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Puertas-Bartolomé M, Venegas-Bustos D, Acosta S, Rodríguez-Cabello JC. Contribution of the ELRs to the development of advanced in vitro models. Front Bioeng Biotechnol 2024; 12:1363865. [PMID: 38650751 PMCID: PMC11033926 DOI: 10.3389/fbioe.2024.1363865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
Developing in vitro models that accurately mimic the microenvironment of biological structures or processes holds substantial promise for gaining insights into specific biological functions. In the field of tissue engineering and regenerative medicine, in vitro models able to capture the precise structural, topographical, and functional complexity of living tissues, prove to be valuable tools for comprehending disease mechanisms, assessing drug responses, and serving as alternatives or complements to animal testing. The choice of the right biomaterial and fabrication technique for the development of these in vitro models plays an important role in their functionality. In this sense, elastin-like recombinamers (ELRs) have emerged as an important tool for the fabrication of in vitro models overcoming the challenges encountered in natural and synthetic materials due to their intrinsic properties, such as phase transition behavior, tunable biological properties, viscoelasticity, and easy processability. In this review article, we will delve into the use of ELRs for molecular models of intrinsically disordered proteins (IDPs), as well as for the development of in vitro 3D models for regenerative medicine. The easy processability of the ELRs and their rational design has allowed their use for the development of spheroids and organoids, or bioinks for 3D bioprinting. Thus, incorporating ELRs into the toolkit of biomaterials used for the fabrication of in vitro models, represents a transformative step forward in improving the accuracy, efficiency, and functionality of these models, and opening up a wide range of possibilities in combination with advanced biofabrication techniques that remains to be explored.
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Affiliation(s)
- María Puertas-Bartolomé
- Technical Proteins Nanobiotechnology, S.L. (TPNBT), Valladolid, Spain
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - Desiré Venegas-Bustos
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - Sergio Acosta
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
| | - José Carlos Rodríguez-Cabello
- Bioforge Lab (Group for Advanced Materials and Nanobiotechnology), CIBER's Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Edificio LUCIA, Universidad de Valladolid, Valladolid, Spain
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Miserez A, Yu J, Mohammadi P. Protein-Based Biological Materials: Molecular Design and Artificial Production. Chem Rev 2023; 123:2049-2111. [PMID: 36692900 PMCID: PMC9999432 DOI: 10.1021/acs.chemrev.2c00621] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.
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Affiliation(s)
- Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,School of Biological Sciences, NTU, Singapore637551
| | - Jing Yu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,Institute for Digital Molecular Analytics and Science (IDMxS), NTU, 50 Nanyang Avenue, Singapore637553
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., Espoo, UusimaaFI-02044, Finland
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3
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Zhou J, Wu Y, Xu X, Zhang Y, Zhang X, Chen H, Zhuang J, Chen J, Teng Y. Identification and characterization of novel elastin gene mutations in eleven families with supravalvular aortic stenosis. Front Genet 2022; 13:1059640. [PMID: 36518217 PMCID: PMC9742416 DOI: 10.3389/fgene.2022.1059640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/11/2022] [Indexed: 11/09/2023] Open
Abstract
Background: Supravalvular aortic stenosis (SVAS) is a rare congenital heart disease affecting approximately 1 in 25,000 live births. In some patients it is accompanied by pulmonary artery stenosis, particularly of pulmonary artery branches. Chronic stenosis can lead to cardiac hypertrophy and even circulatory failure. Familial autosomal dominant SVAS is frequently associated with elastin (ELN) gene mutations, whereas Williams-Beuren syndrome is a complex developmental disorder caused by heterozygous microdeletions of 26-28 genes at 7q11.23, including ELN. Methods: Whole-exome sequencing was performed in 42 individuals from 11 Chinese families with SVAS to identify the pathogenic gene mutations involved. Aortic tissue was obtained for histological analyses, and quantitative reverse-transcription-PCR and western blotting were used to verify the expression of elastin molecules. Results: Five point mutations and six frameshift mutations in the ELN gene were detected in the peripheral blood of all investigated families. Nine were nonsense mutations that result in premature stop codons, and the other two were missense mutations. All variants were heterozygous. Nine of the variants were novel, and have not been included in databases or previously reported. One mutation occurred in individuals from two different families. Reduced elastin protein expression was evident in patients' aortic tissue. Conclusions: The novel mutations of ELN were found to be pathogenic, which confirmed by reduced elastin expression and leads to SVAS. Thus, detailed cardiac testing and genetic counseling are warranted for patients and asymptomatic individuals with these mutations.
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Affiliation(s)
- Jianrong Zhou
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of Cardiovascular Surgery of Guangzhou First People’s Hospital, Guangzhou, China
| | - Yueheng Wu
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiaoli Xu
- State Key Laboratory of Medical Genomics, Key Laboratory for Endocrine and Metabolic Diseases of Ministry of Health, National Clinical Research Center for Metabolic Diseases, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong Zhang
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiong Zhang
- Department of Cardiovascular Surgery of Guangzhou First People’s Hospital, Guangzhou, China
| | - Haisheng Chen
- Department of Cardiovascular Surgery of Guangzhou First People’s Hospital, Guangzhou, China
| | - Jian Zhuang
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jimei Chen
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yun Teng
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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Procknow SS, Kozel BA. Emerging mechanisms of elastin transcriptional regulation. Am J Physiol Cell Physiol 2022; 323:C666-C677. [PMID: 35816641 PMCID: PMC9448287 DOI: 10.1152/ajpcell.00228.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 11/22/2022]
Abstract
Elastin provides recoil to tissues that stretch such as the lung, blood vessels, and skin. It is deposited in a brief window starting in the prenatal period and extending to adolescence in vertebrates, and then slowly turns over. Elastin insufficiency is seen in conditions such as Williams-Beuren syndrome and elastin-related supravalvar aortic stenosis, which are associated with a range of vascular and connective tissue manifestations. Regulation of the elastin (ELN) gene occurs at multiple levels including promoter activation/inhibition, mRNA stability, interaction with microRNAs, and alternative splicing. However, these mechanisms are incompletely understood. Better understanding of the processes controlling ELN gene expression may improve medicine's ability to intervene in these rare conditions, as well as to replace age-associated losses by re-initiating elastin production. This review describes what is known about the ELN gene promoter structure, transcriptional regulation by cytokines and transcription factors, and posttranscriptional regulation via mRNA stability and micro-RNA and highlights new approaches that may influence regenerative medicine.
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Affiliation(s)
- Sara S Procknow
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Beth A Kozel
- Translational Vascular Medicine Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
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5
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Kolel-Veetil MK, Kant A, Shenoy VB, Buehler MJ. SARS-CoV-2 Infection-Of Music and Mechanics of Its Spikes! A Perspective. ACS NANO 2022; 16:6949-6955. [PMID: 35512182 PMCID: PMC9092193 DOI: 10.1021/acsnano.1c11491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/26/2022] [Indexed: 05/11/2023]
Abstract
The COVID-19 pandemic has been inflicted upon humanity by the SARS-CoV-2 virus, the latest insidious incarnation of the coronaviruses group. While in its wake intense scientific research has produced breakthrough vaccines and cures, there still exists an immediate need to further understand the origin, mechanobiology and biochemistry, and destiny of this virus so that future pandemics arising from similar coronaviruses may be contained more effectively. In this Perspective, we discuss the various evidential findings of virus propagation and connect them to respective underpinning cellular biomechanical states leading to corresponding manifestations of the viral activity. We further propose avenues to tackle the virus, including from a "musical" vantage point, and contain its relentless strides that are currently afflicting the global populace.
