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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Yang C, Tarakanova A. Biomechanics and molecular mechanisms of aging in elastin. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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Madani M, Lin K, Tarakanova A. DSResSol: A Sequence-Based Solubility Predictor Created with Dilated Squeeze Excitation Residual Networks. Int J Mol Sci 2021; 22:13555. [PMID: 34948354 PMCID: PMC8704505 DOI: 10.3390/ijms222413555] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
Protein solubility is an important thermodynamic parameter that is critical for the characterization of a protein's function, and a key determinant for the production yield of a protein in both the research setting and within industrial (e.g., pharmaceutical) applications. Experimental approaches to predict protein solubility are costly, time-consuming, and frequently offer only low success rates. To reduce cost and expedite the development of therapeutic and industrially relevant proteins, a highly accurate computational tool for predicting protein solubility from protein sequence is sought. While a number of in silico prediction tools exist, they suffer from relatively low prediction accuracy, bias toward the soluble proteins, and limited applicability for various classes of proteins. In this study, we developed a novel deep learning sequence-based solubility predictor, DSResSol, that takes advantage of the integration of squeeze excitation residual networks with dilated convolutional neural networks and outperforms all existing protein solubility prediction models. This model captures the frequently occurring amino acid k-mers and their local and global interactions and highlights the importance of identifying long-range interaction information between amino acid k-mers to achieve improved accuracy, using only protein sequence as input. DSResSol outperforms all available sequence-based solubility predictors by at least 5% in terms of accuracy when evaluated by two different independent test sets. Compared to existing predictors, DSResSol not only reduces prediction bias for insoluble proteins but also predicts soluble proteins within the test sets with an accuracy that is at least 13% higher than existing models. We derive the key amino acids, dipeptides, and tripeptides contributing to protein solubility, identifying glutamic acid and serine as critical amino acids for protein solubility prediction. Overall, DSResSol can be used for the fast, reliable, and inexpensive prediction of a protein's solubility to guide experimental design.
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Affiliation(s)
- Mohammad Madani
- Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269, USA;
- Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, USA;
| | - Kaixiang Lin
- Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, USA;
| | - Anna Tarakanova
- Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269, USA;
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Marshall L, Tarakanova A, Szarek P, Pierce DM. Cartilage and collagen mechanics under large-strain shear within in vivo and at supraphysiogical temperatures. J Mech Behav Biomed Mater 2020; 103:103595. [PMID: 32090923 DOI: 10.1016/j.jmbbm.2019.103595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/13/2019] [Accepted: 12/10/2019] [Indexed: 11/28/2022]
Abstract
Human joints, particularly those of extremities, experience a significant range of temperatures in vivo. Joint temperature influences the mechanics of both joint and cartilage, and the mechanics of cartilage can affect the temperature of both joint and cartilage. Thermal treatments and tissue repairs, such as thermal chondroplasty, and ex vivo tissue engineering may also expose cartilage to supraphysiological temperatures. Furthermore, although cartilage undergoes principally compressive loads in vivo, shear strain plays a significant role at larger compressive strains. Thus, we aimed to determine whether and how the bulk mechanical responses of cartilage undergoing large-strain shear change (1) within the range of temperatures relevant in vivo, and (2) both during and after supraphysiological thermal treatments. We completed large-strain shear tests (10 and 15%) at four thermal conditions: 24∘C and 40∘C to span the in vivo range, and 70∘C and 24∘C repeated after 70∘C to explore mechanics during and after potential treatments. We calculated the bulk mechanical responses (strain-energy dissipation densities, peak-to-peak shear stresses, and peak-effective shear moduli) as of function of temperature and used statistical methods to probe significant differences. To probe the mechanisms underlying differences we assessed specimens, principally the type II collagen, with imaging (second harmonic generation and transmission electron microscopies, and histology) and assessed the temperature-dependent mechanics of type II collagen molecules within cartilage using steered molecular dynamics simulations. Our results suggest that the bulk mechanical responses of cartilage depend significantly on temperature both within the in vivo range and at supraphysiological temperatures, showing significant reductions in all mechanical measures with increasing temperature. Using imaging and simulations we determined that one underlying mechanism explaining our results may be changes in the molecular deformation profiles of collagen molecules versus temperature, likely compounded at larger length scales. These new insights into the mechanics of cartilage and collagen may suggest new treatment targets for damaged or osteoarthritic cartilage.
