51
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Sidhu MS, Kumar B, Singh KP. The processing and heterostructuring of silk with light. NATURE MATERIALS 2017; 16:938-945. [PMID: 28805825 DOI: 10.1038/nmat4942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/20/2017] [Indexed: 06/07/2023]
Abstract
Spider silk is a tough, elastic and lightweight biomaterial, although there is a lack of tools available for non-invasive processing of silk structures. Here we show that nonlinear multiphoton interactions of silk with few-cycle femtosecond pulses allow the processing and heterostructuring of the material in ambient air. Two qualitatively different responses, bulging by multiphoton absorption and plasma-assisted ablation, are observed for low- and high-peak intensities, respectively. Plasma ablation allows us to make localized nanocuts, microrods, nanotips and periodic patterns with minimal damage while preserving molecular structure. The bulging regime facilitates confined bending and microwelding of silk with materials such as metal, glass and Kevlar with strengths comparable to pristine silk. Moreover, analysis of Raman bands of microwelded joints reveals that the polypeptide backbone remains intact while perturbing its weak hydrogen bonds. Using this approach, we fabricate silk-based functional topological microstructures, such as Mobiüs strips, chiral helices and silk-based sensors.
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Affiliation(s)
- Mehra S Sidhu
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, Manauli 140306, India
| | - Bhupesh Kumar
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, Manauli 140306, India
| | - Kamal P Singh
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, Manauli 140306, India
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52
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Harris J, Böhm CF, Wolf SE. Universal structure motifs in biominerals: a lesson from nature for the efficient design of bioinspired functional materials. Interface Focus 2017. [PMID: 28630670 DOI: 10.1166/jctn.2008.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Biominerals are typically indispensable structures for their host organism in which they serve varying functions, such as mechanical support and protection, mineral storage, detoxification site, or as a sensor or optical guide. In this perspective article, we highlight the occurrence of both structural diversity and uniformity within these biogenic ceramics. For the first time, we demonstrate that the universality-diversity paradigm, which was initially introduced for proteins by Buehler et al. (Cranford & Buehler 2012 Biomateriomics; Cranford et al. 2013 Adv. Mater.25, 802-824 (doi:10.1002/adma.201202553); Ackbarow & Buehler 2008 J. Comput. Theor. Nanosci.5, 1193-1204 (doi:10.1166/jctn.2008.001); Buehler & Yung 2009 Nat. Mater.8, 175-188 (doi:10.1038/nmat2387)), is also valid in the realm of biomineralization. A nanogranular composite structure is shared by most biominerals which rests on a common, non-classical crystal growth mechanism. The nanogranular composite structure affects various properties of the macroscale biogenic ceramic, a phenomenon we attribute to emergence. Emergence, in turn, is typical for hierarchically organized materials. This is a clear call to renew comparative studies of even distantly related biomineralizing organisms to identify further universal design motifs and their associated emergent properties. Such universal motifs with emergent macro-scale properties may represent an unparalleled toolbox for the efficient design of bioinspired functional materials.
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Affiliation(s)
- Joe Harris
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany
| | - Corinna F Böhm
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany
| | - Stephan E Wolf
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany.,Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Haberstrasse 9a, 91058 Erlangen, Germany
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53
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Harris J, Böhm CF, Wolf SE. Universal structure motifs in biominerals: a lesson from nature for the efficient design of bioinspired functional materials. Interface Focus 2017; 7:20160120. [PMID: 28630670 PMCID: PMC5474032 DOI: 10.1098/rsfs.2016.0120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Biominerals are typically indispensable structures for their host organism in which they serve varying functions, such as mechanical support and protection, mineral storage, detoxification site, or as a sensor or optical guide. In this perspective article, we highlight the occurrence of both structural diversity and uniformity within these biogenic ceramics. For the first time, we demonstrate that the universality-diversity paradigm, which was initially introduced for proteins by Buehler et al. (Cranford & Buehler 2012 Biomateriomics; Cranford et al. 2013 Adv. Mater.25, 802-824 (doi:10.1002/adma.201202553); Ackbarow & Buehler 2008 J. Comput. Theor. Nanosci.5, 1193-1204 (doi:10.1166/jctn.2008.001); Buehler & Yung 2009 Nat. Mater.8, 175-188 (doi:10.1038/nmat2387)), is also valid in the realm of biomineralization. A nanogranular composite structure is shared by most biominerals which rests on a common, non-classical crystal growth mechanism. The nanogranular composite structure affects various properties of the macroscale biogenic ceramic, a phenomenon we attribute to emergence. Emergence, in turn, is typical for hierarchically organized materials. This is a clear call to renew comparative studies of even distantly related biomineralizing organisms to identify further universal design motifs and their associated emergent properties. Such universal motifs with emergent macro-scale properties may represent an unparalleled toolbox for the efficient design of bioinspired functional materials.
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Affiliation(s)
- Joe Harris
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany
| | - Corinna F. Böhm
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany
| | - Stephan E. Wolf
- Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Haberstrasse 9a, 91058 Erlangen, Germany
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54
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Lipner J, Boyle JJ, Xia Y, Birman V, Genin GM, Thomopoulos S. Toughening of fibrous scaffolds by mobile mineral deposits. Acta Biomater 2017; 58:492-501. [PMID: 28532898 DOI: 10.1016/j.actbio.2017.05.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 05/10/2017] [Accepted: 05/15/2017] [Indexed: 10/19/2022]
Abstract
Partially mineralized fibrous tissue situated between tendon and bone is believed to be tougher than either tendon or bone, possibly serving as a compliant, energy absorptive, protective barrier between the two. This tissue does not reform following surgical repair (e.g., rotator cuff tendon-to-bone re-attachment) and might be a factor in the poor outcomes following such surgeries. Towards our long-term goal of tissue engineered solutions to functional tendon-to-bone re-attachment, we tested the hypotheses that partially mineralized fibrous matrices can derive toughness from mobility of mineral along their fibers, and that in such cases toughness is maximized at levels of mineralization sufficiently low to allow substantial mobility. Nanofibrous electrospun poly(lactic-co-glycolic acid) (PLGA) scaffolds mineralized for prescribed times were fabricated as model systems to test these hypotheses. Tensile tests performed at varying angles relative to the dominant fiber direction confirmed that mineral cross-linked PLGA nanofibers without adhering to them. Peel tests revealed that fracture toughness increased with mineralization time up to a peak value, then subsequently decreased with increasing mineralization time back to the baseline toughness of unmineralized scaffolds. These experimental results were predicted by a theoretical model combining mineral growth kinetics with fracture energetics, suggesting that toughness increased with mineralization time until mineral mobility was attenuated by steric hindrance, then returned to baseline levels following the rigid percolation threshold. Results supported our hypotheses, and motivate further study of the roles of mobile mineral particles in toughening the tendon-to-bone attachment. STATEMENT OF SIGNIFICANCE Effective surgical repair of interfaces between tendon and bone remains an unmet clinical need, in part due to a lack of understanding of how toughness is achieved in the healthy tissue. Using combined synthesis, experiment, and modeling approaches, the current work supported the hypothesis that toughening of a fibrous scaffold arises from brittle mineral particles that crosslink the fibers, but only if the particles are free to slide relative to the fibers. In the case of the tendon-to-bone interface, this suggests that partially mineralized tissue between tendon and bone, with mobile mineral but relatively low stiffness, may serve as a compliant, energy-absorbing barrier that guards against injury. These results suggest an opportunity for fabrication of tough and strong fibrous scaffolds for tissue engineering applications.
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55
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Kurniawan NA, Vos BE, Biebricher A, Wuite GJL, Peterman EJG, Koenderink GH. Fibrin Networks Support Recurring Mechanical Loads by Adapting their Structure across Multiple Scales. Biophys J 2017; 111:1026-34. [PMID: 27602730 DOI: 10.1016/j.bpj.2016.06.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/01/2016] [Accepted: 06/29/2016] [Indexed: 12/11/2022] Open
Abstract
Tissues and cells sustain recurring mechanical loads that span a wide range of loading amplitudes and timescales as a consequence of exposure to blood flow, muscle activity, and external impact. Both tissues and cells derive their mechanical strength from fibrous protein scaffolds, which typically have a complex hierarchical structure. In this study, we focus on a prototypical hierarchical biomaterial, fibrin, which is one of the most resilient naturally occurring biopolymers and forms the structural scaffold of blood clots. We show how fibrous networks composed of fibrin utilize irreversible changes in their hierarchical structure at different scales to maintain reversible stress stiffening up to large strains. To trace the origin of this paradoxical resilience, we systematically tuned the microstructural parameters of fibrin and used a combination of optical tweezers and fluorescence microscopy to measure the interactions of single fibrin fibers for the first time, to our knowledge. We demonstrate that fibrin networks adapt to moderate strains by remodeling at the network scale through the spontaneous formation of new bonds between fibers, whereas they adapt to high strains by plastic remodeling of the fibers themselves. This multiscale adaptation mechanism endows fibrin gels with the remarkable ability to sustain recurring loads due to shear flows and wound stretching. Our findings therefore reveal a microscopic mechanism by which tissues and cells can balance elastic nonlinearity and plasticity, and thus can provide microstructural insights into cell-driven remodeling of tissues.
