C, Weiss AS, Buehler MJ. Tropoelastin is a Flexible Molecule that Retains its Canonical Shape. Macromol Biosci 2018; 19:e1800250. [DOI: 10.1002/mabi.201800250] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/03/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics Department of Civil and Environmental Engineering Massachusetts Institute of Technology 02139 Cambridge MA USA
| | - Giselle C. Yeo
- School of Life and Environmental Sciences The University of Sydney 2006 Sydney NSW Australia
- Charles Perkins Centre The University of Sydney 2006 Sydney NSW Australia
| | - Clair Baldock
- Wellcome Trust Centre for Cell‐Matrix Research Division of Cell Matrix Biology and Regenerative Medicine School of Biological Sciences Manchester Academic Health Science Centre The University of Manchester M13 9PL Manchester UK
| | - Anthony S. Weiss
- School of Life and Environmental Sciences The University of Sydney 2006 Sydney NSW Australia
- Charles Perkins Centre The University of Sydney 2006 Sydney NSW Australia
- Bosch Institute The University of Sydney 2006 Sydney NSW Australia
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics Department of Civil and Environmental Engineering Massachusetts Institute of Technology 02139 Cambridge MA USA
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6
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Yeo G, Baldock C, Wise SG, Weiss AS. Targeted Modulation of Tropoelastin Structure and Assembly. ACS Biomater Sci Eng 2017; 3:2832-2844. [PMID: 29152561 PMCID: PMC5686564 DOI: 10.1021/acsbiomaterials.6b00564] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/06/2016] [Indexed: 12/17/2022]
Abstract
Tropoelastin, as the monomer unit of elastin, assembles into elastic fibers that impart strength and resilience to elastic tissues. Tropoelastin is also widely used to manufacture versatile materials with specific mechanical and biological properties. The assembly of tropoelastin into elastic fibers or biomaterials is crucially influenced by key submolecular regions and specific residues within these domains. In this work, we identify the functional contributions of two rarely occurring negatively charged residues, glutamate 345 in domain 19 and glutamate 414 in domain 21, in jointly maintaining the native conformation of the tropoelastin hinge, bridge and foot regions. Alanine substitution of E345 and/or E414 variably alters the positioning and interactive accessibility of these regions, as illustrated by nanostructural studies and detected by antibody and cell probes. These structural changes are associated with a lower propensity for monomer coacervation, cross-linking into morphologically and functionally atypical hydrogels, and markedly impaired and abnormal elastic fiber formation. Our work indicates the crucial significance of both E345 and E414 residues in modulating specific local structure and higher-order assembly of human tropoelastin.
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Affiliation(s)
- Giselle
C. Yeo
- Charles Perkins Centre, School of Life and
Environmental Sciences, School of Physics, Sydney Medical School, and Bosch Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Clair Baldock
- Wellcome
Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine
and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Steven G. Wise
- Charles Perkins Centre, School of Life and
Environmental Sciences, School of Physics, Sydney Medical School, and Bosch Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
- The
Heart Research Institute, 7 Eliza Street, Newtown, New South Wales 2050, Australia
| | - Anthony S. Weiss
- Charles Perkins Centre, School of Life and
Environmental Sciences, School of Physics, Sydney Medical School, and Bosch Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
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7
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Single nucleotide polymorphisms and domain/splice variants modulate assembly and elastomeric properties of human elastin. Implications for tissue specificity and durability of elastic tissue. Biopolymers 2017; 107. [DOI: 10.1002/bip.23007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/23/2016] [Accepted: 12/03/2016] [Indexed: 12/13/2022]
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8
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Abstract
Elastin is the dominant mammalian elastic protein found in soft tissue. Elastin-based biomaterials have the potential to repair elastic tissues by improving local elasticity and providing appropriate cellular interactions and signaling. Studies that combine these biomaterials with mesenchymal stem cells have demonstrated their capacity to also regenerate non-elastic tissue. Mesenchymal stem cell differentiation can be controlled by their immediate environment, and their sensitivity to elasticity makes them an ideal candidate for combining with elastin-based biomaterials. With the growing accessibility of the elastin precursor, tropoelastin, and elastin-derived materials, the amount of research interest in combining these two fields has increased and, subsequently, is leading to the realization of a potentially new strategy for regenerative medicine.