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Affiliation(s)
- Lauren Marshall
- Department of Mechanical Engineering, University of Connecticut, 191 Auditorium Road, Unit 3139, Storrs, CT, 06269, USA
| | - Anna Tarakanova
- Department of Mechanical Engineering, University of Connecticut, 191 Auditorium Road, Unit 3139, Storrs, CT, 06269, USA; Department of Biomedical Engineering, University of Connecticut, 260 Glenbrook Road, Unit 3247, Storrs, CT, 06269, USA
| | - Phoebe Szarek
- Department of Biomedical Engineering, University of Connecticut, 260 Glenbrook Road, Unit 3247, Storrs, CT, 06269, USA
| | - David M Pierce
- Department of Mechanical Engineering, University of Connecticut, 191 Auditorium Road, Unit 3139, Storrs, CT, 06269, USA; Department of Biomedical Engineering, University of Connecticut, 260 Glenbrook Road, Unit 3247, Storrs, CT, 06269, USA.
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Madani M, Tarakanova A. Characterization of Mechanics and Tunability of Resilin Protein by Molecular Dynamics Simulation. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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López Barreiro D, Yeo J, Tarakanova A, Martin‐Martinez FJ, Buehler MJ. Multiscale Modeling of Silk and Silk‐Based Biomaterials—A Review. Macromol Biosci 2019. [DOI: 10.1002/mabi.201970007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Liu D, Tarakanova A, Hsu CC, Yu M, Zheng S, Yu L, Liu J, He Y, Dunstan DJ, Buehler MJ. Spider dragline silk as torsional actuator driven by humidity. Sci Adv 2019; 5:eaau9183. [PMID: 30838327 PMCID: PMC6397028 DOI: 10.1126/sciadv.aau9183] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 05/25/2023]
Abstract
Self-powered actuation driven by ambient humidity is of practical interest for applications such as hygroscopic artificial muscles. We demonstrate that spider dragline silk exhibits a humidity-induced torsional deformation of more than 300°/mm. When the relative humidity reaches a threshold of about 70%, the dragline silk starts to generate a large twist deformation independent of spider species. The torsional actuation can be precisely controlled by regulating the relative humidity. The behavior of humidity-induced twist is related to the supercontraction behavior of spider dragline silk. Specifically, molecular simulations of MaSp1 and MaSp2 proteins in dragline silk reveal that the unique torsional property originates from the presence of proline in MaSp2. The large proline rings also contribute to steric exclusion and disruption of hydrogen bonding in the molecule. This property of dragline silk and its structural origin can inspire novel design of torsional actuators or artificial muscles and enable the development of designer biomaterials.