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Affiliation(s)
- Nicholas A Kurniawan
- Department of Systems Biophysics, FOM Institute AMOLF, Amsterdam, The Netherlands; Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bart E Vos
- Department of Systems Biophysics, FOM Institute AMOLF, Amsterdam, The Netherlands
| | - Andreas Biebricher
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijsje H Koenderink
- Department of Systems Biophysics, FOM Institute AMOLF, Amsterdam, The Netherlands.
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56
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Cossio P, Hummer G, Szabo A. Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy. Biophys J 2017; 111:832-840. [PMID: 27558726 DOI: 10.1016/j.bpj.2016.05.054] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/06/2016] [Accepted: 05/13/2016] [Indexed: 12/18/2022] Open
Abstract
Ductile materials can absorb spikes in mechanical force, whereas brittle ones fail catastrophically. Here we develop a theory to quantify the kinetic ductility of single molecules from force spectroscopy experiments, relating force-spike resistance to the differential responses of the intact protein and the unfolding transition state to an applied mechanical force. We introduce a class of unistable one-dimensional potential surfaces that encompass previous models as special cases and continuously cover the entire range from ductile to brittle. Compact analytic expressions for force-dependent rates and rupture-force distributions allow us to analyze force-clamp and force-ramp pulling experiments. We find that the force-transmitting protein domains of filamin and titin are kinetically ductile when pulled from their two termini, making them resistant to force spikes. For the mechanostable muscle protein titin, a highly ductile model reconciles data over 10 orders of magnitude in force loading rate from experiment and simulation.
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Affiliation(s)
- Pilar Cossio
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Attila Szabo
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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57
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Rossetti L, Kuntz LA, Kunold E, Schock J, Müller KW, Grabmayr H, Stolberg-Stolberg J, Pfeiffer F, Sieber SA, Burgkart R, Bausch AR. The microstructure and micromechanics of the tendon-bone insertion. NATURE MATERIALS 2017; 16:664-670. [PMID: 28250445 DOI: 10.1038/nmat4863] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 01/17/2017] [Indexed: 05/28/2023]
Abstract
The exceptional mechanical properties of the load-bearing connection of tendon to bone rely on an intricate interplay of its biomolecular composition, microstructure and micromechanics. Here we identify that the Achilles tendon-bone insertion is characterized by an interface region of ∼500 μm with a distinct fibre organization and biomolecular composition. Within this region, we identify a heterogeneous mechanical response by micromechanical testing coupled with multiscale confocal microscopy. This leads to localized strains that can be larger than the remotely applied strain. The subset of fibres that sustain the majority of loading in the interface area changes with the angle of force application. Proteomic analysis detects enrichment of 22 proteins in the interfacial region that are predominantly involved in cartilage and skeletal development as well as proteoglycan metabolism. The presented mechanisms mark a guideline for further biomimetic strategies to rationally design hard-soft interfaces.
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Affiliation(s)
- L Rossetti
- Lehrstuhl für Zellbiophysik, Technische Universität München, D-85748 Garching, Germany
| | - L A Kuntz
- Lehrstuhl für Zellbiophysik, Technische Universität München, D-85748 Garching, Germany
- Klinik für Orthopädie und Sportorthopädie, Klinikum rechts der Isar, Technische Universität München, D-81675 München, Germany
| | - E Kunold
- Center for Integrated Protein Science (CIPSM), Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
| | - J Schock
- Lehrstuhl für Biomedizinische Physik, Physik-Department &Institut für Medizintechnik, Technische Universität München, D-85748 Garching, Germany
| | - K W Müller
- Institute for Computational Mechanics, Technische Universität München, D-85748 Garching, Germany
- Structural and Applied Mechanics Group, Computational Engineering Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, California 94550, USA
| | - H Grabmayr
- Lehrstuhl für Zellbiophysik, Technische Universität München, D-85748 Garching, Germany
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, D-80539 Munich, Germany
| | - J Stolberg-Stolberg
- Klinik für Orthopädie und Sportorthopädie, Klinikum rechts der Isar, Technische Universität München, D-81675 München, Germany
- University Hospital Münster, Department of Trauma-, Hand- and Reconstructive Surgery, Albert-Schweitzer-Campus 1, Building W1, D-48149 Münster, Germany
| | - F Pfeiffer
- Lehrstuhl für Biomedizinische Physik, Physik-Department &Institut für Medizintechnik, Technische Universität München, D-85748 Garching, Germany
- Institut für diagnostische und interventionelle Radiologie, Klinikum rechts der Isar, Technische Universität München, D-81675 München, Germany
| | - S A Sieber
- Center for Integrated Protein Science (CIPSM), Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
| | - R Burgkart
- Klinik für Orthopädie und Sportorthopädie, Klinikum rechts der Isar, Technische Universität München, D-81675 München, Germany
| | - A R Bausch
- Lehrstuhl für Zellbiophysik, Technische Universität München, D-85748 Garching, Germany
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58
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Chang HJ, Lee M, Kim JI, Yoon G, Na S. Mechanical and vibrational characterization of amyloid-like HET-s nanosheets based on the skewed plate theory. Phys Chem Chem Phys 2017; 19:11492-11501. [PMID: 28425516 DOI: 10.1039/c7cp01418j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pathological amyloidogenic prion proteins have a toxic effect on functional cells in the human cerebrum because of poor degradability and the tendency to accumulate in an uncontrolled manner under physiological conditions. HET-s, a fungal prion protein, is known to undergo conformational variations from fibrillar to nanosheet structures during a change from low to high pH conditions. It has been said that this conformational change can lead to self-propagation by nucleating on the lateral surface of singlet fibrils. Efforts have been made toward the mechanical characterization of fibrillar amyloids, but a global understanding of amyloid-like HET-s nanosheet structures is lacking. In this study, we analyzed the mechanical and vibrational characteristics of the skewed HET-s nanosheet structures that developed under neutral pH conditions by performing various molecular dynamics simulations. By applying the skewed plate theory to HET-s nanosheets for various length scales with numerous pores inside the structures, we found that the skewed HET-s nanosheet structure has mechanical properties comparable to those of previously reported biological film materials and nanomaterials. Considering the inherent characteristics of structural stability, our observation provides valuable and detailed structural information on skewed amyloid-like HET-s nanosheets.
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Affiliation(s)
- Hyun Joon Chang
- Department of Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea.