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Affiliation(s)
- Manoj K. Kolel-Veetil
- Chemistry Division, Naval Research
Laboratory, Washington, D.C. 20375, United States
| | - Aayush Kant
- NSF Science and Technology Center for Engineering
Mechanobiology, University of Pennsylvania, Philadelphia,
Pennsylvania 19104, United States
| | - Vivek B. Shenoy
- NSF Science and Technology Center for Engineering
Mechanobiology, University of Pennsylvania, Philadelphia,
Pennsylvania 19104, United States
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM),
Massachusetts Institute of Technology, Cambridge,
Massachusetts 02139, United States
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6
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Lau K, Reichheld S, Sharpe S, Cerruti M. Globule and fiber formation with elastin-like polypeptides: a balance of coacervation and crosslinking. SOFT MATTER 2022; 18:3257-3266. [PMID: 35404375 DOI: 10.1039/d2sm00049k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Elastic fiber assembly is a complex process that requires the coacervation and cross-linking of the protein building block tropoelastin. To date, the order, timing, and interplay of coacervation and crosslinking is not completely understood, despite a great number of advances into understanding the molecular structure and functions of the many proteins involved in elastic fiber assembly. With a simple in vitro model using elastin-like polypeptides and the natural chemical crosslinker genipin, we demonstrate the strong influence of the timing and kinetics of crosslinking reaction on the coacervation, crosslinking extent, and resulting morphology of elastin. We also outline a method for analyzing elastin droplet network formation as a heuristic for measuring the propensity for elastic fiber formation. From this we show that adding crosslinker during peak coacervation dramatically increases the propensity for droplet network formation.
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Affiliation(s)
- Kirklann Lau
- Department of Materials Engineering, McGill University, 3610 University Street Wong Building, 2250 Montreal, QC H3A 2B2, Canada.
| | - Sean Reichheld
- Molecular Medicine, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay St., Room 20.9714, Toronto, ON M5G 1X8, Canada.
| | - Simon Sharpe
- Molecular Medicine, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay St., Room 20.9714, Toronto, ON M5G 1X8, Canada.
| | - Marta Cerruti
- Department of Materials Engineering, McGill University, 3610 University Street Wong Building, 2250 Montreal, QC H3A 2B2, Canada.
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7
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Zhang X, Alanazi YF, Jowitt TA, Roseman AM, Baldock C. Elastic Fibre Proteins in Elastogenesis and Wound Healing. Int J Mol Sci 2022; 23:4087. [PMID: 35456902 PMCID: PMC9027394 DOI: 10.3390/ijms23084087] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 12/30/2022] Open
Abstract
As essential components of our connective tissues, elastic fibres give tissues such as major blood vessels, skin and the lungs their elasticity. Their formation is complex and co-ordinately regulated by multiple factors. In this review, we describe key players in elastogenesis: fibrillin-1, tropoelastin, latent TGFβ binding protein-4, and fibulin-4 and -5. We summarise their roles in elastogenesis, discuss the effect of their mutations on relevant diseases, and describe their interactions involved in forming the elastic fibre network. Moreover, we look into their roles in wound repair for a better understanding of their potential application in tissue regeneration.
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Affiliation(s)
- Xinyang Zhang
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (X.Z.); (T.A.J.)
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK;
| | - Yasmene F. Alanazi
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Thomas A. Jowitt
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (X.Z.); (T.A.J.)
| | - Alan M. Roseman
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK;
| | - Clair Baldock
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (X.Z.); (T.A.J.)
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK;
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8
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Yang C, Weiss AS, Tarakanova A. Changes in elastin structure and extensibility induced by hypercalcemia and hyperglycemia. Acta Biomater 2022; 163:131-145. [PMID: 35364318 DOI: 10.1016/j.actbio.2022.03.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 12/15/2022]
Abstract
Elastin is a key elastomeric protein responsible for the elasticity of many organs, including heart, skin, and blood vessels. Due to its intrinsic long life and low turnover rate, damage in elastin induced by pathophysiological conditions, such as hypercalcemia and hyperglycemia, accumulates during biological aging and in aging-associated diseases, such as diabetes mellitus and atherosclerosis. Prior studies have shown that calcification induced by hypercalcemia deteriorates the function of aortic tissues. Glycation of elastin is triggered by hyperglycemia and associated with elastic tissue damage and loss of mechanical functions via the accumulation of advanced glycation end products. To evaluate the effects on elastin's structural conformations and elasticity by hypercalcemia and hyperglycemia at the molecular scale, we perform classical atomistic and steered molecular dynamics simulations on tropoelastin, the soluble precursor of elastin, under different conditions. We characterize the interaction sites of glucose and calcium and associated structural conformational changes. Additionally, we find that elevated levels of calcium ions and glucose hinder the extensibility of tropoelastin by rearranging structural domains and altering hydrogen bonding patterns, respectively. Overall, our investigation helps to reveal the behavior of tropoelastin and the biomechanics of elastin biomaterials in these physiological environments. STATEMENT OF SIGNIFICANCE: Elastin is a key component of elastic fibers which endow many important tissues and organs, from arteries and veins, to skin and heart, with strength and elasticity. During aging and aging-associated diseases, such as diabetes mellitus and atherosclerosis, physicochemical stressors, including hypercalcemia and hyperglycemia, induce accumulated irreversible damage in elastin, and consequently alter mechanical function. Yet, molecular mechanisms associated with these processes are still poorly understood. Here, we present the first study on how these changes in elastin structure and extensibility are induced by hypercalcemia and hyperglycemia at the molecular scale, revealing the essential roles that calcium and glucose play in triggering structural alterations and mechanical stiffness. Our findings yield critical insights into the first steps of hypercalcemia- and hyperglycemia-mediated aging.
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Affiliation(s)
- Chengeng Yang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
| | - Anthony S Weiss
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia; Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
| | - Anna Tarakanova
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA; Department of Mechanical Engineering, University of Connecticut, Storrs, CT, USA.
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9
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Fast and reversible crosslinking of a silk elastin-like polymer. Acta Biomater 2022; 141:14-23. [PMID: 34971785 PMCID: PMC8898266 DOI: 10.1016/j.actbio.2021.12.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022]
Abstract
Elastin-like polymers (ELPs) and their chimeric subfamily the silk elastin-like polymers (SELPs) exhibit a lower critical solvation temperature (LCST) behavior in water which has been extensively studied from theoretical, computational and experimental perspectives. The inclusion of silk domains in the backbone of the ELPs effects the molecular dynamics of the elastin-like domains in response to increased temperature above its transition temperature and confers gelation ability. This response has been studied in terms of initial and long-term changes in structures, however, intermediate transition states have been less investigated. Moreover, little is known about the effects of reversible hydration on the elastin versus silk domains in the physical crosslinks. We used spectroscopic techniques to analyze initial, intermediate and long-term states of the crosslinks in SELPs. A combination of thermoanalytical and rheological measurements demonstrated that the fast reversible rehydration of the elastin motifs adjacent to the relatively small silk domains was capable of breaking the silk physical crosslinks. This feature can be exploited to tailor the dynamics of these types of crosslinks in SELPs. STATEMENT OF SIGNIFICANCE: The combination of silk and elastin in a single molecule results in synergy via their interactions to impact the protein polymer properties. The ability of the silk domains to crosslink affects the thermoresponsive properties of the elastin domains. These interactions have been studied at early and late states of the physical crosslinking, while the intermediate states were the focus of the present study to understand the reversible phase-transitions of the elastin domains over the silk physical crosslinking. The thermoresponsive properties of the elastin domains at the initial, intermediate and late states of silk crosslinking were characterized to demonstrate that reversible hydration of the elastin domains influenced the reversibility of the silk crosslinks.