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Affiliation(s)
- Jazmin Ozsvar
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia ; Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
| | - Suzanne M Mithieux
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia ; Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
| | - Richard Wang
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia ; Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
| | - Anthony S Weiss
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia ; Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
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9
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Heinz A, Schräder CU, Baud S, Keeley FW, Mithieux SM, Weiss AS, Neubert RHH, Schmelzer CEH. Molecular-level characterization of elastin-like constructs and human aortic elastin. Matrix Biol 2014; 38:12-21. [PMID: 25068896 DOI: 10.1016/j.matbio.2014.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 01/09/2023]
Abstract
This study aimed to characterize the structures of two elastin-like constructs, one composed of a cross-linked elastin-like polypeptide and the other one of cross-linked tropoelastin, and native aortic elastin. The structures of the insoluble materials and human aortic elastin were investigated using scanning electron microscopy. Additionally, all samples were digested with enzymes of different specificities, and the resultant peptide mixtures were characterized by ESI mass spectrometry and MALDI mass spectrometry. The MS(2) data was used to sequence linear peptides, and cross-linked species were analyzed with the recently developed software PolyLinX. This enabled the identification of two intramolecularly cross-linked peptides containing allysine aldols in the two constructs. The presence of the tetrafunctional cross-link desmosine was shown for all analyzed materials and its quantification revealed that the cross-linking degree of the two in vitro cross-linked materials was significantly lower than that of native elastin. Molecular dynamics simulations were performed, based on molecular species identified in the samples, to follow the formation of elastin cross-links. The results provide evidence for the significance of the GVGTP hinge region of domain 23 for the formation of elastin cross-links. Overall, this work provides important insight into structural similarities and differences between elastin-like constructs and native elastin. Furthermore, it represents a step toward the elucidation of the complex cross-linking pattern of mature elastin.
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Affiliation(s)
- Andrea Heinz
- Institute of Pharmacy, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
| | - Christoph U Schräder
- Institute of Pharmacy, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Stéphanie Baud
- Laboratoire SiRMa, FRE CNRS/URCA 3481, Université de Reims Champagne-Ardenne, Reims, France; Plateforme de Modélisation Moléculaire Multi-échelle, UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne, Reims, France
| | - Fred W Keeley
- Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada
| | | | - Anthony S Weiss
- School of Molecular Bioscience, University of Sydney, Sydney, Australia; Bosch Institute, University of Sydney, Sydney, Australia; Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Reinhard H H Neubert
- Institute of Pharmacy, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Christian E H Schmelzer
- Institute of Pharmacy, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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10
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Muiznieks LD, Cirulis JT, van der Horst A, Reinhardt DP, Wuite GJ, Pomès R, Keeley FW. Modulated growth, stability and interactions of liquid-like coacervate assemblies of elastin. Matrix Biol 2014; 36:39-50. [DOI: 10.1016/j.matbio.2014.03.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/26/2014] [Accepted: 03/27/2014] [Indexed: 11/25/2022]
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11
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Wise SG, Yeo GC, Hiob MA, Rnjak-Kovacina J, Kaplan DL, Ng MKC, Weiss AS. Tropoelastin: a versatile, bioactive assembly module. Acta Biomater 2014; 10:1532-41. [PMID: 23938199 DOI: 10.1016/j.actbio.2013.08.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/24/2013] [Accepted: 08/01/2013] [Indexed: 12/27/2022]
Abstract
Elastin provides structural integrity, biological cues and persistent elasticity to a range of important tissues, including the vasculature and lungs. Its critical importance to normal physiology makes it a desirable component of biomaterials that seek to repair or replace these tissues. The recent availability of large quantities of the highly purified elastin monomer, tropoelastin, has allowed for a thorough characterization of the mechanical and biological mechanisms underpinning the benefits of mature elastin. While tropoelastin is a flexible molecule, a combination of optical and structural analyses has defined key regions of the molecule that directly contribute to the elastomeric properties and control the cell interactions of the protein. Insights into the structure and behavior of tropoelastin have translated into increasingly sophisticated elastin-like biomaterials, evolving from classically manufactured hydrogels and fibers to new forms, stabilized in the absence of incorporated cross-linkers. Tropoelastin is also compatible with synthetic and natural co-polymers, expanding the applications of its potential use beyond traditional elastin-rich tissues and facilitating finer control of biomaterial properties and the design of next-generation tailored bioactive materials.
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Affiliation(s)
- Steven G Wise
- The Heart Research Institute, Sydney, NSW 2042, Australia; Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - Giselle C Yeo
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - Matti A Hiob
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; The Heart Research Institute, Sydney, NSW 2042, Australia
| | - Jelena Rnjak-Kovacina
- Department of Biomedical Engineering, School of Engineering, Tufts University, Medford, MA 02155, USA
| | - David L Kaplan
- Department of Biomedical Engineering, School of Engineering, Tufts University, Medford, MA 02155, USA
| | - Martin K C Ng
- The Heart Research Institute, Sydney, NSW 2042, Australia; Department of Cardiology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Anthony S Weiss
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Bosch Institute, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia.