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59
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Liu M, Gao P, Wan Q, Deng F, Wei Y, Zhang X. Recent Advances and Future Prospects of Aggregation-induced Emission Carbohydrate Polymers. Macromol Rapid Commun 2017; 38. [DOI: 10.1002/marc.201600575] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/25/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Meiying Liu
- Department of Chemistry; Nanchang University; 999 Xuefu Avenue Nanchang 330031 China
| | - Peng Gao
- Department of Chemistry; Nanchang University; 999 Xuefu Avenue Nanchang 330031 China
| | - Qing Wan
- Department of Chemistry; Nanchang University; 999 Xuefu Avenue Nanchang 330031 China
| | - Fengjie Deng
- Department of Chemistry; Nanchang University; 999 Xuefu Avenue Nanchang 330031 China
| | - Yen Wei
- Department of Chemistry and the Tsinghua Center for Frontier Polymer Research; Tsinghua University; Beijing 100084 P. R. China
| | - Xiaoyong Zhang
- Department of Chemistry; Nanchang University; 999 Xuefu Avenue Nanchang 330031 China
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60
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De Falco P, Barbieri E, Pugno N, Gupta HS. Staggered Fibrils and Damageable Interfaces Lead Concurrently and Independently to Hysteretic Energy Absorption and Inhomogeneous Strain Fields in Cyclically Loaded Antler Bone. ACS Biomater Sci Eng 2017; 3:2779-2787. [DOI: 10.1021/acsbiomaterials.6b00637] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- P. De Falco
- School of Engineering and Material Science, Queen Mary University of London, London E1 4NS, United Kingdom
| | - E. Barbieri
- School of Engineering and Material Science, Queen Mary University of London, London E1 4NS, United Kingdom
| | - N. Pugno
- School of Engineering and Material Science, Queen Mary University of London, London E1 4NS, United Kingdom
- Laboratory
of Bio-Inspired and Graphene Nanomechanics, Department of Civil, Environmental
and Mechanical Engineering, University of Trento, Trento 38122, Italy
- Center
for Materials and Microsystems, Fondazione Bruno Kessler, Povo, Trento 38122, Italy
| | - H. S. Gupta
- School of Engineering and Material Science, Queen Mary University of London, London E1 4NS, United Kingdom
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61
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Lee M, Chang HJ, Baek I, Na S. Structural analysis of oligomeric and protofibrillar Aβ amyloid pair structures considering F20L mutation effects using molecular dynamics simulations. Proteins 2016; 85:580-592. [PMID: 28019690 DOI: 10.1002/prot.25232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/12/2016] [Accepted: 11/23/2016] [Indexed: 12/20/2022]
Abstract
Aβ amyloid proteins are involved in neuro-degenerative diseases such as Alzheimer's, Parkinson's, and so forth. Because of its structurally stable feature under physiological conditions, Aβ amyloid protein disrupts the normal cell function. Because of these concerns, understanding the structural feature of Aβ amyloid protein in detail is crucial. There have been some efforts on lowering the structural stabilities of Aβ amyloid fibrils by decreasing the aromatic residues characteristic and hydrophobic effect. Yet, there is a lack of understanding of Aβ amyloid pair structures considering those effects. In this study, we provide the structural characteristics of wildtype (WT) and phenylalanine residue mutation to leucine (F20L) Aβ amyloid pair structures using molecular dynamics simulation in detail. We also considered the polymorphic feature of F20L and WT Aβ pair amyloids based on the facing β-strand directions between the amyloid pairs. As a result, we were able to observe the varying effects of mutation, polymorphism, and protofibril lengths on the structural stability of pair amyloids. Furthermore, we have also found that opposite structural stability exists on a certain polymorphic Aβ pair amyloids depending on its oligomeric or protofibrillar state, which can be helpful for understanding the amyloid growth mechanism via repetitive fragmentation and elongation mechanism. Proteins 2017; 85:580-592. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Myeongsang Lee
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Hyun Joon Chang
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Inchul Baek
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
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62
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Sun L, Deng WQ. Recent developments of first-principles force fields. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1282] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Lei Sun
- State Key Laboratory of Molecular Reaction Dynamics, Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Wei-Qiao Deng
- State Key Laboratory of Molecular Reaction Dynamics, Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
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63
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Kumar V, Krishna KV, Khanna S, Joshi KB. Aggregation propensity of amyloidogenic and elastomeric dipeptides constituents. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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64
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Sim S, Niwa T, Taguchi H, Aida T. Supramolecular Nanotube of Chaperonin GroEL: Length Control for Cellular Uptake Using Single-Ring GroEL Mutant as End-Capper. J Am Chem Soc 2016; 138:11152-5. [PMID: 27545864 DOI: 10.1021/jacs.6b07925] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
How to modulate supramolecular protein nanotubes without sacrificing their thermodynamic stability? This challenging issue emerged with an enhanced reality since our successful development of a protein nanotube of chaperonin GroELMC as a novel ATP-responsive 1D nanocarrier because the nanotube length may potentially affect the cellular uptake efficiency. Herein, we report a molecularly engineered protein end-capper (SRMC) that firmly binds to the nanotube termini since the end-capper originates from GroEL. According to the single-ring mutation of GroEL, we obtained a single-ring version of GroEL bearing cysteine mutations (GroELCys) and modified its 14 apical cysteine residues with merocyanine (MC). Whereas SRMC self-dimerizes upon treatment with Mg(2+), we confirmed that SRMC serves as the efficient end-capper for the Mg(2+)-mediated supramolecular polymerization of GroELMC and allows for modulating the average nanotube length over a wide range from 320 to 40 nm by increasing the feed molar ratio SRMC/GroELMC up to 5.4. We also found that the nanotubes shorter than 100 nm are efficiently taken up into HEP3B cells.
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Affiliation(s)
- Seunghyun Sim
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tatsuya Niwa
- Research Unit for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology , Midori-ku, Yokohama 226-8501, Japan
| | - Hideki Taguchi
- Research Unit for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology , Midori-ku, Yokohama 226-8501, Japan
| | - Takuzo Aida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,RIKEN Center for Emergent Matter Science , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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65
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Ling S, Zhang Q, Kaplan DL, Omenetto F, Buehler MJ, Qin Z. Printing of stretchable silk membranes for strain measurements. LAB ON A CHIP 2016; 16:2459-66. [PMID: 27241909 PMCID: PMC4968584 DOI: 10.1039/c6lc00519e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Quantifying the deformation of biological tissues under mechanical loading is crucial to understand its biomechanical response in physiological conditions and important for designing materials and treatments for biomedical applications. However, strain measurements for biological tissues subjected to large deformations and humid environments are challenging for conventional methods due to several limitations such as strain range, boundary conditions, surface bonding and biocompatibility. Here we propose the use of silk solutions and printing to synthesize prototype strain gauges for large strain measurements in biological tissues. The study shows that silk-based strain gauges can be stretched up to 1300% without failure, which is more than two orders of magnitude larger than conventional strain gauges, and the mechanics can be tuned by adjusting ion content. We demonstrate that the printing approach can accurately provide well bonded fluorescent features on the silk membranes using designs which can accurately measure strain in the membrane. The results show that these new strain gauges measure large deformations in the materials by eliminating the effects of sliding from the boundaries, making the measurements more accurate than direct outputs from tensile machines.
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Affiliation(s)
- Shengjie Ling
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Qiang Zhang
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
- School of Textile Science and Engineering, Wuhan Textile University, Wuhan, 430073, China
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Fiorenzo Omenetto
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Markus J. Buehler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Center for Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
- Center for Computational Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Zhao Qin
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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66
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Chen CL, Zuckermann RN, DeYoreo JJ. Surface-Directed Assembly of Sequence-Defined Synthetic Polymers into Networks of Hexagonally Patterned Nanoribbons with Controlled Functionalities. ACS NANO 2016; 10:5314-5320. [PMID: 27136277 DOI: 10.1021/acsnano.6b01333] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The exquisite self-assembly of proteins and peptides in nature into highly ordered functional materials has inspired innovative approaches to the design and synthesis of biomimetic materials. While sequence-defined polymers hold great promise to mimic proteins and peptides for functions, controlled assembly of them on surfaces still remains underdeveloped. Here, we report the assembly of 12-mer peptoids containing alternating acidic and aromatic monomers into networks of hexagonally patterned nanoribbons on mica surfaces. Ca(2+)-carboxylate coordination creates peptoid-peptoid and peptoid-mica interactions that control self-assembly. In situ atomic force microscopy (AFM) shows that peptoids first assemble into discrete nanoparticles; these particles then transform into hexagonally patterned nanoribbons on mica surfaces. AFM-based dynamic force spectroscopy studies show that peptoid-mica interactions are much stronger than peptoid-peptoid interactions, illuminating the driving forces for mica-directed peptoid assembly. We further demonstrate the display of functional domains at the N-terminus of assembling peptoids to produce extended networks with similar hierarchical structures. This research demonstrates that surface-directed peptoid assembly can be used as a robust platform to develop biomimetic coating materials for applications.
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Affiliation(s)
- Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Ronald N Zuckermann
- Molecular Foundry, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - James J DeYoreo
- Physical Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Departments of Materials Science and Engineering and of Chemistry, University of Washington , Seattle, Washington 98195, United States
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67
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Prakash SS. Cavitation of tumoral basement membrane as onset of cancer invasion and metastasis: physics of oncogenic homeorhesis via nonlinear mechano-metabolomics. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2016. [DOI: 10.1088/2057-1739/2/1/015001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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68
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Bruekers SMC, Jaspers M, Hendriks JMA, Kurniawan NA, Koenderink GH, Kouwer PHJ, Rowan AE, T S Huck W. Fibrin-fiber architecture influences cell spreading and differentiation. Cell Adh Migr 2016; 10:495-504. [PMID: 26910190 DOI: 10.1080/19336918.2016.1151607] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The mechanical and structural properties of the extracellular matrix (ECM) play an important role in regulating cell fate. The natural ECM has a complex fibrillar structure and shows nonlinear mechanical properties, which are both difficult to mimic synthetically. Therefore, systematically testing the influence of ECM properties on cellular behavior is very challenging. In this work we show two different approaches to tune the fibrillar structure and mechanical properties of fibrin hydrogels. Addition of extra thrombin before gelation increases the protein density within the fibrin fibers without significantly altering the mechanical properties of the resulting hydrogel. On the other hand, by forming a composite hydrogel with a synthetic biomimetic polyisocyanide network the protein density within the fibrin fibers decreases, and the mechanics of the composite material can be tuned by the PIC/fibrin mass ratio. The effect of the changes in gel structure and mechanics on cellular behavior are investigated, by studying human mesenchymal stem cell (hMSC) spreading and differentiation on these gels. We find that the trends observed in cell spreading and differentiation cannot be explained by the bulk mechanics of the gels, but correlate to the density of the fibrin fibers the gels are composed of. These findings strongly suggest that the microscopic properties of individual fibers in fibrous networks play an essential role in determining cell behavior.