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10
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Gonzalez-Obeso C, Backlund FG, Kaplan DL. Charge-Modulated Accessibility of Tyrosine Residues for Silk-Elastin Copolymer Cross-Linking. Biomacromolecules 2022; 23:760-765. [PMID: 35113522 PMCID: PMC9211056 DOI: 10.1021/acs.biomac.1c01192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The modulation of reaction kinetics with horseradish peroxidase (HRP)-catalyzed cross-linking of proteins remains a useful strategy to modulate hydrogel formation. Here, we demonstrate that the presence of positively charged lysines in silk-elastin-like polymers impacts the thermal transition temperature of these proteins, while the location in the primary sequence modulates the reactivity of the tyrosines. The positively charged lysine side chains decreased π-π interactions among the tyrosines and reduced the rate of formation and number of HRP-mediated dityrosine bonds, dependent on the proximity of the charged group to the tyrosine. The results suggest that the location of repulsive charges can be used to tailor the reaction kinetics for enzymatic cross-linking, providing further control of gelation rates for in situ gel formation and the resulting protein-based gel characteristics.
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Affiliation(s)
- Constancio Gonzalez-Obeso
- Department of Biomedical Engineering Tufts University, 4, Colby Street, Medford, Massachusetts 02155, United States
| | - Fredrik G Backlund
- Department of Biomedical Engineering Tufts University, 4, Colby Street, Medford, Massachusetts 02155, United States
| | - David L Kaplan
- Department of Biomedical Engineering Tufts University, 4, Colby Street, Medford, Massachusetts 02155, United States
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11
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Singh M, Becker M, Godwin AR, Baldock C. Structural studies of elastic fibre and microfibrillar proteins. Matrix Biol Plus 2021; 12:100078. [PMID: 34355160 PMCID: PMC8322146 DOI: 10.1016/j.mbplus.2021.100078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 11/27/2022] Open
Abstract
Elastic tissues owe their functional properties to the composition of their extracellular matrices, particularly the range of extracellular, multidomain extensible elastic fibre and microfibrillar proteins. These proteins include elastin, fibrillin, latent TGFβ binding proteins (LTBPs) and collagens, where their biophysical and biochemical properties not only give the matrix structural integrity, but also play a vital role in the mechanisms that underlie tissue homeostasis. Thus far structural information regarding the structure and hierarchical assembly of these molecules has been challenging and the resolution has been limited due to post-translational modification and their multidomain nature leading to flexibility, which together result in conformational and structural heterogeneity. In this review, we describe some of the matrix proteins found in elastic fibres and the new emerging techniques that can shed light on their structure and dynamic properties.
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Affiliation(s)
- Mukti Singh
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Mark Becker
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Alan R.F. Godwin
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Clair Baldock
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
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12
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Florio G, Pugno NM, Buehler MJ, Puglisi G. A coarse-grained mechanical model for folding and unfolding of tropoelastin with possible mutations. Acta Biomater 2021; 134:477-489. [PMID: 34303013 DOI: 10.1016/j.actbio.2021.07.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 01/10/2023]
Abstract
We propose a simple general framework to predict folding, native states, energy barriers, protein unfolding, as well as mutation induced diseases and other protein structural analyses. The model should not be considered as an alternative to classical approaches (Molecular Dynamics or Monte Carlo) because it neglects low scale details and rather focuses on global features of proteins and structural information. We aim at the description of phenomena that are out of the range of classical molecular modeling approaches due to the large computational cost: multimolecular interactions, cyclic behavior under variable external interactions, and similar. To demonstrate the effectiveness of the approach in a real case, we focus on the folding and unfolding behavior of tropoelastin and its mutations. Specifically, we derive a discrete mechanical model whose structure is deduced based on a coarse graining approach that allows us to group the amino acids sequence in a smaller number of `equivalent' masses. Nearest neighbor energy terms are then introduced to reproduce the interaction of such amino acid groups. Nearest and non-nearest neighbor energy terms, inter and intra functional blocks are phenomenologically added in the form of Morse potentials. As we show, the resulting system reproduces important properties of the folding-unfolding mechanical response, including the monotonic and cyclic force-elongation behavior, representing a physiologically important information for elastin. The comparison with the experimental behavior of mutated tropoelastin confirms the predictivity of the model. STATEMENT OF SIGNIFICANCE: Classical approaches to the study of phenomena at the molecular scale such as Molecular Dynamics (MD) represent an incredible tool to unveil mechanical and conformational properties of macromolecules, in particular for biological and medical applications. On the other hand, due to the computational cost, the time and spatial scales are limited. Focusing of the real case of tropoelastin, we propose a new approach based on a careful coarse graining of the system, able to describe the overall properties of the macromolecule and amenable of extension to larger scale effects (protein bundles, protein-protein interactions, cyclic loading). The comparison with tropoelastin behavior, also for mutations, is very promising.
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13
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López Barreiro D, Minten IJ, Thies JC, Sagt CMJ. Structure-Property Relationships of Elastin-like Polypeptides: A Review of Experimental and Computational Studies. ACS Biomater Sci Eng 2021. [PMID: 34251181 DOI: 10.1021/acsbiomaterials.1c00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Elastin is a structural protein with outstanding mechanical properties (e.g., elasticity and resilience) and biologically relevant functions (e.g., triggering responses like cell adhesion or chemotaxis). It is formed from its precursor tropoelastin, a 60-72 kDa water-soluble and temperature-responsive protein that coacervates at physiological temperature, undergoing a phenomenon termed lower critical solution temperature (LCST). Inspired by this behavior, many scientists and engineers are developing recombinantly produced elastin-inspired biopolymers, usually termed elastin-like polypeptides (ELPs). These ELPs are generally comprised of repetitive motifs with the sequence VPGXG, which corresponds to repeats of a small part of the tropoelastin sequence, X being any amino acid except proline. ELPs display LCST and mechanical properties similar to tropoelastin, which renders them promising candidates for the development of elastic and stimuli-responsive protein-based materials. Unveiling the structure-property relationships of ELPs can aid in the development of these materials by establishing the connections between the ELP amino acid sequence and the macroscopic properties of the materials. Here we present a review of the structure-property relationships of ELPs and ELP-based materials, with a focus on LCST and mechanical properties and how experimental and computational studies have aided in their understanding.