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12
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Gronau G, Krishnaji ST, Kinahan ME, Giesa T, Wong JY, Kaplan DL, Buehler MJ. A review of combined experimental and computational procedures for assessing biopolymer structure-process-property relationships. Biomaterials 2012; 33:8240-55. [PMID: 22938765 DOI: 10.1016/j.biomaterials.2012.06.054] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 06/22/2012] [Indexed: 02/08/2023]
Abstract
Tailored biomaterials with tunable functional properties are desirable for many applications ranging from drug delivery to regenerative medicine. To improve the predictability of biopolymer materials functionality, multiple design parameters need to be considered, along with appropriate models. In this article we review the state of the art of synthesis and processing related to the design of biopolymers, with an emphasis on the integration of bottom-up computational modeling in the design process. We consider three prominent examples of well-studied biopolymer materials - elastin, silk, and collagen - and assess their hierarchical structure, intriguing functional properties and categorize existing approaches to study these materials. We find that an integrated design approach in which both experiments and computational modeling are used has rarely been applied for these materials due to difficulties in relating insights gained on different length- and time-scales. In this context, multiscale engineering offers a powerful means to accelerate the biomaterials design process for the development of tailored materials that suit the needs posed by the various applications. The combined use of experimental and computational tools has a very broad applicability not only in the field of biopolymers, but can be exploited to tailor the properties of other polymers and composite materials in general.
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Affiliation(s)
- Greta Gronau
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA
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13
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Rauscher S, Pomès R. Structural disorder and protein elasticity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:159-83. [PMID: 22399324 DOI: 10.1007/978-1-4614-0659-4_10] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
An emerging class of disordered proteins underlies the elasticity of many biological tissues. Elastomeric proteins are essential to the function of biological machinery as diverse as the human arterial wall, the capture spiral of spider webs and the jumping mechanism of fleas. In this chapter, we review what is known about the molecular basis and the functional role of structural disorder in protein elasticity. In general, the elastic recoil of proteins is due to a combination of internal energy and entropy. In rubber-like elastomeric proteins, the dominant driving force is the increased entropy of the relaxed state relative to the stretched state. Aggregates of these proteins are intrinsically disordered or fuzzy, with high polypeptide chain entropy. We focus our discussion on the sequence, structure and function of five rubber-like elastomeric proteins, elastin, resilin, spider silk, abductin and ColP. Although we group these disordered elastomers together into one class of proteins, they exhibit a broad range of sequence motifs, mechanical properties and biological functions. Understanding how sequence modulates both disorder and elasticity will help advance the rational design of elastic biomaterials such as artificial skin and vascular grafts.
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Affiliation(s)
- Sarah Rauscher
- Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada
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14
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Cranford S, Buehler MJ. Materiomics: biological protein materials, from nano to macro. Nanotechnol Sci Appl 2010; 3:127-48. [PMID: 24198478 PMCID: PMC3781696 DOI: 10.2147/nsa.s9037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Materiomics is an emerging field of science that provides a basis for multiscale material system characterization, inspired in part by natural, for example, protein-based materials. Here we outline the scope and explain the motivation of the field of materiomics, as well as demonstrate the benefits of a materiomic approach in the understanding of biological and natural materials as well as in the design of de novo materials. We discuss recent studies that exemplify the impact of materiomics - discovering Nature's complexity through a materials science approach that merges concepts of material and structure throughout all scales and incorporates feedback loops that facilitate sensing and resulting structural changes at multiple scales. The development and application of materiomics is illustrated for the specific case of protein-based materials, which constitute the building blocks of a variety of biological systems such as tendon, bone, skin, spider silk, cells, and tissue, as well as natural composite material systems (a combination of protein-based and inorganic constituents) such as nacre and mollusk shells, and other natural multiscale systems such as cellulose-based plant and wood materials. An important trait of these materials is that they display distinctive hierarchical structures across multiple scales, where molecular details are exhibited in macroscale mechanical responses. Protein materials are intriguing examples of materials that balance multiple tasks, representing some of the most sustainable material solutions that integrate structure and function despite severe limitations in the quality and quantity of material building blocks. However, up until now, our attempts to analyze and replicate Nature's materials have been hindered by our lack of fundamental understanding of these materials' intricate hierarchical structures, scale-bridging mechanisms, and complex material components that bestow protein-based materials their unique properties. Recent advances in analytical tools and experimental methods allow a holistic view of such a hierarchical biological material system. The integration of these approaches and amalgamation of material properties at all scale levels to develop a complete description of a material system falls within the emerging field of materiomics. Materiomics is the result of the convergence of engineering and materials science with experimental and computational biology in the context of natural and synthetic materials. Through materiomics, fundamental advances in our understanding of structure-property-process relations of biological systems contribute to the mechanistic understanding of certain diseases and facilitate the development of novel biological, biologically inspired, and completely synthetic materials for applications in medicine (biomaterials), nanotechnology, and engineering.