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Affiliation(s)
- Stéphanie M C Bruekers
- a Institute for Molecules and Materials, Radboud University , Nijmegen , The Netherlands
| | - Maarten Jaspers
- a Institute for Molecules and Materials, Radboud University , Nijmegen , The Netherlands
| | - José M A Hendriks
- a Institute for Molecules and Materials, Radboud University , Nijmegen , The Netherlands
| | - Nicholas A Kurniawan
- b Systems Biophysics Department, FOM Institute AMOLF , Amsterdam , The Netherlands.,c Department of Biomedical Engineering , Eindhoven University of Technology , Eindhoven , The Netherlands
| | - Gijsje H Koenderink
- b Systems Biophysics Department, FOM Institute AMOLF , Amsterdam , The Netherlands
| | - Paul H J Kouwer
- a Institute for Molecules and Materials, Radboud University , Nijmegen , The Netherlands
| | - Alan E Rowan
- a Institute for Molecules and Materials, Radboud University , Nijmegen , The Netherlands.,d Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane , Australia
| | - Wilhelm T S Huck
- a Institute for Molecules and Materials, Radboud University , Nijmegen , The Netherlands
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69
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Conformational changes of Aβ (1-42) monomers in different solvents. J Mol Graph Model 2016; 65:8-14. [PMID: 26896721 DOI: 10.1016/j.jmgm.2016.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 01/16/2016] [Accepted: 02/06/2016] [Indexed: 11/21/2022]
Abstract
Amyloid proteins are known to be the main cause of numerous degenerative and neurodegenerative diseases. In general, amyloids are misfolded from monomers and they tend to have β-strand formations. These misfolded monomers are then transformed into oligomers, fibrils, and plaques. It is important to understand the forming mechanism of amyloids in order to prevent degenerative diseases to occur. Aβ protein is a highly noticeable protein which causes Alzheimer's disease. It is reported that solvents affect the forming mechanism of Aβ amyloids. In this research, Aβ1-42 was analyzed using an all-atom MD simulation with the consideration of effects induced by two disparate solvents: water and DMSO. As a result, two different conformation changes of Aβ1-42 were exhibited in each solvent. It was found that salt-bridge of Asp23 and Lys28 in Aβ1-42 was the key for amyloid folding based on the various analysis including hydrogen bond, electrostatic interaction energy and salt-bridge distance. Since this salt-bridge region plays a crucial role in initiating the misfolding of Aβ1-42, this research may shed a light for studies related in amyloid folding and misfolding.
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70
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Buehler MJ, Genin GM. Integrated multiscale biomaterials experiment and modelling: a perspective. Interface Focus 2016; 6:20150098. [PMID: 28981126 DOI: 10.1098/rsfs.2015.0098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Advances in multiscale models and computational power have enabled a broad toolset to predict how molecules, cells, tissues and organs behave and develop. A key theme in biological systems is the emergence of macroscale behaviour from collective behaviours across a range of length and timescales, and a key element of these models is therefore hierarchical simulation. However, this predictive capacity has far outstripped our ability to validate predictions experimentally, particularly when multiple hierarchical levels are involved. The state of the art represents careful integration of multiscale experiment and modelling, and yields not only validation, but also insights into deformation and relaxation mechanisms across scales. We present here a sampling of key results that highlight both challenges and opportunities for integrated multiscale experiment and modelling in biological systems.
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Affiliation(s)
- Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guy M Genin
- Department of Mechanical Engineering and Materials Science, and Department of Neurological Surgery, Washington University, St Louis, MO 63130, USA
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71
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Zanuy D, Poater J, Solà M, Hamley IW, Alemán C. Fmoc–RGDS based fibrils: atomistic details of their hierarchical assembly. Phys Chem Chem Phys 2016; 18:1265-78. [DOI: 10.1039/c5cp04269k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We describe the 3D supramolecular structure of Fmoc–RGDS fibrils, where Fmoc and RGDS refer to the hydrophobic N-(fluorenyl-9-methoxycarbonyl) group and the hydrophilic Arg-Gly-Asp-Ser peptide sequence, respectively.
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Affiliation(s)
- David Zanuy
- Departament d'Enginyeria Química
- ETSEIB
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - Jordi Poater
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling
- Vrije Universiteit Amsterdam
- NL-1081HV Amsterdam
- The Netherlands
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química
- Universitat de Girona
- E-17071 Girona
- Spain
| | - Ian W. Hamley
- School of Chemistry
- Pharmacy and Food Biosciences
- University of Reading
- Reading
- UK
| | - Carlos Alemán
- Departament d'Enginyeria Química
- ETSEIB
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
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72
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Baek I, Lee M, Na S. Understanding structural characteristics of out-of-register hIAPP amyloid proteins via molecular dynamics. RSC Adv 2016. [DOI: 10.1039/c6ra19100b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We investigated characteristics of out-of-register (OOR) hIAPP amyloids. By varying the length size of OOR hIAPP, we found 8 layers is most stable. In addition, OOR hIAPP has relative structural instability than in-register hAIPP.
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Affiliation(s)
- Inchul Baek
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| | - Myeongsang Lee
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
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73
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Yoon G, Lee M, Kim K, In Kim J, Joon Chang H, Baek I, Eom K, Na S. Morphology and mechanical properties of multi-stranded amyloid fibrils probed by atomistic and coarse-grained simulations. Phys Biol 2015; 12:066021. [DOI: 10.1088/1478-3975/12/6/066021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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74
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Lee M, Na S. End Capping Alters the Structural Characteristics and Mechanical Properties of Transthyretin (105-115) Amyloid Protofibrils. Chemphyschem 2015; 17:425-32. [DOI: 10.1002/cphc.201500945] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/16/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Myeongsang Lee
- Department of Mechanical Engineering; Korea University; Seoul 02841 Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering; Korea University; Seoul 02841 Republic of Korea
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75
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Velmurugan P, Jonnalagadda RR, Sankaranarayanan K, Dhathathreyan A. Does L to D-amino acid substitution trigger helix→sheet conformations in collagen like peptides adsorbed to surfaces? MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 57:249-56. [PMID: 26354261 DOI: 10.1016/j.msec.2015.07.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 06/22/2015] [Accepted: 07/28/2015] [Indexed: 11/18/2022]
Abstract
The present work reports on the structural order, self assembling behaviour and the role in adsorption to hydrophilic or hydrophobic solid surfaces of modified sequence from the triple helical peptide model of the collagenase cleavage site in type I collagen (Uniprot accession number P02452 residues from 935 to 970) using (D)Ala and (D)Ile substitutions as given in the models below: Model-1: GSOGADGPAGAOGTOGPQGIAGQRGVV GLOGQRGER. Model-2: GSOGADGP(D)AGAOGTOGPQGIAGQRGVVGLOGQRGER. Model-3: GSOGADGPAGAOGTOGPQG(D)IAGQRGVVGLOGQRGER. Collagenase is an important enzyme that plays an important role in degrading collagen in wound healing, cancer metastasis and even in embryonic development. However, the mechanism by which this degradation occurs is not completely understood. Our results show that adsorption of the peptides to the solid surfaces, specifically hydrophobic triggers a helix to beta transition with order increasing in peptide models 2 and 3. This restricts the collagenolytic behaviour of collagenase and may find application in design of peptides and peptidomimetics for enzyme-substrate interaction, specifically with reference to collagen and other extra cellular matrix proteins.
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Affiliation(s)
- Punitha Velmurugan
- Council of Scientific and Industrial Research-Central Leather Research Institute, Chemical Laboratory, Adyar, Chennai 600 020, India; University of Madras, Centre for Advanced Study in Crystallography and Biophysics, Guindy Campus, Chennai 600 025, India
| | - Raghava Rao Jonnalagadda
- Council of Scientific and Industrial Research-Central Leather Research Institute, Chemical Laboratory, Adyar, Chennai 600 020, India.
| | - Kamatchi Sankaranarayanan
- Council of Scientific and Industrial Research-Central Leather Research Institute, Chemical Laboratory, Adyar, Chennai 600 020, India
| | - Aruna Dhathathreyan
- Council of Scientific and Industrial Research-Central Leather Research Institute, Biophysics Laboratory, Adyar, Chennai 600 020, India
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76
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Falzone TT, Robertson-Anderson RM. Active Entanglement-Tracking Microrheology Directly Couples Macromolecular Deformations to Nonlinear Microscale Force Response of Entangled Actin. ACS Macro Lett 2015; 4:1194-1199. [PMID: 35614836 DOI: 10.1021/acsmacrolett.5b00673] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We track the deformation of discrete entangled actin segments while simultaneously measuring the resistive force the deformed filaments exert in response to an optically driven microsphere. We precisely map the network deformation field to show that local microscale stresses can induce filament deformations that propagate beyond mesoscopic length scales (60 μm, >3 persistence lengths lp). We show that the filament persistence length controls the critical length scale at which distinct entanglement deformations become driven by collective network mechanics. Mesoscale propagation beyond lp is coupled with nonlinear local stresses arising from steric entanglements mimicking cross-links.