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Affiliation(s)
- Diego López Barreiro
- DSM Biotechnology Center, DSM, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Inge J Minten
- DSM Materials Science Center - Applied Science Center, DSM, Urmonderbaan 22, 6160 BB, Geleen, The Netherlands
| | - Jens C Thies
- DSM Biomedical, DSM, Koestraat 1, 6167 RA, Geleen, The Netherlands
| | - Cees M J Sagt
- DSM Biotechnology Center, DSM, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
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14
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Ozsvar J, Wang R, Tarakanova A, Buehler MJ, Weiss AS. Fuzzy binding model of molecular interactions between tropoelastin and integrin alphaVbeta3. Biophys J 2021; 120:3138-3151. [PMID: 34197806 DOI: 10.1016/j.bpj.2021.04.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 12/30/2022] Open
Abstract
Tropoelastin is the highly flexible monomer subunit of elastin, required for the resilience of the extracellular matrix in elastic tissues. To elicit biological signaling, multiple sites on tropoelastin bind to cell surface integrins in a poorly understood multifactorial process. We constructed a full atomistic molecular model of the interactions between tropoelastin and integrin αvβ3 using ensemble-based computational methodologies. Conformational changes of integrin αvβ3 associated with outside-in signaling were more frequently facilitated in an ensemble in which tropoelastin bound the integrin's α1 helix rather than the upstream canonical binding site. Our findings support a model of fuzzy binding, whereby many tropoelastin conformations and defined sites cooperatively interact with multiple αvβ3 regions. This model explains prior experimental binding to distinct tropoelastin regions, domains 17 and 36, and points to the cooperative participation of domain 20. Our study highlights the utility of ensemble-based approaches in helping to understand the interactive mechanisms of functionally significant flexible proteins.
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Affiliation(s)
- Jazmin Ozsvar
- Charles Perkins Centre, The University of Sydney, Sydney, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Richard Wang
- Charles Perkins Centre, The University of Sydney, Sydney, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Anna Tarakanova
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut; Department of Mechanical Engineering, University of Connecticut, Storrs, Connecticut
| | - Markus J Buehler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Anthony S Weiss
- Charles Perkins Centre, The University of Sydney, Sydney, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia; Sydney Nano Institute, The University of Sydney, Sydney, Australia.
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15
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Ozsvar J, Yang C, Cain SA, Baldock C, Tarakanova A, Weiss AS. Tropoelastin and Elastin Assembly. Front Bioeng Biotechnol 2021; 9:643110. [PMID: 33718344 PMCID: PMC7947355 DOI: 10.3389/fbioe.2021.643110] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
Elastic fibers are an important component of the extracellular matrix, providing stretch, resilience, and cell interactivity to a broad range of elastic tissues. Elastin makes up the majority of elastic fibers and is formed by the hierarchical assembly of its monomer, tropoelastin. Our understanding of key aspects of the assembly process have been unclear due to the intrinsic properties of elastin and tropoelastin that render them difficult to study. This review focuses on recent developments that have shaped our current knowledge of elastin assembly through understanding the relationship between tropoelastin’s structure and function.
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Affiliation(s)
- Jazmin Ozsvar
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Chengeng Yang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, United States
| | - Stuart A Cain
- Wellcome Trust Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Clair Baldock
- Wellcome Trust Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Anna Tarakanova
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, United States.,Department of Mechanical Engineering, University of Connecticut, Storrs, CT, United States
| | - Anthony S Weiss
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
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16
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Lockhart-Cairns MP, Newandee H, Thomson J, Weiss AS, Baldock C, Tarakanova A. Transglutaminase-Mediated Cross-Linking of Tropoelastin to Fibrillin Stabilises the Elastin Precursor Prior to Elastic Fibre Assembly. J Mol Biol 2020; 432:5736-5751. [PMID: 32898582 PMCID: PMC7610145 DOI: 10.1016/j.jmb.2020.08.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/07/2020] [Accepted: 08/26/2020] [Indexed: 02/05/2023]
Abstract
Elastic fibres are essential components of all mammalian elastic tissues such as blood vessels, lung and skin, and are critically important for the mechanical properties they endow. The main components of elastic fibres are elastin and fibrillin, where correct formation of elastic fibres requires a fibrillin microfibril scaffold for the deposition of elastin. It has been demonstrated previously that the interaction between fibrillin and tropoelastin, the elastin precursor, increases the rate of assembly of tropoelastin. Furthermore, tropoelastin and fibrillin can be cross-linked by transglutaminase-2, but the function of cross-linking on their elastic properties is yet to be elucidated. Here we show that transglutaminase cross-linking supports formation of a 1:1 stoichiometric fibrillin-tropoelastin complex. SAXS data show that the complex retains features of the individual proteins but is elongated supporting end-to-end assembly. Elastic network models were constructed to compare the dynamics of tropoelastin and fibrillin individually as well as in the cross-linked complex. Normal mode analysis was performed to determine the structures' most energetically favourable, biologically accessible motions which show that within the complex, tropoelastin is less mobile and this molecular stabilisation extends along the length of the tropoelastin molecule to regions remote from the cross-linking site. Together, these data suggest a long-range stabilising effect of cross-linking that occurs due to the covalent linkage of fibrillin to tropoelastin. This work provides insight into the interactions of tropoelastin and fibrillin and how cross-link formation stabilises the elastin precursor so it is primed for elastic fibre assembly.
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Affiliation(s)
- Michael P Lockhart-Cairns
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Helena Newandee
- Department of Biomedical Engineering, School of Engineering, University of Connecticut, Storrs-Mansfield, CT 06269-3139, USA
| | - Jennifer Thomson
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Anthony S Weiss
- School of Molecular Bioscience, Bosch Institute, Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
| | - Clair Baldock
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK.
| | - Anna Tarakanova
- Department of Biomedical Engineering, School of Engineering, University of Connecticut, Storrs-Mansfield, CT 06269-3139, USA; Department of Mechanical Engineering, School of Engineering, University of Connecticut, Storrs-Mansfield, CT 06269-3139, USA.
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17
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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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18
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Sequence variants of human tropoelastin affecting assembly, structural characteristics and functional properties of polymeric elastin in health and disease. Matrix Biol 2019; 84:68-80. [DOI: 10.1016/j.matbio.2019.06.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/23/2019] [Accepted: 06/25/2019] [Indexed: 12/19/2022]
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19
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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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20
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Almeida H, Domingues RMA, Mithieux SM, Pires RA, Gonçalves AI, Gómez-Florit M, Reis RL, Weiss AS, Gomes ME. Tropoelastin-Coated Tendon Biomimetic Scaffolds Promote Stem Cell Tenogenic Commitment and Deposition of Elastin-Rich Matrix. ACS APPLIED MATERIALS & INTERFACES 2019; 11:19830-19840. [PMID: 31088069 DOI: 10.1021/acsami.9b04616] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Tendon tissue engineering strategies that recreate the biophysical and biochemical native microenvironment have a greater potential to achieve regeneration. Here, we developed tendon biomimetic scaffolds using mechanically competent yarns of poly-ε-caprolactone, chitosan, and cellulose nanocrystals to recreate the inherent tendon hierarchy from a nano-to-macro scale. These were then coated with tropoelastin (TROPO) through polydopamine (PDA) linking, to mimic the native extracellular matrix (ECM) composition and elasticity. Both PDA and TROPO coatings decreased surface stiffness without masking the underlying substrate. We found that human adipose-derived stem cells (hASCs) seeded onto these TROPO biomimetic scaffolds more rapidly acquired their spindle-shape morphology and high aspect ratio characteristic of tenocytes. Immunocytochemistry shows that the PDA and TROPO-coated surfaces boosted differentiation of hASCs toward the tenogenic lineage, with sustained expression of the tendon-related markers scleraxis and tenomodulin up to 21 days of culture. Furthermore, these surfaces enabled the deposition of a tendon-like ECM, supported by the expression of collagens type I and III, tenascin, and decorin. Gene expression analysis revealed a downregulation of osteogenic and fibrosis markers in the presence of TROPO when compared with the control groups, suggesting proper ECM deposition. Remarkably, differentiated cells exposed to TROPO acquired an elastogenic profile due to the evident elastin synthesis and deposition, contributing to the formation of a more mimetic matrix in comparison with the PDA-coated and uncoated conditions. In summary, our biomimetic substrates combining biophysical and biological cues modulate stem cell behavior potentiating their long-term tenogenic commitment and the production of an elastin-rich ECM.