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Affiliation(s)
- Dabiao Liu
- Department of Mechanics, Huazhong University of Science and Technology, Wuhan 430074, China
- Hubei Key Laboratory of Engineering Structural Analysis and Safety Assessment, Wuhan 430074, China
- School of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
| | - Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Claire C. Hsu
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Miao Yu
- Department of Mechanics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shimin Zheng
- Department of Mechanics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Longteng Yu
- Department of Mechanics, Huazhong University of Science and Technology, Wuhan 430074, China
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Jie Liu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yuming He
- Department of Mechanics, Huazhong University of Science and Technology, Wuhan 430074, China
- Hubei Key Laboratory of Engineering Structural Analysis and Safety Assessment, Wuhan 430074, China
| | - D. J. Dunstan
- School of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
| | - Markus 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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Tarakanova A. Molecular Models of Human Elastin and Elastin Biomaterials. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Roberts EG, Rim NG, Huang W, Tarakanova A, Yeo J, Buehler MJ, Kaplan DL, Wong JY. Fabrication and Characterization of Recombinant Silk-Elastin-Like-Protein (SELP) Fiber. Macromol Biosci 2018; 18:e1800265. [PMID: 30417967 PMCID: PMC6960454 DOI: 10.1002/mabi.201800265] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/28/2018] [Indexed: 11/06/2022]
Abstract
Silk-elastin-like-protein polymers (SELPs) are genetically engineered recombinant protein sequences consisting of repeating units of silk-like and elastin-like blocks. By combining these entities, it is shown that both the characteristic strength of silk and the temperature-dependent responsiveness of elastin can be leveraged to create an enhanced stimuli-responsive material. It is hypothesized that SELP behavior can be influenced by varying the silk-to-elastin ratio. If the responsiveness of the material at different ratios is significantly different, this would allow for the design of materials with specific temperature-based swelling and mechanical properties. This study demonstrates that SELP fiber properties can be controlled via a temperature transition dependent on the ratio of silk-to-elastin in the material. SELP fibers are experimentally wet spun from polymers with different ratios of silk-to-elastin and conditioned in either a below or above transition temperature (T t ) water bath prior to characterization. The fibers with higher elastin content showed more stimuli-responsive behavior compared to the fibers with lower elastin content in the hot (57-60 °C) versus cold (4-7 °C) environment, both computationally and experimentally. This work builds a foundation for developing SELP materials with well-characterized mechanical properties and responsive features.
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Affiliation(s)
- Erin G Roberts
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Nae-Gyune Rim
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Wenwen Huang
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Anna Tarakanova
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jingjie Yeo
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Institute of High Performance Computing, A∗STAR, 1 Fusionopolis Way, Singapore, 138632, Singapore
| | - Markus J Buehler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Joyce Y Wong
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
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15
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López Barreiro D, Yeo J, Tarakanova A, Martin-Martinez FJ, Buehler MJ. Multiscale Modeling of Silk and Silk-Based Biomaterials-A Review. Macromol Biosci 2018; 19:e1800253. [PMID: 30375164 DOI: 10.1002/mabi.201800253] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/20/2018] [Indexed: 12/25/2022]
Abstract
Silk embodies outstanding material properties and biologically relevant functions achieved through a delicate hierarchical structure. It can be used to create high-performance, multifunctional, and biocompatible materials through mild processes and careful rational material designs. To achieve this goal, computational modeling has proven to be a powerful platform to unravel the causes of the excellent mechanical properties of silk, to predict the properties of the biomaterials derived thereof, and to assist in devising new manufacturing strategies. Fine-scale modeling has been done mainly through all-atom and coarse-grained molecular dynamics simulations, which offer a bottom-up description of silk. In this work, a selection of relevant contributions of computational modeling is reviewed to understand the properties of natural silk, and to the design of silk-based materials, especially combined with experimental methods. Future research directions are also pointed out, including approaches such as 3D printing and machine learning, that may enable a high throughput design and manufacturing of silk-based biomaterials.
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Affiliation(s)
- Diego López Barreiro
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 1-290, Cambridge, MA, 02139, USA
| | - Jingjie Yeo
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 1-290, Cambridge, MA, 02139, USA.,Institute of High Performance Computing, A*STAR, 1 Fusionopolis Way, Singapore, 138632, Singapore.,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, 77 Massachusetts Avenue, 1-290, Cambridge, MA, 02139, USA
| | - Francisco J Martin-Martinez
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 1-290, Cambridge, MA, 02139, USA
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 1-290, Cambridge, MA, 02139, USA
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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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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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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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 Mech Lett 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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Tarakanova A, Huang W, Weiss AS, Kaplan DL, Buehler MJ. Computational smart polymer design based on elastin protein mutability. Biomaterials 2017; 127:49-60. [DOI: 10.1016/j.biomaterials.2017.01.041] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 01/13/2017] [Accepted: 01/28/2017] [Indexed: 12/16/2022]
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21
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Abstract
Soluble elastin-like peptides (ELPs) can be engineered into a range of physical forms, from hydrogels and scaffolds to fibers and artificial tissues, finding numerous applications in medicine and engineering as "smart polymers". Elastin-like peptides are attractive candidates as a platform for novel biomaterial design because they exhibit a highly tunable response spectrum, with reversible phase transition capabilities. Here, we report the design of the first virtual library of elastin-like protein models using methods for enhanced sampling to study the effect of peptide chemistry, chain length, and salt concentration on the structural transitions of ELPs, exposing associated molecular mechanisms. We describe the behavior of the local molecular structure under increasing temperatures and the effect of peptide interactions with nearest hydration shell water molecules on peptide mobility and propensity to exhibit structural transitions. Shifts in the magnitude of structural transitions at the single-molecule scale are explained from the perspective of peptide-ion-water interactions in a library of four unique elastin-like peptide systems. Predictions of structural transitions are subsequently validated in experiment. This library is a valuable resource for recombinant protein design and synthesis as it elucidates mechanisms at the single-molecule level, paving a feedback path between simulation and experiment for smart material designs, with applications in biomedicine and diagnostic devices.
