1
|
Guo HB, Huntington B, Perminov A, Smith K, Hastings N, Dennis P, Kelley-Loughnane N, Berry R. AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein. PLoS One 2024; 19:e0301866. [PMID: 38739602 PMCID: PMC11090348 DOI: 10.1371/journal.pone.0301866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/23/2024] [Indexed: 05/16/2024] Open
Abstract
We use AlphaFold2 (AF2) to model the monomer and dimer structures of an intrinsically disordered protein (IDP), Nvjp-1, assisted by molecular dynamics (MD) simulations. We observe relatively rigid dimeric structures of Nvjp-1 when compared with the monomer structures. We suggest that protein conformations from multiple AF2 models and those from MD trajectories exhibit a coherent trend: the conformations of an IDP are deviated from each other and the conformations of a well-folded protein are consistent with each other. We use a residue-residue interaction network (RIN) derived from the contact map which show that the residue-residue interactions in Nvjp-1 are mainly transient; however, those in a well-folded protein are mainly persistent. Despite the variation in 3D shapes, we show that the AF2 models of both disordered and ordered proteins exhibit highly consistent profiles of the pLDDT (predicted local distance difference test) scores. These results indicate a potential protocol to justify the IDPs based on multiple AF2 models and MD simulations.
Collapse
Affiliation(s)
- Hao-Bo Guo
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
- UES Inc., Dayton, OH, United States of America
| | - Baxter Huntington
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
- Miami University, Oxford, OH, United States of America
| | - Alexander Perminov
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
- Miami University, Oxford, OH, United States of America
| | - Kenya Smith
- United States Air Force Academy, Colorado Springs, CO, United States of America
| | - Nicholas Hastings
- United States Air Force Academy, Colorado Springs, CO, United States of America
| | - Patrick Dennis
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
| | - Nancy Kelley-Loughnane
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
| | - Rajiv Berry
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
| |
Collapse
|
2
|
Matsumura Y, Krings W, Kovalev A, Gorb SN. The puncture mechanics: an example from the bed bug Cimex lectularius showing traumatic insemination using the paramere. J R Soc Interface 2024; 21:20240108. [PMID: 38807525 DOI: 10.1098/rsif.2024.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/09/2024] [Indexed: 05/30/2024] Open
Abstract
Cimicidae are well-known for traumatic insemination, and males pierce females with their parameres and transfer sperm through them. The shape of parameres is relatively stable in the family, but in some genera, the paramere is elongated, appearing less resistant against lateral deflection. To understand the mechanical limitations of the paramere, we studied its penetration mechanics of the common bed bug, Cimex lectularius. We examined the post-abdominal morphology, paramere geometry and material properties and conducted breaking stress experiments on the paramere under wet and dry conditions. Mechanical property gradients are present with the paramere tip as the stiffest region and the base as the most flexible one. These mechanical properties relate to the presence of Ca, Zn and Si. The basal wing-shaped structure is flexible, enabling it to interlock with the anal region during mating. The paramere is slightly twisted; the tip region is circular in cross-section, and the geometry of the rest is rather complex. In the mechanical tests, wet parameres mainly buckled, while dried parameres broke off. The level of structural failures depended on directions from which the compression forces were applied. Structural, material and mechanical strengthening mechanisms preventing the paramere from mechanical failure are discussed.