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Affiliation(s)
- Helena Almeida
- 3B's Research Group, I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics , University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine , AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra , Barco, 4805-017 Guimarães , Portugal
- ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães , Portugal
| | - Rui M A Domingues
- 3B's Research Group, I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics , University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine , AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra , Barco, 4805-017 Guimarães , Portugal
- ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães , Portugal
- The Discoveries Centre for Regenerative and Precision Medicine , Headquarters at University of Minho , Avepark , Barco, 4805-017 Guimarães , Portugal
| | | | - Ricardo A Pires
- 3B's Research Group, I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics , University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine , AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra , Barco, 4805-017 Guimarães , Portugal
- ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães , Portugal
- The Discoveries Centre for Regenerative and Precision Medicine , Headquarters at University of Minho , Avepark , Barco, 4805-017 Guimarães , Portugal
| | - Ana I Gonçalves
- 3B's Research Group, I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics , University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine , AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra , Barco, 4805-017 Guimarães , Portugal
- ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães , Portugal
| | - Manuel Gómez-Florit
- 3B's Research Group, I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics , University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine , AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra , Barco, 4805-017 Guimarães , Portugal
- ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães , Portugal
| | - Rui L Reis
- 3B's Research Group, I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics , University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine , AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra , Barco, 4805-017 Guimarães , Portugal
- ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães , Portugal
- The Discoveries Centre for Regenerative and Precision Medicine , Headquarters at University of Minho , Avepark , Barco, 4805-017 Guimarães , Portugal
| | | | - Manuela E Gomes
- 3B's Research Group, I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics , University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine , AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra , Barco, 4805-017 Guimarães , Portugal
- ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães , Portugal
- The Discoveries Centre for Regenerative and Precision Medicine , Headquarters at University of Minho , Avepark , Barco, 4805-017 Guimarães , Portugal
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21
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Tarakanova A, Ozsvar J, Weiss A, Buehler M. Coarse-grained model of tropoelastin self-assembly into nascent fibrils. Mater Today Bio 2019; 3:100016. [PMID: 32159149 PMCID: PMC7061556 DOI: 10.1016/j.mtbio.2019.100016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 12/30/2022] Open
Abstract
Elastin is the dominant building block of elastic fibers that impart structural integrity and elasticity to a range of important tissues, including the lungs, blood vessels, and skin. The elastic fiber assembly process begins with a coacervation stage where tropoelastin monomers reversibly self-assemble into coacervate aggregates that consist of multiple molecules. In this paper, an atomistically based coarse-grained model of tropoelastin assembly is developed. Using the previously determined atomistic structure of tropoelastin, the precursor molecule to elastic fibers, as the basis for coarse-graining, the atomistic model is mapped to a MARTINI-based coarse-grained framework to account for chemical details of protein-protein interactions, coupled to an elastic network model to stabilize the structure. We find that self-assembly of monomers generates up to ∼70 nm of dense aggregates that are distinct at different temperatures, displaying high temperature sensitivity. Resulting assembled structures exhibit a combination of fibrillar and globular substructures within the bulk aggregates. The results suggest that the coalescence of tropoelastin assemblies into higher order structures may be reinforced in the initial stages of coacervation by directed assembly, supporting the experimentally observed presence of heterogeneous cross-linking. Self-assembly of tropoelastin is driven by interactions of specific hydrophobic domains and the reordering of water molecules in the system. Domain pair orientation analysis throughout the self-assembly process at different temperatures suggests coacervation is a driving force to orient domains for heterogeneous downstream cross-linking. The model provides a framework to characterize macromolecular self-assembly for elastin, and the formulation could easily be adapted to similar assembly systems.
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Affiliation(s)
- A. Tarakanova
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering and Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
| | - J. Ozsvar
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - A.S. Weiss
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Bosch Institute, The University of Sydney, Sydney, NSW, Australia
- Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
| | - M.J. Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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23
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Qin Z, Buehler MJ. Analysis of the vibrational and sound spectrum of over 100,000 protein structures and application in sonification. EXTREME MECHANICS LETTERS 2019; 29:100460. [PMID: 32832588 PMCID: PMC7437953 DOI: 10.1016/j.eml.2019.100460] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report a high-throughput method that enables us to automatically compute the vibrational spectra of more than 100,000 proteins available in the Protein Data Bank to date, in a consistent manner. Using this new algorithm we report a comprehensive database of the normal mode frequencies of all known protein structures, which has not been available before. We then use the resulting frequency spectra of the proteins to generate audible sound by overlaying the molecular vibrations and translating them to the audible frequency range using the music theoretic concept of transpositional equivalence. The method, implemented as a Max audio device for use in a digital audio workstation (DAW), provides unparalleled insights into the rich vibrational signatures of protein structures, and offers a new way for creative expression by using it as a new type of musical instrument. This musical instrument is fully defined by the vibrational feature of almost all known protein structures, making it fundamentally different from all the traditional instruments that are limited by the material properties of a few types of conventional engineering materials, such as wood, metals or polymers.