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Affiliation(s)
- Tobias T. Falzone
- Department of Physics, University of San Diego, San Diego, California 92110, United States
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77
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Andriotis OG, Chang SW, Vanleene M, Howarth PH, Davies DE, Shefelbine SJ, Buehler MJ, Thurner PJ. Structure-mechanics relationships of collagen fibrils in the osteogenesis imperfecta mouse model. J R Soc Interface 2015; 12:20150701. [PMID: 26468064 PMCID: PMC4614505 DOI: 10.1098/rsif.2015.0701] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/24/2015] [Indexed: 12/13/2022] Open
Abstract
The collagen molecule, which is the building block of collagen fibrils, is a triple helix of two α1(I) chains and one α2(I) chain. However, in the severe mouse model of osteogenesis imperfecta (OIM), deletion of the COL1A2 gene results in the substitution of the α2(I) chain by one α1(I) chain. As this substitution severely impairs the structure and mechanics of collagen-rich tissues at the tissue and organ level, the main aim of this study was to investigate how the structure and mechanics are altered in OIM collagen fibrils. Comparing results from atomic force microscopy imaging and cantilever-based nanoindentation on collagen fibrils from OIM and wild-type (WT) animals, we found a 33% lower indentation modulus in OIM when air-dried (bound water present) and an almost fivefold higher indentation modulus in OIM collagen fibrils when fully hydrated (bound and unbound water present) in phosphate-buffered saline solution (PBS) compared with WT collagen fibrils. These mechanical changes were accompanied by an impaired swelling upon hydration within PBS. Our experimental and atomistic simulation results show how the structure and mechanics are altered at the individual collagen fibril level as a result of collagen gene mutation in OIM. We envisage that the combination of experimental and modelling approaches could allow mechanical phenotyping at the collagen fibril level of virtually any alteration of collagen structure or chemistry.
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Affiliation(s)
- O G Andriotis
- Institute for Lightweight Design and Structural Biomechanics, Vienna University of Technology, Getreidemarkt 9, Vienna 1060, Austria Bioengineering Research Group, Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, UK
| | - S W Chang
- Department of Civil Engineering, National Taiwan University, Taipei 10617, Taiwan, Republic of China Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - M Vanleene
- Department of Bioengineering, Imperial College London, London, UK
| | - P H Howarth
- The Brooke Laboratories, Division of Infection, Inflammation and Immunity, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - D E Davies
- The Brooke Laboratories, Division of Infection, Inflammation and Immunity, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - S J Shefelbine
- Department of Bioengineering, Imperial College London, London, UK Department of Mechanical and Industrial Engineering, Northeastern University, Boston, MA, USA
| | - M J Buehler
- Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA Center for Computational Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - P J Thurner
- Institute for Lightweight Design and Structural Biomechanics, Vienna University of Technology, Getreidemarkt 9, Vienna 1060, Austria Bioengineering Research Group, Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, UK
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78
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Valbuena A, Mateu MG. Quantification and modification of the equilibrium dynamics and mechanics of a viral capsid lattice self-assembled as a protein nanocoating. NANOSCALE 2015; 7:14953-14964. [PMID: 26302823 DOI: 10.1039/c5nr04023j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Self-assembling, protein-based bidimensional lattices are being developed as functionalizable, highly ordered biocoatings for multiple applications in nanotechnology and nanomedicine. Unfortunately, protein assemblies are soft materials that may be too sensitive to mechanical disruption, and their intrinsic conformational dynamism may also influence their applicability. Thus, it may be critically important to characterize, understand and manipulate the mechanical features and dynamic behavior of protein assemblies in order to improve their suitability as nanomaterials. In this study, the capsid protein of the human immunodeficiency virus was induced to self-assemble as a continuous, single layered, ordered nanocoating onto an inorganic substrate. Atomic force microscopy (AFM) was used to quantify the mechanical behavior and the equilibrium dynamics ("breathing") of this virus-based, self-assembled protein lattice in close to physiological conditions. The results uniquely provided: (i) evidence that AFM can be used to directly visualize in real time and quantify slow breathing motions leading to dynamic disorder in protein nanocoatings and viral capsid lattices; (ii) characterization of the dynamics and mechanics of a viral capsid lattice and protein-based nanocoating, including flexibility, mechanical strength and remarkable self-repair capacity after mechanical damage; (iii) proof of principle that chemical additives can modify the dynamics and mechanics of a viral capsid lattice or protein-based nanocoating, and improve their applied potential by increasing their mechanical strength and elasticity. We discuss the implications for the development of mechanically resistant and compliant biocoatings precisely organized at the nanoscale, and of novel antiviral agents acting on fundamental physical properties of viruses.
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Affiliation(s)
- Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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79
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Chang HJ, Baek I, Lee M, Na S. Influence of Aromatic Residues on the Material Characteristics of Aβ Amyloid Protofibrils at the Atomic Scale. Chemphyschem 2015; 16:2403-14. [DOI: 10.1002/cphc.201500244] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/27/2015] [Indexed: 11/06/2022]
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80
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Yahyazadehfar M, Arola D. The role of organic proteins on the crack growth resistance of human enamel. Acta Biomater 2015; 19:33-45. [PMID: 25805107 PMCID: PMC4499056 DOI: 10.1016/j.actbio.2015.03.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/06/2015] [Accepted: 03/05/2015] [Indexed: 11/18/2022]
Abstract
With only 1% protein by weight, tooth enamel is the most highly mineralized tissue in mammals. The focus of this study was to evaluate contributions of the proteins on the fracture resistance of this unique structural material. Sections of enamel were obtained from the cusps of human molars and the crack growth resistance was quantified using a conventional fracture mechanics approach with complementary finite element analysis. In selected specimens the proteins were extracted using a potassium hydroxide treatment. Removal of the proteins resulted in approximately 40% decrease in the fracture toughness with respect to the fully proteinized control. The loss of organic content was most detrimental to the extrinsic toughening mechanisms, causing over 80% reduction in their contribution to the total energy to fracture. This degradation occurred by embrittlement of the unbroken bridging ligaments and consequent reduction in the crack closure stress. Although the organic content of tooth enamel is very small, it is essential to crack growth toughening by facilitating the formation of unbroken ligaments and in fortifying their potency. Replicating functions of the organic content will be critical to the successful development of bio-inspired materials that are designed for fracture resistance.
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Affiliation(s)
- Mobin Yahyazadehfar
- Department of Material Science and Engineering, University of Washington, Seattle, WA, USA; Department of Mechanical Engineering, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Dwayne Arola
- Department of Material Science and Engineering, University of Washington, Seattle, WA, USA; Department of Restorative Dentistry, School of Dentistry, University of Washington, Seattle, WA, USA.
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81
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Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, Faure G, Rebehmed J, Ghozlane A, Swapna LS, Bhaskara RM, Barnoud J, Téletchéa S, Jallu V, Cerny J, Schneider B, Etchebest C, Srinivasan N, Gelly JC, de Brevern AG. Protein flexibility in the light of structural alphabets. Front Mol Biosci 2015; 2:20. [PMID: 26075209 PMCID: PMC4445325 DOI: 10.3389/fmolb.2015.00020] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/30/2015] [Indexed: 01/01/2023] Open
Abstract
Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases.