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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, USA
| | - Wenwen Huang
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Anthony S Weiss
- School of Life and Environmental Sciences and Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Markus 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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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Tarakanova A, Huang W, Qin Z, Kaplan DL, Buehler MJ. Modeling and Experiment Reveal Structure and Nanomechanics across the Inverse Temperature Transition in B. mori Silk-Elastin-like Protein Polymers. ACS Biomater Sci Eng 2017; 3:2889-2899. [PMID: 33418710 DOI: 10.1021/acsbiomaterials.6b00688] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Silk and elastin are exemplary protein materials that exhibit exceptional material properties. Silk is uniquely strong, surpassing engineering materials such as Kevlar and steel, while elastin has exquisite flexibility and can reversibly fold into a more structured form at high temperatures when many other proteins would unfold and denature. This phenomenon in elastin is termed the inverse temperature transition. It is a reversible, controllable process that motivates applications in drug delivery, shape change materials, and biomimetic devices. Silk-elastinlike protein polymers (SELPs), which combine repeating B. mori silk and elastin blocks, have been introduced as biologically inspired materials that combine the distinctive properties of the component parts to achieve strong and extensible, tunable biomaterials. Here, we considered a single SELP sequence to examine temperature transition effects at the molecular scale. SELP molecular models were created using Replica Exchange Molecular Dynamics, an accelerated sampling method, and confirmed in experiment by comparing secondary structure distributions. A molecular collapse of the SELP molecule was observed with increased temperature in both molecular simulation and experiment. Temperature-specific differences were observed in the mechanical properties and the unfolding pathways of the polypeptide. Using the Bell-Evans model, we analyzed the free energy landscape associated with molecular unfolding at temperatures below and above the transition temperature range (Tt) of the polypeptide. We found that at physiological pulling rates, the energy barrier to unfold SELPs was counterintuitively higher above Tt. Our findings offer a foundational perspective on the molecular scale mechanisms of temperature-induced phase transition in SELPs, and suggest a novel approach to combine simulation and experiment to study materials for multifunctional biomimetic applications.
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Affiliation(s)
- Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 1-290, Cambridge, Massachusetts 02139, United States
| | - Wenwen Huang
- Department of Biomedical Engineering, Tufts University, Science & Technology Center, Room 251, Medford, Massachusetts 02155, United States
| | - Zhao Qin
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 1-290, Cambridge, Massachusetts 02139, United States
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Science & Technology Center, Room 251, Medford, Massachusetts 02155, United States
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 1-290, Cambridge, Massachusetts 02139, United States
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24
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Huang W, Tarakanova A, Dinjaski N, Wang Q, Xia X, Chen Y, Wong JY, Buehler MJ, Kaplan DL. Design of Multistimuli Responsive Hydrogels Using Integrated Modeling and Genetically Engineered Silk-Elastin-Like Proteins. Adv Funct Mater 2016; 26:4113-4123. [PMID: 28670244 PMCID: PMC5488272 DOI: 10.1002/adfm.201600236] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Elastomeric, robust, and biocompatible hydrogels are rare, while the need for these types of biomaterials in biomedical-related uses remains high. Here, a new family of genetically engineered silk-elastin copolymers (SELPs) with encoded enzymatic crosslinking sites is developed for a new generation of stimuli-responsive yet robust hydrogels. Input into the designs is guided by simulation, and realized via genetic engineering strategies. The avoidance of gamma irradiation or chemical crosslinking during gel fabrication, in lieu of an enzymatic process, expands the versatility of these new gels for the incorporation of labile proteins and cells. In the present study, the new SELP hydrogels offers sequence dependent, reversible stimuli-responsive features. Their stiffness covers almost the full range of the elasticity of soft tissues. Further, physical modification of the silk domains provided a secondary control point to fine-tune mechanical stiffness while preserving stimuli-responsive features, with implications for a variety of biomedical materials and device needs.