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Affiliation(s)
- Zhao Qin
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave. 1-290, Cambridge, Massachusetts 02139, United States of America
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave. 1-290, Cambridge, Massachusetts 02139, United States of America
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24
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Ozsvar J, Tarakanova A, Wang R, Buehler MJ, Weiss AS. Allysine modifications perturb tropoelastin structure and mobility on a local and global scale. Matrix Biol Plus 2019; 2:100002. [PMID: 33543005 PMCID: PMC7852328 DOI: 10.1016/j.mbplus.2019.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/10/2019] [Accepted: 03/10/2019] [Indexed: 11/20/2022] Open
Abstract
Elastin provides elastic tissues with resilience through stretch and recoil cycles, and is primarily made of its extensively cross-linked monomer, tropoelastin. Here, we leverage the recently published full atomistic model of tropoelastin to assess how allysine modifications, which are essential to cross-linking, contribute to the dynamics and structural changes that occur in tropoelastin in the context of elastin assembly. We used replica exchange molecular dynamics to generate structural ensembles of allysine containing tropoelastin. We conducted principal component analysis on these ensembles and found that the molecule departs from the canonical structural ensemble. Furthermore, we showed that, while the canonical scissors-twist movement was retained, new movements emerged that deviated from those of the wild type protein, providing evidence for the involvement of a variety of molecular motions in elastin assembly. Additionally, we highlighted secondary structural changes and linked these perturbations to the longevity of specific salt bridges. We propose a model where allysines in tropoelastin contribute to hierarchical elastin assembly through global and local perturbations to molecular structure and dynamics. converting lysine to allysine by lysyl oxidases is needed to generate crosslinks between tropoelastin molecules in order to make elastin structural changes in the intact tropoelastin molecule ensue where modified tropoelastin molecules structurally depart from the canonical ensemble new molecular motions deviate from those of unmodified tropoelastin persistence times of specific salt bridges contribute to these perturbations allysines in tropoelastin contribute to hierarchical elastin assembly through global and local perturbations to molecular structure and dynamics
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Key Words
- 5ALK, tropoelastin containing 5 allysine residues
- ALK353, tropoelastin containing allysine at residue 353
- ALK353, tropoelastin containing allysine at residue 507
- ALL, allysine aldol
- ANM, anisotropic network model
- Assembly
- ECM, extracellular matrix
- Elastin
- LNL, lysinonorleucine
- MD, molecular dynamics
- Molecular dynamics
- NMA, normal mode analysis
- PCA, principal component analysis
- REMD, replica exchange molecular dynamics
- RMSD, root mean square deviation
- Replica exchange molecular dynamics
- SASA, solvent accessible surface area
- WT, wild type tropoelastin
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Affiliation(s)
- Jazmin Ozsvar
- Charles Perkins Centre, the University of Sydney, 2006 Sydney, NSW, Australia.,School of Life and Environmental Sciences, The University of Sydney, 2006 Sydney, NSW, Australia.,Cell Therapy Manufacturing Cooperative Research Centre, Adelaide, 5000, SA, Australia
| | - Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Richard Wang
- Charles Perkins Centre, the University of Sydney, 2006 Sydney, NSW, Australia.,School of Life and Environmental Sciences, The University of Sydney, 2006 Sydney, NSW, Australia
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anthony S Weiss
- Charles Perkins Centre, the University of Sydney, 2006 Sydney, NSW, Australia.,School of Life and Environmental Sciences, The University of Sydney, 2006 Sydney, NSW, Australia.,Cell Therapy Manufacturing Cooperative Research Centre, Adelaide, 5000, SA, Australia.,Bosch Institute, The University of Sydney, 2006 Sydney, NSW, Australia.,Sydney Nano Institute, The University of Sydney, 2006 Sydney, NSW, Australia
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25
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Soluble matrix protein is a potent modulator of mesenchymal stem cell performance. Proc Natl Acad Sci U S A 2019; 116:2042-2051. [PMID: 30659152 DOI: 10.1073/pnas.1812951116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We challenge the conventional designation of structural matrix proteins primarily as supporting scaffolds for resident cells. The extracellular matrix protein tropoelastin is classically regarded as a structural component that confers mechanical strength and resilience to tissues subject to repetitive elastic deformation. Here we describe how tropoelastin inherently induces a range of biological responses, even in cells not typically associated with elastic tissues and in a manner unexpected of typical substrate-dependent matrix proteins. We show that tropoelastin alone drives mesenchymal stem cell (MSC) proliferation and phenotypic maintenance, akin to the synergistic effects of potent growth factors such as insulin-like growth factor 1 and basic fibroblast growth factor. In addition, tropoelastin functionally surpasses these growth factors, as well as fibronectin, in allowing substantial media serum reduction without loss of proliferative potential. We further demonstrate that tropoelastin elicits strong mitogenic and cell-attractive responses, both as an immobilized substrate and as a soluble additive, via direct interactions with cell surface integrins αvβ3 and αvβ5. This duality of action converges the long-held mechanistic dichotomy between adhesive matrix proteins and soluble growth factors and uncovers the powerful, untapped potential of tropoelastin for clinical MSC expansion and therapeutic MSC recruitment. We propose that the potent, growth factor-like mitogenic and motogenic abilities of tropoelastin are biologically rooted in the need for rapid stem cell homing and proliferation during early development and/or wound repair.
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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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27
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Yeo GC, Kosobrodova E, Kondyurin A, McKenzie DR, Bilek MM, Weiss AS. Plasma‐Activated Substrate with a Tropoelastin Anchor for the Maintenance and Delivery of Multipotent Adult Progenitor Cells. Macromol Biosci 2018; 19:e1800233. [DOI: 10.1002/mabi.201800233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/19/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Giselle C. Yeo
- Charles Perkins CentreUniversity of Sydney NSW 2006 Australia
- School of Life and Environmental SciencesUniversity of Sydney NSW 2006 Australia
- Bosch InstituteUniversity of Sydney NSW 2006 Australia
- The Cooperative Research Centre for Cell Therapy ManufacturingUniversity of South Australia City West Campus Adelaide SA 5000 Australia
| | - Elena Kosobrodova
- School of PhysicsUniversity of Sydney NSW 2006 Australia
- School of AerospaceMechanical and Mechatronic EngineeringUniversity of Sydney NSW 2006 Australia
- The Cooperative Research Centre for Cell Therapy ManufacturingUniversity of South Australia City West Campus Adelaide SA 5000 Australia
| | - Alexey Kondyurin
- School of PhysicsUniversity of Sydney NSW 2006 Australia
- The Cooperative Research Centre for Cell Therapy ManufacturingUniversity of South Australia City West Campus Adelaide SA 5000 Australia
| | - David R. McKenzie
- School of PhysicsUniversity of Sydney NSW 2006 Australia
- The Cooperative Research Centre for Cell Therapy ManufacturingUniversity of South Australia City West Campus Adelaide SA 5000 Australia
| | - Marcela M. Bilek
- Charles Perkins CentreUniversity of Sydney NSW 2006 Australia
- School of PhysicsUniversity of Sydney NSW 2006 Australia
- School of AerospaceMechanical and Mechatronic EngineeringUniversity of Sydney NSW 2006 Australia
- Australian Institute of Nanoscale Science and TechnologyUniversity of Sydney NSW 2006 Australia
- The Cooperative Research Centre for Cell Therapy ManufacturingUniversity of South Australia City West Campus Adelaide SA 5000 Australia
| | - Anthony S. Weiss
- Charles Perkins CentreUniversity of Sydney NSW 2006 Australia
- School of Life and Environmental SciencesUniversity of Sydney NSW 2006 Australia
- Bosch InstituteUniversity of Sydney NSW 2006 Australia
- The Cooperative Research Centre for Cell Therapy ManufacturingUniversity of South Australia City West Campus Adelaide SA 5000 Australia
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28
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Tarakanova A, Yeo GC, Baldock C, Weiss AS, Buehler MJ. Molecular model of human tropoelastin and implications of associated mutations. Proc Natl Acad Sci U S A 2018; 115:7338-7343. [PMID: 29946030 PMCID: PMC6048532 DOI: 10.1073/pnas.1801205115] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein folding poses unique challenges for large, disordered proteins due to the low resolution of structural data accessible in experiment and on the basis of short time scales and limited sampling attainable in computation. Such molecules are uniquely suited to accelerated-sampling molecular dynamics algorithms due to a flat-energy landscape. We apply these methods to report here the folded structure in water from a fully extended chain of tropoelastin, a 698-amino acid molecular precursor to elastic fibers that confer elasticity and recoil to tissues, finding good agreement with experimental data. We then study a series of artificial and disease-related mutations, yielding molecular mechanisms to explain structural differences and variation in hierarchical assembly observed in experiment. The present model builds a framework for studying assembly and disease and yields critical insight into molecular mechanisms behind these processes. These results suggest that proteins with disordered regions are suitable candidates for characterization by this approach.