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Affiliation(s)
- Pierrick Craveur
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Agnel P Joseph
- Rutherford Appleton Laboratory, Science and Technology Facilities Council Didcot, UK
| | - Jeremy Esque
- Institut National de la Santé et de la Recherche Médicale U964,7 UMR Centre National de la Recherche Scientifique 7104, IGBMC, Université de Strasbourg Illkirch, France
| | - Tarun J Narwani
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Floriane Noël
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Nicolas Shinada
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Matthieu Goguet
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Sylvain Leonard
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Pierre Poulain
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Ets Poulain Pointe-Noire, Congo
| | - Olivier Bertrand
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Guilhem Faure
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health Bethesda, MD, USA
| | - Joseph Rebehmed
- Centre National de la Recherche Scientifique UMR7590, Sorbonne Universités, Université Pierre et Marie Curie - MNHN - IRD - IUC Paris, France
| | | | - Lakshmipuram S Swapna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Hospital for Sick Children, and Departments of Biochemistry and Molecular Genetics, University of Toronto Toronto, ON, Canada
| | - Ramachandra M Bhaskara
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Department of Theoretical Biophysics, Max Planck Institute of Biophysics Frankfurt, Germany
| | - Jonathan Barnoud
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Laboratoire de Physique, École Normale Supérieure de Lyon, Université de Lyon, Centre National de la Recherche Scientifique UMR 5672 Lyon, France
| | - Stéphane Téletchéa
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Faculté des Sciences et Techniques, Université de Nantes, Unité Fonctionnalité et Ingénierie des Protéines, Centre National de la Recherche Scientifique UMR 6286, Université Nantes Nantes, France
| | - Vincent Jallu
- Platelet Unit, Institut National de la Transfusion Sanguine Paris, France
| | - Jiri Cerny
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Catherine Etchebest
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | | | - Jean-Christophe Gelly
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Alexandre G de Brevern
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
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82
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Kim JI, Lee M, Baek I, Yoon G, Na S. The mechanical response of hIAPP nanowires based on different bending direction simulations. Phys Chem Chem Phys 2015; 16:18493-500. [PMID: 25073067 DOI: 10.1039/c4cp02494j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Amyloid proteins, implicated in numerous aging-related diseases, possess remarkable mechanical properties. Polymorphism leads to different arrangements of β sheets in amyloid fibrils, which changes the characteristics of the hydrogen bond network that determines their mechanical properties and structural characteristics. We performed bending simulations using molecular dynamics methods under constant-velocity conditions in different bending directions. Two different fibril structures, parallel/homo and parallel/hetero, of hIAPP amyloids were considered. Though the bending configuration influences the toughness of the material, our results indicate that the basic material behavior is affected by the β-sheet arrangement that is determined by the type of polymorphism in amyloid fibrils.
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Affiliation(s)
- J I Kim
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Republic of Korea.
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83
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Sim S, Miyajima D, Niwa T, Taguchi H, Aida T. Tailoring Micrometer-Long High-Integrity 1D Array of Superparamagnetic Nanoparticles in a Nanotubular Protein Jacket and Its Lateral Magnetic Assembling Behavior. J Am Chem Soc 2015; 137:4658-61. [DOI: 10.1021/jacs.5b02144] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seunghyun Sim
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Daigo Miyajima
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tatsuya Niwa
- Department
of Biomolecular Engineering, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Hideki Taguchi
- Department
of Biomolecular Engineering, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Takuzo Aida
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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84
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Casares L, Vincent R, Zalvidea D, Campillo N, Navajas D, Arroyo M, Trepat X. Hydraulic fracture during epithelial stretching. NATURE MATERIALS 2015; 14:343-51. [PMID: 25664452 PMCID: PMC4374166 DOI: 10.1038/nmat4206] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 12/23/2014] [Indexed: 05/07/2023]
Abstract
The origin of fracture in epithelial cell sheets subject to stretch is commonly attributed to excess tension in the cells' cytoskeleton, in the plasma membrane, or in cell-cell contacts. Here, we demonstrate that for a variety of synthetic and physiological hydrogel substrates the formation of epithelial cracks is caused by tissue stretching independently of epithelial tension. We show that the origin of the cracks is hydraulic; they result from a transient pressure build-up in the substrate during stretch and compression manoeuvres. After pressure equilibration, cracks heal readily through actomyosin-dependent mechanisms. The observed phenomenology is captured by the theory of poroelasticity, which predicts the size and healing dynamics of epithelial cracks as a function of the stiffness, geometry and composition of the hydrogel substrate. Our findings demonstrate that epithelial integrity is determined in a tension-independent manner by the coupling between tissue stretching and matrix hydraulics.
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Affiliation(s)
- Laura Casares
- Institute for Bioengineering of Catalonia, Barcelona, Spain
| | | | | | - Noelia Campillo
- Institute for Bioengineering of Catalonia, Barcelona, Spain
- Unitat de Biofísica i Bioenginyeria, Facultat de Medicina, Universitat de Barcelona, and CIBERES, Spain
| | - Daniel Navajas
- Institute for Bioengineering of Catalonia, Barcelona, Spain
- Unitat de Biofísica i Bioenginyeria, Facultat de Medicina, Universitat de Barcelona, and CIBERES, Spain
| | - Marino Arroyo
- Universitat Politècnica de Catalunya-BarcelonaTech, Spain
- Corresponding authors: Marino Arroyo, Universitat Politècnica de Catalunya, Carrer Jordi Girona 1, 08034, Barcelona, Spain, (+34) 934 011 805, ; Xavier Trepat, Institute for Bioengineering of Catalonia, Ed. Hèlix, Baldiri i Reixac, 15-21, 08028, Barcelona, Spain, (+34) 934 020 265,
| | - Xavier Trepat
- Institute for Bioengineering of Catalonia, Barcelona, Spain
- Unitat de Biofísica i Bioenginyeria, Facultat de Medicina, Universitat de Barcelona, and CIBERES, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Corresponding authors: Marino Arroyo, Universitat Politècnica de Catalunya, Carrer Jordi Girona 1, 08034, Barcelona, Spain, (+34) 934 011 805, ; Xavier Trepat, Institute for Bioengineering of Catalonia, Ed. Hèlix, Baldiri i Reixac, 15-21, 08028, Barcelona, Spain, (+34) 934 020 265,
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85
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Meyer A, Pugno NM, Cranford SW. Compliant threads maximize spider silk connection strength and toughness. J R Soc Interface 2015; 11:20140561. [PMID: 25008083 DOI: 10.1098/rsif.2014.0561] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Millions of years of evolution have adapted spider webs to achieve a range of functionalities, including the well-known capture of prey, with efficient use of material. One feature that has escaped extensive investigation is the silk-on-silk connection joints within spider webs, particularly from a structural mechanics perspective. We report a joint theoretical and computational analysis of an idealized silk-on-silk fibre junction. By modifying the theory of multiple peeling, we quantitatively compare the performance of the system while systematically increasing the rigidity of the anchor thread, by both scaling the stress-strain response and the introduction of an applied pre-strain. The results of our study indicate that compliance is a virtue-the more extensible the anchorage, the tougher and stronger the connection becomes. In consideration of the theoretical model, in comparison with rigid substrates, a compliant anchorage enormously increases the effective adhesion strength (work required to detach), independent of the adhered thread itself, attributed to a nonlinear alignment between thread and anchor (contact peeling angle). The results can direct novel engineering design principles to achieve possible load transfer from compliant fibre-to-fibre anchorages, be they silk-on-silk or another, as-yet undeveloped, system.
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Affiliation(s)
- Avery Meyer
- Laboratory for Nanotechnology in Civil Engineering (NICE), Department of Civil and Environmental Engineering, Northeastern University, 400 Snell Engineering, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Nicola M Pugno
- Laboratory of Bio-Inspired and Graphene Nanomechanics, Department of Civil, Environmental and Mechanical Engineering, Università di Trento, via Mesiano 77, 38123 Trento, Italy Center for Materials and Microsystems, Fondazione Bruno Kessler, Via Sommarive 18, 38123 Povo (Trento), Italy
| | - Steven W Cranford
- Laboratory for Nanotechnology in Civil Engineering (NICE), Department of Civil and Environmental Engineering, Northeastern University, 400 Snell Engineering, 360 Huntington Avenue, Boston, MA 02115, USA
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86
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Kim JI, Chang HJ, Na S. Identification of tail binding effect of kinesin-1 using an elastic network model. Biomech Model Mechanobiol 2015; 14:1107-17. [PMID: 25676575 DOI: 10.1007/s10237-015-0657-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 02/05/2015] [Indexed: 12/15/2022]
Abstract
Kinesin is a motor protein that delivers cargo inside a cell. Kinesin has many different families, but they perform basically same function and have same motions. The walking motion of kinesin enables the cargo delivery inside the cell. Autoinhibition of kinesin is important because it explains how function of kinesin inside a cell is stopped. Former researches showed that tail binding is related to autoinhibition of kinesin. In this work, we performed normal mode analysis with elastic network model using different conformation of kinesin to determine the effect of tail binding by considering four models such as functional form, autoinhibited form, autoinhibited form without tail, and autoinhibited form with carbon structure. Our calculation of the thermal fluctuation and cross-correlation shows the change of tail-binding region in structural motion. Also strain energy of kinesin showed that elimination of tail binding effect leads the structure to have energetically similar behavior with the functional form.