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Affiliation(s)
- Steven Cranford
- Center for Materials Science and Engineering, Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Markus J Buehler
- Center for Materials Science and Engineering, Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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15
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Muiznieks LD, Weiss AS, Keeley FW. Structural disorder and dynamics of elastin. Biochem Cell Biol 2010; 88:239-50. [PMID: 20453927 DOI: 10.1139/o09-161] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Elastin is a self-assembling, extracellular-matrix protein that is the major provider of tissue elasticity. Here we review structural studies of elastin from over four decades, and draw together evidence for solution flexibility and conformational disorder that is inherent in all levels of structural organization. The characterization of disorder is consistent with an entropy-driven mechanism of elastic recoil. We conclude that conformational disorder is a constitutive feature of elastin structure and function.
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Affiliation(s)
- Lisa D Muiznieks
- Research Institute, Hospital for Sick Children, 555 University Ave., Toronto, ON M5G 1X8, Canada.
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16
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Dyksterhuis LB, Weiss AS. Homology models for domains 21-23 of human tropoelastin shed light on lysine crosslinking. Biochem Biophys Res Commun 2010; 396:870-3. [PMID: 20457133 DOI: 10.1016/j.bbrc.2010.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 05/04/2010] [Indexed: 10/19/2022]
Abstract
The contiguous crosslinking domain at the center of human tropoelastin encoded by exons 21-23 contains an unusual 'hinge' region thought to adopt both open and closed conformations. Key lysines 425 and 437 have been implicated in both artificial and lysyl oxidase mediated crosslinks. We have examined the importance of hinge conformation to the proximity of these lysines and their ability to undergo intramolecular and intermolecular crosslinks using homology models. The results, counter intuitively, indicate that the more open hinge conformations favor intramolecular crosslinking, while the more closed conformations favor intermolecular crosslinking. We also present evidence that the sidechains of lysines 425 and 437 are able to make direct contact enabling an intramolecular lysyl oxidase mediated crosslink.
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Affiliation(s)
- L B Dyksterhuis
- Molecular and Health Technologies, CSIRO, Victoria 3168, Australia.
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Heinz A, Jung MC, Duca L, Sippl W, Taddese S, Ihling C, Rusciani A, Jahreis G, Weiss AS, Neubert RHH, Schmelzer CEH. Degradation of tropoelastin by matrix metalloproteinases--cleavage site specificities and release of matrikines. FEBS J 2010; 277:1939-56. [PMID: 20345904 DOI: 10.1111/j.1742-4658.2010.07616.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To provide a basis for the development of approaches to treat elastin-degrading diseases, the aim of this study was to investigate the degradation of the natural substrate tropoelastin by the elastinolytic matrix metalloproteinases MMP-7, MMP-9, and MMP-12 and to compare the cleavage site specificities of the enzymes using complementary MS techniques and molecular modeling. Furthermore, the ability of the three proteases to release bioactive peptides was studied. Tropoelastin was readily degraded by all three MMPs. Eighty-nine cleavage sites in tropoelastin were identified for MMP-12, whereas MMP-7 and MMP-9 were found to cleave at only 58 and 63 sites, respectively. Cleavages occurred predominantly in the N-terminal and C-terminal regions of tropoelastin. With respect to the cleavage site specificities, the study revealed that all three MMPs similarly tolerate hydrophobic and/or aliphatic amino acids, including Pro, Gly, Ile, and Val, at P(1)'. MMP-7 shows a strong preference for Leu at P(1)', which is also well accepted by MMP-9 and MMP-12. Of all three MMPs, MMP-12 best tolerates bulky charged and aromatic amino acids at P(1)'. All three MMPs showed a clear preference for Pro at P(3) that could be structurally explained by molecular modeling. Analysis of the generated peptides revealed that all three MMPs show a similar ability to release bioactive sequences, with MMP-12 producing the highest number of these peptides. Furthermore, the generated peptides YTTGKLPYGYGPGG, YGARPGVGVGGIP, and PGFGAVPGA, containing GxxPG motifs that have not yet been proven to be bioactive, were identified as new matrikines upon biological activity testing.
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Affiliation(s)
- Andrea Heinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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