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Affiliation(s)
- Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239
| | - Giselle C Yeo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, 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, Manchester M13 9PT, United Kingdom
| | - Anthony S Weiss
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239;
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29
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Yeo J, Huang W, Tarakanova A, Zhang YW, Kaplan DL, Buehler MJ. Unraveling the Molecular Mechanisms of Thermo-responsive Properties of Silk-Elastin-Like Proteins by Integrating Multiscale Modeling and Experiment. J Mater Chem B 2018; 6:3727-3734. [PMID: 30467524 PMCID: PMC6241539 DOI: 10.1039/c8tb00819a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Adaptive hydrogels tailor-made from silk-elastin-like proteins (SELPs) possess excellent biocompatibility and biodegradability with properties that are tunable and responsive to multiple simultaneous external stimuli. To unravel the molecular mechanisms of their physical response to external stimuli in tandem with experiments, here we predict and measure the variation in structural properties as a function of temperature through coarse-grained (CG) modeling of individual and crosslinked SE8Y and S4E8Y molecules, which have ratios of 1:8 and 4:8 of silk to elastin blocks respectively. Extensive structural reshuffling in single SE8Y molecules led to the increased compactness of the structure, whereas S4E8Y molecules did not experience any significant changes as they already adopted very compact structures at low temperatures. Crosslinking of SE8Y molecules at high concentrations impeded their structural transition at high temperatures that drastically reduced the degree of deswelling through extensive suppression of the structural shuffling and the trapping of the molecules in high potential energy states due to inter-molecular constraints. This integrative experimental and computational understanding of the thermal response in single molecules of SELPs and their crosslinked networks should lead to further improvements in the properties of SELP hydrogels through predictive designs and their wider applications in biomaterials and tissue engineering.
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Affiliation(s)
- Jingjie Yeo
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute of High Performance Computing, ASTAR, 1 Fusionopolis Way, Singapore 138632, Singapore
| | - Wenwen Huang
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yong-Wei Zhang
- Institute of High Performance Computing, ASTAR, 1 Fusionopolis Way, Singapore 138632, Singapore
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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30
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Yeo J, Jung GS, Martín-Martínez FJ, Ling S, Gu GX, Qin Z, Buehler MJ. Materials-by-Design: Computation, Synthesis, and Characterization from Atoms to Structures. PHYSICA SCRIPTA 2018; 93:053003. [PMID: 31866694 PMCID: PMC6924929 DOI: 10.1088/1402-4896/aab4e2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In the 50 years that succeeded Richard Feynman's exposition of the idea that there is "plenty of room at the bottom" for manipulating individual atoms for the synthesis and manufacturing processing of materials, the materials-by-design paradigm is being developed gradually through synergistic integration of experimental material synthesis and characterization with predictive computational modeling and optimization. This paper reviews how this paradigm creates the possibility to develop materials according to specific, rational designs from the molecular to the macroscopic scale. We discuss promising techniques in experimental small-scale material synthesis and large-scale fabrication methods to manipulate atomistic or macroscale structures, which can be designed by computational modeling. These include recombinant protein technology to produce peptides and proteins with tailored sequences encoded by recombinant DNA, self-assembly processes induced by conformational transition of proteins, additive manufacturing for designing complex structures, and qualitative and quantitative characterization of materials at different length scales. We describe important material characterization techniques using numerous methods of spectroscopy and microscopy. We detail numerous multi-scale computational modeling techniques that complements these experimental techniques: DFT at the atomistic scale; fully atomistic and coarse-grain molecular dynamics at the molecular to mesoscale; continuum modeling at the macroscale. Additionally, we present case studies that utilize experimental and computational approaches in an integrated manner to broaden our understanding of the properties of two-dimensional materials and materials based on silk and silk-elastin-like proteins.
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Affiliation(s)
- Jingjie Yeo
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore 138632
| | - Gang Seob Jung
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Francisco J. Martín-Martínez
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shengjie Ling
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Grace X. Gu
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhao Qin
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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31
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Yeo J, Jung G, Tarakanova A, Martín-Martínez FJ, Qin Z, Cheng Y, Zhang YW, Buehler MJ. Multiscale modeling of keratin, collagen, elastin and related human diseases: Perspectives from atomistic to coarse-grained molecular dynamics simulations. EXTREME MECHANICS LETTERS 2018; 20:112-124. [PMID: 33344740 PMCID: PMC7745951 DOI: 10.1016/j.eml.2018.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Scleroproteins are an important category of proteins within the human body that adopt filamentous, elongated conformations in contrast with typical globular proteins. These include keratin, collagen, and elastin, which often serve a common mechanical function in structural support of cells and tissues. Genetic mutations alter these proteins, disrupting their functions and causing diseases. Computational characterization of these mutations has proven to be extremely valuable in identifying the intricate structure-function relationships of scleroproteins from the molecular scale up, especially if combined with multiscale experimental analysis and the synthesis of model proteins to test specific structure-function relationships. In this work, we review numerous critical diseases that are related to keratin, collagen, and elastin, and through several case studies, we propose ways of extensively utilizing multiscale modeling, from atomistic to coarse-grained molecular dynamics simulations, to uncover the molecular origins for some of these diseases and to aid in the development of novel cures and therapies. As case studies, we examine the effects of the genetic disease Epidermolytic Hyperkeratosis (EHK) on the structure and aggregation of keratins 1 and 10; we propose models to understand the diseases of Osteogenesis Imperfecta (OI) and Alport syndrome (AS) that affect the mechanical and aggregation properties of collagen; and we develop atomistic molecular dynamics and elastic network models of elastin to determine the role of mutations in diseases such as Cutis Laxa and Supravalvular Aortic Stenosis on elastin's structure and molecular conformational motions and implications for assembly.
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Affiliation(s)
- Jingjie Yeo
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore 138632
| | - GangSeob Jung
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Francisco J. Martín-Martínez
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhao Qin
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuan Cheng
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore 138632
| | - Yong-Wei Zhang
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore 138632
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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32
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Duque Lasio ML, Kozel BA. Elastin-driven genetic diseases. Matrix Biol 2018; 71-72:144-160. [PMID: 29501665 DOI: 10.1016/j.matbio.2018.02.021] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/23/2018] [Accepted: 02/23/2018] [Indexed: 02/08/2023]
Abstract
Elastic fibers provide recoil to tissues that undergo repeated deformation, such as blood vessels, lungs and skin. Composed of elastin and its accessory proteins, the fibers are produced within a restricted developmental window and are stable for decades. Their eventual breakdown is associated with a loss of tissue resiliency and aging. Rare alteration of the elastin (ELN) gene produces disease by impacting protein dosage (supravalvar aortic stenosis, Williams Beuren syndrome and Williams Beuren region duplication syndrome) and protein function (autosomal dominant cutis laxa). This review highlights aspects of the elastin molecule and its assembly process that contribute to human disease and also discusses potential therapies aimed at treating diseases of elastin insufficiency.
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Affiliation(s)
| | - Beth A Kozel
- National Institutes of Health, National Heart Lung and Blood Institute, Bethesda, MD, USA.