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Affiliation(s)
- Jae In Kim
- Department of Mechanical Engineering, Korea University, Seoul, 136-701, Republic of Korea
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87
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Relationship between structural composition and material properties of polymorphic hIAPP fibrils. Biophys Chem 2015; 199:1-8. [PMID: 25682214 DOI: 10.1016/j.bpc.2015.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/14/2015] [Accepted: 02/02/2015] [Indexed: 01/21/2023]
Abstract
Amyloid proteins are misfolded, denatured proteins that are responsible for causing several degenerative and neuro-degenerative diseases. Determining the mechanical stability of these amyloids is crucial for understanding the disease mechanisms, which will guide us in treatment. Furthermore, many research groups recognized amyloid proteins as functional biological materials that can be used in nanosensors, bacterial biofilms, coatings, etc. Many in vitro studies have been carried out to determine the characteristics of amyloid proteins via force spectroscopy methods, atomic force microscopy, and optical tweezers. However, computational methods (e.g. molecular dynamics and elastic network model) not only reveal the mechanical properties of the amyloid proteins, but also provide more in-depth information about the amyloids by presenting a visualization of their conformational changes. In this study, we evaluated the various material properties and behaviors of four different polymorphic structures of human islet amyloid polypeptide (hIAPP) by using steered molecular dynamics (SMD) simulations under tensile conditions. From our results, we examined how these mechanical properties may differ with respect to the structural formation of amyloid proteins.
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88
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Masic A, Bertinetti L, Schuetz R, Chang SW, Metzger TH, Buehler MJ, Fratzl P. Osmotic pressure induced tensile forces in tendon collagen. Nat Commun 2015; 6:5942. [PMID: 25608644 PMCID: PMC4354200 DOI: 10.1038/ncomms6942] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/21/2014] [Indexed: 11/12/2022] Open
Abstract
Water is an important component of collagen in tendons, but its role for the function of this load-carrying protein structure is poorly understood. Here we use a combination of multi-scale experimentation and computation to show that water is an integral part of the collagen molecule, which changes conformation upon water removal. The consequence is a shortening of the molecule that translates into tensile stresses in the range of several to almost 100 MPa, largely surpassing those of about 0.3 MPa generated by contractile muscles. Although a complete drying of collagen would be relevant for technical applications, such as the fabrication of leather or parchment, stresses comparable to muscle contraction already occur at small osmotic pressures common in biological environments. We suggest, therefore, that water-generated tensile stresses may play a role in living collagen-based materials such as tendon or bone.
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Affiliation(s)
- Admir Masic
- Department of Biomaterials, Max Planck Institute for Colloids and Interfaces, Research Campus Golm, 14424 Potsdam, Germany
| | - Luca Bertinetti
- Department of Biomaterials, Max Planck Institute for Colloids and Interfaces, Research Campus Golm, 14424 Potsdam, Germany
| | - Roman Schuetz
- Department of Biomaterials, Max Planck Institute for Colloids and Interfaces, Research Campus Golm, 14424 Potsdam, Germany
| | - Shu-Wei Chang
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - Till Hartmut Metzger
- Department of Biomaterials, Max Planck Institute for Colloids and Interfaces, Research Campus Golm, 14424 Potsdam, Germany
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - Peter Fratzl
- Department of Biomaterials, Max Planck Institute for Colloids and Interfaces, Research Campus Golm, 14424 Potsdam, Germany
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89
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Mechanical Properties and Failure of Biopolymers: Atomistic Reactions to Macroscale Response. Top Curr Chem (Cham) 2015; 369:317-43. [PMID: 26108895 DOI: 10.1007/128_2015_643] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The behavior of chemical bonding under various mechanical loadings is an intriguing mechanochemical property of biological materials, and the property plays a critical role in determining their deformation and failure mechanisms. Because of their astonishing mechanical properties and roles in constituting the basis of a variety of physiologically relevant materials, biological protein materials have been intensively studied. Understanding the relation between chemical bond networks (structures) and their mechanical properties offers great possibilities to enable new materials design in nanotechnology and new medical treatments for human diseases. Here we focus on how the chemical bonds in biological systems affect mechanical properties and how they change during mechanical deformation and failure. Three representative cases of biomaterials related to the human diseases are discussed in case studies, including: amyloids, intermediate filaments, and collagen, each describing mechanochemical features and how they relate to the pathological conditions at multiple scales.
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90
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Meersman F, McMillan PF. High hydrostatic pressure: a probing tool and a necessary parameter in biophysical chemistry. Chem Commun (Camb) 2014; 50:766-75. [PMID: 24286104 DOI: 10.1039/c3cc45844j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High pressures extending up to several thousands of atmospheres provide extreme conditions for biological organisms to survive. Recent studies are investigating the survival mechanisms and biological function of microorganisms under natural and laboratory conditions extending into the GigaPascal range, with applications to understanding the Earth's deep biosphere and food technology. High pressure has also emerged as a useful tool and physical parameter for probing changes in the structure and functional properties of biologically important macromolecules and polymers encountered in soft matter science. Here we highlight some areas of current interest in high pressure biophysics and physical chemistry that are emerging at the frontier of this cross-disciplinary field.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, UK.
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91
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Kwan K, Cranford SW. Quantifying Cooperativity via Geometric Gyration-Based Metrics of Coupled Macromolecules. JOURNAL OF NANOMECHANICS AND MICROMECHANICS 2014. [DOI: 10.1061/(asce)nm.2153-5477.0000095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Kenny Kwan
- Graduate Research Assistant, Laboratory of Nanotechnology in Civil Engineering, Dept. of Civil and Environmental Engineering, Northeastern Univ., Boston, MA 02115
| | - Steven W. Cranford
- Assistant Professor, Laboratory of Nanotechnology in Civil Engineering, Dept. of Civil and Environmental Engineering, Northeastern Univ., Boston, MA 02115 (corresponding author)
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92
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Mechanics of fragmentation of crocodile skin and other thin films. Sci Rep 2014; 4:4966. [PMID: 24862190 PMCID: PMC4034009 DOI: 10.1038/srep04966] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 03/19/2014] [Indexed: 12/03/2022] Open
Abstract
Fragmentation of thin layers of materials is mediated by a network of cracks on its surface. It is commonly seen in dehydrated paintings or asphalt pavements and even in graphene or other two-dimensional materials, but is also observed in the characteristic polygonal pattern on a crocodile's head. Here, we build a simple mechanical model of a thin film and investigate the generation and development of fragmentation patterns as the material is exposed to various modes of deformation. We find that the characteristic size of fragmentation, defined by the mean diameter of polygons, is strictly governed by mechanical properties of the film material. Our result demonstrates that skin fragmentation on the head of crocodiles is dominated by that it features a small ratio between the fracture energy and Young's modulus, and the patterns agree well with experimental observations. Understanding this mechanics-driven process could be applied to improve the lifetime and reliability of thin film coatings by mimicking crocodile skin.
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93
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Eckes K, Mu X, Ruehle MA, Ren P, Suggs LJ. β sheets not required: combined experimental and computational studies of self-assembly and gelation of the ester-containing analogue of an Fmoc-dipeptide hydrogelator. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:5287-96. [PMID: 24786493 PMCID: PMC4020586 DOI: 10.1021/la500679b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 03/31/2014] [Indexed: 05/24/2023]
Abstract
In our work toward developing ester-containing self-assembling peptides as soft biomaterials, we have found that a fluorenylmethoxycarbonyl (Fmoc)-conjugated alanine-lactic acid (Ala-Lac) sequence self-assembles into nanostructures that gel in water. This process occurs despite Fmoc-Ala-Lac's inability to interact with other Fmoc-Ala-Lac molecules via β-sheet-like amide-amide hydrogen bonding, a condition previously thought to be crucial to the self-assembly of Fmoc-conjugated peptides. Experimental comparisons of Fmoc-Ala-Lac to its self-assembling peptide sequence analogue Fmoc-Ala-Ala using a variety of microscopic, spectroscopic, and bulk characterization techniques demonstrate distinct features of the two systems and show that while angstrom-scale self-assembled structures are similar, their nanometer-scale size and morphological properties diverge and give rise to different bulk mechanical properties. Molecular dynamics simulations were performed to gain more insight into the differences between the two systems. An analysis of the hydrogen-bonding and solvent-surface interface properties of the simulated fibrils revealed that Fmoc-Ala-Lac fibrils are stronger and less hydrophilic than Fmoc-Ala-Ala fibrils. We propose that this difference in fibril amphiphilicity gives rise to differences in the higher-order assembly of fibrils into nanostructures seen in TEM. Importantly, we confirm experimentally that β-sheet-type hydrogen bonding is not crucial to the self-assembly of short, conjugated peptides, and we demonstrate computationally that the amide bond in such systems may act mainly to mediate the solvation of the self-assembled single fibrils and therefore regulate a more extensive higher-order aggregation of fibrils. This work provides a basic understanding for future research in designing highly degradable self-assembling materials with peptide-like bioactivity for biomedical applications.