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Affiliation(s)
- 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
| | - Nina Dinjaski
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Qin Wang
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Xiaoxia Xia
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Ying Chen
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Joyce Y Wong
- Departments of Biomedical Engineering and Materials Science and Engineering, Boston University, Boston, MA 02215, 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
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
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25
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Yeo GC, Tarakanova A, Baldock C, Wise SG, Buehler MJ, Weiss AS. Subtle balance of tropoelastin molecular shape and flexibility regulates dynamics and hierarchical assembly. Sci Adv 2016; 2:e1501145. [PMID: 26998516 PMCID: PMC4795673 DOI: 10.1126/sciadv.1501145] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 11/20/2015] [Indexed: 05/02/2023]
Abstract
The assembly of the tropoelastin monomer into elastin is vital for conferring elasticity on blood vessels, skin, and lungs. Tropoelastin has dual needs for flexibility and structure in self-assembly. We explore the structure-dynamics-function interplay, consider the duality of molecular order and disorder, and identify equally significant functional contributions by local and global structures. To study these organizational stratifications, we perturb a key hinge region by expressing an exon that is universally spliced out in human tropoelastins. We find a herniated nanostructure with a displaced C terminus and explain by molecular modeling that flexible helices are replaced with substantial β sheets. We see atypical higher-order cross-linking and inefficient assembly into discontinuous, thick elastic fibers. We explain this dysfunction by correlating local and global structural effects with changes in the molecule's assembly dynamics. This work has general implications for our understanding of elastomeric proteins, which balance disordered regions with defined structural modules at multiple scales for functional assembly.
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Affiliation(s)
- Giselle C. Yeo
- Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales 2006, Australia
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Clair Baldock
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Steven G. Wise
- The Heart Research Institute, Newtown, New South Wales 2050, Australia
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Anthony S. Weiss
- Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales 2006, Australia
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
- Bosch Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
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26
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Abstract
Among a myriad of spider web geometries, the orb web presents a fascinating, exquisite example in architecture and evolution. Orb webs can be divided into two categories according to the capture silk used in construction: cribellate orb webs (composed of pseudoflagelliform silk) coated with dry cribellate threads and ecribellate orb webs (composed of flagelliform silk fibres) coated by adhesive glue droplets. Cribellate capture silk is generally stronger but less-extensible than viscid capture silk, and a body of phylogenic evidence suggests that cribellate capture silk is more closely related to the ancestral form of capture spiral silk. Here, we use a coarse-grained web model to investigate how the mechanical properties of spiral capture silk affect the behaviour of the whole web, illustrating that more elastic capture spiral silk yields a decrease in web system energy absorption, suggesting that the function of the capture spiral shifted from prey capture to other structural roles. Additionally, we observe that in webs with more extensible capture silk, the effect of thread strength on web performance is reduced, indicating that thread elasticity is a dominant driving factor in web diversification.
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Affiliation(s)
- Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Cranford SW, Tarakanova A, Pugno NM, Buehler MJ. Nonlinear material behaviour of spider silk yields robust webs. Nature 2012; 482:72-6. [DOI: 10.1038/nature10739] [Citation(s) in RCA: 331] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 11/25/2011] [Indexed: 11/09/2022]
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