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33
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Casaril AM, Ignasiak MT, Chuang CY, Vieira B, Padilha NB, Carroll L, Lenardão EJ, Savegnago L, Davies MJ. Selenium-containing indolyl compounds: Kinetics of reaction with inflammation-associated oxidants and protective effect against oxidation of extracellular matrix proteins. Free Radic Biol Med 2017; 113:395-405. [PMID: 29055824 DOI: 10.1016/j.freeradbiomed.2017.10.344] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/14/2017] [Accepted: 10/16/2017] [Indexed: 12/27/2022]
Abstract
Activated white blood cells generate multiple oxidants in response to invading pathogens. Thus, hypochlorous acid (HOCl) is generated via the reaction of myeloperoxidase (from neutrophils and monocytes) with hydrogen peroxide, and peroxynitrous acid (ONOOH), a potent oxidizing and nitrating agent is formed from superoxide radicals and nitric oxide, generated by stimulated macrophages. Excessive or misplaced production of these oxidants has been linked to multiple human pathologies, including cardiovascular disease. Atherosclerosis is characterized by chronic inflammation and the presence of oxidized materials, including extracellular matrix (ECM) proteins, within the artery wall. Here we investigated the potential of selenium-containing indoles to afford protection against these oxidants, by determining rate constants (k) for their reaction, and quantifying the extent of damage on isolated ECM proteins and ECM generated by human coronary artery endothelial cells (HCAECs). The novel selenocompounds examined react with HOCl with k 0.2-1.0 × 108M-1s-1, and ONOOH with k 4.5-8.6 - × 105M-1s-1. Reaction with H2O2 is considerably slower (k < 0.25M-1s-1). The selenocompound 2-phenyl-3-(phenylselanyl)imidazo[1,2-a]pyridine provided protection to human serum albumin (HSA) against HOCl-mediated damage (as assessed by SDS-PAGE) and damage to isolated matrix proteins induced by ONOOH, with a concomitant decrease in the levels of the biomarker 3-nitrotyrosine. Structural damage and generation of 3-nitroTyr on HCAEC-ECM were also reduced. These data demonstrate that the novel selenium-containing compounds show high reactivity with oxidants and may modulate oxidative and nitrosative damage at sites of inflammation, contributing to a reduction in tissue dysfunction and atherogenesis.
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Affiliation(s)
- Angela M Casaril
- Grupo de Pesquisa em Neurobiotecnologia - GPN - Universidade Federal de Pelotas - UFPel, P.O. Box 354, 96010-900 Pelotas, RS, Brazil
| | - Marta T Ignasiak
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark; Faculty of Chemistry, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Christine Y Chuang
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
| | - Beatriz Vieira
- Laboratório de Síntese Orgânica Limpa - LASOL - Universidade Federal de Pelotas - UFPel, P.O. Box 354, 96010-900 Pelotas, RS, Brazil
| | - Nathalia B Padilha
- Laboratório de Síntese Orgânica Limpa - LASOL - Universidade Federal de Pelotas - UFPel, P.O. Box 354, 96010-900 Pelotas, RS, Brazil
| | - Luke Carroll
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
| | - Eder J Lenardão
- Laboratório de Síntese Orgânica Limpa - LASOL - Universidade Federal de Pelotas - UFPel, P.O. Box 354, 96010-900 Pelotas, RS, Brazil
| | - Lucielli Savegnago
- Grupo de Pesquisa em Neurobiotecnologia - GPN - Universidade Federal de Pelotas - UFPel, P.O. Box 354, 96010-900 Pelotas, RS, Brazil
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark.
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34
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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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35
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Affiliation(s)
- Gang Seob Jung
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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36
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Huang W, Ebrahimi D, Dinjaski N, Tarakanova A, Buehler MJ, Wong JY, Kaplan DL. Synergistic Integration of Experimental and Simulation Approaches for the de Novo Design of Silk-Based Materials. Acc Chem Res 2017; 50:866-876. [PMID: 28191922 DOI: 10.1021/acs.accounts.6b00616] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tailored biomaterials with tunable functional properties are crucial for a variety of task-specific applications ranging from healthcare to sustainable, novel bio-nanodevices. To generate polymeric materials with predictive functional outcomes, exploiting designs from nature while morphing them toward non-natural systems offers an important strategy. Silks are Nature's building blocks and are produced by arthropods for a variety of uses that are essential for their survival. Due to the genetic control of encoded protein sequence, mechanical properties, biocompatibility, and biodegradability, silk proteins have been selected as prototype models to emulate for the tunable designs of biomaterial systems. The bottom up strategy of material design opens important opportunities to create predictive functional outcomes, following the exquisite polymeric templates inspired by silks. Recombinant DNA technology provides a systematic approach to recapitulate, vary, and evaluate the core structure peptide motifs in silks and then biosynthesize silk-based polymers by design. Post-biosynthesis processing allows for another dimension of material design by controlled or assisted assembly. Multiscale modeling, from the theoretical prospective, provides strategies to explore interactions at different length scales, leading to selective material properties. Synergy among experimental and modeling approaches can provide new and more rapid insights into the most appropriate structure-function relationships to pursue while also furthering our understanding in terms of the range of silk-based systems that can be generated. This approach utilizes nature as a blueprint for initial polymer designs with useful functions (e.g., silk fibers) but also employs modeling-guided experiments to expand the initial polymer designs into new domains of functional materials that do not exist in nature. The overall path to these new functional outcomes is greatly accelerated via the integration of modeling with experiment. In this Account, we summarize recent advances in understanding and functionalization of silk-based protein systems, with a focus on the integration of simulation and experiment for biopolymer design. Spider silk was selected as an exemplary protein to address the fundamental challenges in polymer designs, including specific insights into the role of molecular weight, hydrophobic/hydrophilic partitioning, and shear stress for silk fiber formation. To expand current silk designs toward biointerfaces and stimuli responsive materials, peptide modules from other natural proteins were added to silk designs to introduce new functions, exploiting the modular nature of silk proteins and fibrous proteins in general. The integrated approaches explored suggest that protein folding, silk volume fraction, and protein amino acid sequence changes (e.g., mutations) are critical factors for functional biomaterial designs. In summary, the integrated modeling-experimental approach described in this Account suggests a more rationally directed and more rapid method for the design of polymeric materials. It is expected that this combined use of experimental and computational approaches has a broad applicability not only for silk-based systems, but also for other polymer and composite materials.
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Affiliation(s)
- Wenwen Huang
- Department
of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Davoud Ebrahimi
- Laboratory
for Atomistic and Molecular Mechanics (LAMM), Department of Civil
and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nina Dinjaski
- Department
of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Anna Tarakanova
- Laboratory
for Atomistic and Molecular Mechanics (LAMM), Department of Civil
and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Markus J. Buehler
- Laboratory
for Atomistic and Molecular Mechanics (LAMM), Department of Civil
and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Joyce Y. Wong
- Department
of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, United States
| | - David L. Kaplan
- Department
of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
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37
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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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38
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Muiznieks LD, Keeley FW. Biomechanical Design of Elastic Protein Biomaterials: A Balance of Protein Structure and Conformational Disorder. ACS Biomater Sci Eng 2016; 3:661-679. [DOI: 10.1021/acsbiomaterials.6b00469] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lisa D. Muiznieks
- Molecular
Structure and Function Program, Research Institute, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, Canada M5G 0A4
| | - Fred W. Keeley
- Molecular
Structure and Function Program, Research Institute, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, Canada M5G 0A4
- Department
of Biochemistry and Department of Laboratory Medicine and Pathobiology, 1 King’s College Circle, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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39
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Weiss AS. Perspectives on the Molecular and Biological Implications of Tropoelastin in Human Tissue Elasticity. Aust J Chem 2016. [DOI: 10.1071/ch16452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The elasticity of a range of vertebrate and particularly human tissues depends on the dynamic and persistent protein elastin. This elasticity is diverse, and comprises skin, blood vessels, and lung, and is essential for tissue viability. Elastin is predominantly made by assembling tropoelastin, which is an asymmetric 20-nm-long protein molecule. This overview considers tropoelastin’s molecular features and biological interactions in the context of its value in tissue repair.
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