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Affiliation(s)
- Kevin
M. Eckes
- Department
of Biomedical
Engineering, The University of Texas at
Austin, 107 W. Dean Keeton
St. Stop C0800, Austin, Texas 78712, United States
| | - Xiaojia Mu
- Department
of Biomedical
Engineering, The University of Texas at
Austin, 107 W. Dean Keeton
St. Stop C0800, Austin, Texas 78712, United States
| | - Marissa A. Ruehle
- Department
of Biomedical
Engineering, The University of Texas at
Austin, 107 W. Dean Keeton
St. Stop C0800, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department
of Biomedical
Engineering, The University of Texas at
Austin, 107 W. Dean Keeton
St. Stop C0800, Austin, Texas 78712, United States
| | - Laura J. Suggs
- Department
of Biomedical
Engineering, The University of Texas at
Austin, 107 W. Dean Keeton
St. Stop C0800, Austin, Texas 78712, United States
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94
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95
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Qin Z, Dimas L, Adler D, Bratzel G, Buehler MJ. Biological materials by design. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:073101. [PMID: 24451343 DOI: 10.1088/0953-8984/26/7/073101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this topical review we discuss recent advances in the use of physical insight into the way biological materials function, to design novel engineered materials 'from scratch', or from the level of fundamental building blocks upwards and by using computational multiscale methods that link chemistry to material function. We present studies that connect advances in multiscale hierarchical material structuring with material synthesis and testing, review case studies of wood and other biological materials, and illustrate how engineered fiber composites and bulk materials are designed, modeled, and then synthesized and tested experimentally. The integration of experiment and simulation in multiscale design opens new avenues to explore the physics of materials from a fundamental perspective, and using complementary strengths from models and empirical techniques. Recent developments in this field illustrate a new paradigm by which complex material functionality is achieved through hierarchical structuring in spite of simple material constituents.
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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 Avenue, Room 1-290, Cambridge, MA 02139, USA
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96
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Yi X, Shi X, Gao H. A universal law for cell uptake of one-dimensional nanomaterials. NANO LETTERS 2014; 14:1049-55. [PMID: 24459994 DOI: 10.1021/nl404727m] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Understanding cell interaction with one-dimensional nanomaterials, including nanotubes, nanowires, nanofibers, filamentous bacteria, and certain nanoparticle chains, has fundamental importance to many applications such as biomedical diagnostics, therapeutics, and nanotoxicity. Here we show that cell uptake of one-dimensional nanomaterials via receptor-mediated endocytosis is dominated by a single dimensionless parameter that scales with the membrane tension and radius of the nanomaterial and inversely with the membrane bending stiffness. It is shown that as cell membrane internalizes one-dimensional nanomaterials the uptake follows a near-perpendicular entry mode at small membrane tension but it switches to a near-parallel interaction mode at large membrane tension.
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Affiliation(s)
- Xin Yi
- School of Engineering, Brown University , Providence, Rhode Island 02912, United States
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97
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Chen X, Mahadevan L, Driks A, Sahin O. Bacillus spores as building blocks for stimuli-responsive materials and nanogenerators. NATURE NANOTECHNOLOGY 2014; 9:137-141. [PMID: 24463362 DOI: 10.1038/nnano.2013.290] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 12/03/2013] [Indexed: 06/03/2023]
Abstract
Materials that respond mechanically to external chemical stimuli have applications in biomedical devices, adaptive architectural systems, robotics and energy harvesting. Inspired by biological systems, stimuli-responsive materials have been created that can oscillate, transport fluid, provide homeostasis and undergo complex changes in shape. However, the effectiveness of synthetic stimuli-responsive materials in generating work is limited when compared with mechanical actuators. Here, we show that the mechanical response of Bacillus spores to water gradients exhibits an energy density of more than 10 MJ m(-3), which is two orders of magnitude higher than synthetic water-responsive materials. We also identified mutations that can approximately double the energy density of the spores and found that they can self-assemble into dense, submicrometre-thick monolayers on substrates such as silicon microcantilevers and elastomer sheets, creating bio-hybrid hygromorph actuators. To illustrate the potential applications of the spores, we used them to build an energy-harvesting device that can remotely generate electrical power from an evaporating body of water.
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Affiliation(s)
- Xi Chen
- Department of Biological Sciences and Department of Physics, Columbia University, New York, New York 10027, USA
| | - L Mahadevan
- 1] School of Engineering and Applied Sciences, Department of Physics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Kavli Institute for Nanobio Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA [3] Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
| | - Adam Driks
- Department of Microbiology and Immunology, Loyola University Medical Center, 2160 S. First Avenue, Maywood, Illinois 60153, USA
| | - Ozgur Sahin
- 1] Department of Biological Sciences and Department of Physics, Columbia University, New York, New York 10027, USA [2] Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
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98
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Impact tolerance in mussel thread networks by heterogeneous material distribution. Nat Commun 2014; 4:2187. [PMID: 23880603 DOI: 10.1038/ncomms3187] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/24/2013] [Indexed: 01/17/2023] Open
Abstract
The Mytilidae, generally known as marine mussels, are known to attach to most substrates including stone, wood, concrete and iron by using a network of byssus threads. Mussels are subjected to severe mechanical impacts caused by waves. However, how the network of byssus threads keeps the mussel attached in this challenging mechanical environment is puzzling, as the dynamical forces far exceed the measured strength of byssus threads and their attachment to the environment. Here we combine experiment and simulation, and show that the heterogeneous material distribution in byssus threads has a critical role in decreasing the effect of impact loading. We find that a combination of stiff and soft materials at an 80:20 ratio enables mussels to rapidly and effectively dissipate impact energy. Notably, this facilitates a significantly enhanced strength under dynamical loading over 900% that of the strength under static loading.
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99
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Liu Y, Thomopoulos S, Chen C, Birman V, Buehler MJ, Genin GM. Modelling the mechanics of partially mineralized collagen fibrils, fibres and tissue. J R Soc Interface 2013; 11:20130835. [PMID: 24352669 DOI: 10.1098/rsif.2013.0835] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Progressive stiffening of collagen tissue by bioapatite mineral is important physiologically, but the details of this stiffening are uncertain. Unresolved questions about the details of the accommodation of bioapatite within and upon collagen's hierarchical structure have posed a central hurdle, but recent microscopy data resolve several major questions. These data suggest how collagen accommodates bioapatite at the lowest relevant hierarchical level (collagen fibrils), and suggest several possibilities for the progressive accommodation of bioapatite at higher hierarchical length scales (fibres and tissue). We developed approximations for the stiffening of collagen across spatial hierarchies based upon these data, and connected models across hierarchies levels to estimate mineralization-dependent tissue-level mechanics. In the five possible sequences of mineralization studied, percolation of the bioapatite phase proved to be an important determinant of the degree of stiffening by bioapatite. The models were applied to study one important instance of partially mineralized tissue, which occurs at the attachment of tendon to bone. All sequences of mineralization considered reproduced experimental observations of a region of tissue between tendon and bone that is more compliant than either tendon or bone, but the size and nature of this region depended strongly upon the sequence of mineralization. These models and observations have implications for engineered tissue scaffolds at the attachment of tendon to bone, bone development and graded biomimetic attachment of dissimilar hierarchical materials in general.
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Affiliation(s)
- Yanxin Liu
- Department of Mechanical Engineering and Materials Science, Washington University, , St Louis, MO 63130, USA
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100
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Perticaroli S, Nickels JD, Ehlers G, O'Neill H, Zhang Q, Sokolov AP. Secondary structure and rigidity in model proteins. SOFT MATTER 2013; 9:9548-56. [PMID: 26029761 DOI: 10.1039/c3sm50807b] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
There is tremendous interest in understanding the role that secondary structure plays in the rigidity and dynamics of proteins. In this work we analyze nanomechanical properties of proteins chosen to represent different secondary structures: α-helices (myoglobin and bovine serum albumin), β-barrels (green fluorescent protein), and α + β + loop structures (lysozyme). Our experimental results show that in these model proteins, the β motif is a stiffer structural unit than the α-helix in both dry and hydrated states. This difference appears not only in the rigidity of the protein, but also in the amplitude of fast picosecond fluctuations. Moreover, we show that for these examples the secondary structure correlates with the temperature- and hydration-induced changes in the protein dynamics and rigidity. Analysis also suggests a connection between the length of the secondary structure (α-helices) and the low-frequency vibrational mode, the so-called boson peak. The presented results suggest an intimate connection of dynamics and rigidity with the protein secondary structure.
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Affiliation(s)
- Stefania Perticaroli
- aChemical and Materials Sciences Division at Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. E-mail:
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