Collapse
Affiliation(s)
- Yoko Matsumura
- Department of Functional Morphology and Biomechanics, Zoological Institute, Kiel University , Kiel, Germany
- Systematic Entomology, Graduate School of Agriculture, Hokkaido University , Sapporo 060-8589, Japan
- General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald , Greifswald, Germany
| | - Wencke Krings
- Department of Functional Morphology and Biomechanics, Zoological Institute, Kiel University , Kiel, Germany
- Department of Cariology, Endodontology and Periodontology, Universität Leipzig , Leipzig 04103, Germany
- Department of Mammalogy and Paleoanthropology, Leibniz Institute for the Analysis of Biodiversity Change , Hamburg 20146, Germany
- Department of Electron Microscopy, Institute of Cell and Systems Biology of Animals, Universität Hamburg , Hamburg 20146, Germany
| | - Alexander Kovalev
- Department of Functional Morphology and Biomechanics, Zoological Institute, Kiel University , Kiel, Germany
| | - Stanislav N Gorb
- Department of Functional Morphology and Biomechanics, Zoological Institute, Kiel University , Kiel, Germany
| |
Collapse
|
3
|
Klunk CL, Heethoff M, Hammel JU, Gorb SN, Krings W. Mechanical and elemental characterization of ant mandibles: consequences for bite mechanics. Interface Focus 2024; 14:20230056. [PMID: 38618235 PMCID: PMC11008963 DOI: 10.1098/rsfs.2023.0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/16/2024] [Indexed: 04/16/2024] Open
Abstract
Mandible morphology has an essential role in biting performance, but the mandible cuticle can have regional differences in its mechanical properties. The effects of such a heterogeneous distribution of cuticle material properties in the mandible responses to biting loading are still poorly explored in chewing insects. Here, we tested the mechanical properties of mandibles of the ant species Formica cunicularia by nanoindentation and investigated the effects of the cuticular variation in Young's modulus (E) under bite loading with finite-element analysis (FEA). The masticatory margin of the mandible, which interacts with the food, was the hardest and stiffest region. To unravel the origins of the mechanical property gradients, we characterized the elemental composition by energy-dispersive X-ray spectroscopy. The masticatory margin possessed high proportions of Cu and Zn. When incorporated into the FEA, variation in E effectively changed mandible stress patterns, leading to a relatively higher concentration of stresses in the stiffer mandibular regions and leaving the softer mandible blade with relatively lower stress. Our results demonstrated the relevance of cuticle E heterogeneity in mandibles under bite loading, suggesting that the accumulation of transition metals such as Cu and Zn has a relevant correlation with the mechanical characteristics in F. cunicularia mandibles.
Collapse
Affiliation(s)
- Cristian L. Klunk
- Animal Evolutionary Ecology, Technische Universität Darmstadt, Schnittspahnstr. 3, Darmstadt 64287, Germany
| | - Michael Heethoff
- Animal Evolutionary Ecology, Technische Universität Darmstadt, Schnittspahnstr. 3, Darmstadt 64287, Germany
| | - Jörg U. Hammel
- Institute of Materials Physics, Helmholtz-Zentrum Hereon, Geesthacht, Germany
| | - Stanislav N. Gorb
- Department of Functional Morphology and Biomechanics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, Kiel 24118, Germany
| | - Wencke Krings
- Department of Functional Morphology and Biomechanics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, Kiel 24118, Germany
- Department of Cariology, Endodontology and Periodontology, Universität Leipzig, Liebigstraße 12, Leipzig, Germany
- Department of Electron Microscopy, Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King-Platz 3, Hamburg 20146, Germany
| |
Collapse
|
4
|
Birkenfeld V, Gorb SN, Krings W. Mandible elemental composition and mechanical properties from distinct castes of the leafcutter ant Atta laevigata (Attini; Formicidae). Interface Focus 2024; 14:20230048. [PMID: 38618230 PMCID: PMC11008964 DOI: 10.1098/rsfs.2023.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/18/2023] [Indexed: 04/16/2024] Open
Abstract
Leafcutter ant colonies are divided into castes with the individuals performing different tasks, based mostly on size. With the mandibles, the small minims care for the brood or the fungus, whereas the larger minors and mediae cut and transport plant material, with the ant size positively related to the material size. The mechanical properties and composition of the mandible cuticle have been previously tested in the soldiers as the largest caste, revealing that the cutting edges contained high contents of the cross-linking transition metal zinc (Zn). With regard to the smaller castes, no data are present. To study how the mandible size and function relates to its mechanical properties, we here tested the mandibles of minims, minors and mediae by nanoindentation. We found that the hardness (H) and Young's modulus (E) values increased with increasing ant size and that the mandible cutting edges in each caste have the highest H- and E-values. To gain insight into the origins of these properties, we characterized the elemental composition by energy-dispersive X-ray analysis, revealing that minors and mediae possessed higher content of Zn in the cutting edges in contrast to the minims containing significantly less Zn. This shows, that Zn content relates to higher mechanical property values. Additionally, it shows that all of these parameters can differ within a single species.
Collapse
Affiliation(s)
- Valentin Birkenfeld
- Department of Functional Morphology and Biomechanics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| | - Stanislav N. Gorb
- Department of Functional Morphology and Biomechanics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| | - Wencke Krings
- Department of Functional Morphology and Biomechanics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
- Department of Cariology, Endodontology and Periodontology, Universität Leipzig, Liebigstraße 12, 04103 Leipzig, Germany
- Department of Electron Microscopy, Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
- Department of Mammalogy and Palaeoanthropology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| |
Collapse
|
5
|
Krings W, Below P, Gorb SN. Mandible mechanical properties and composition of the larval Glossosoma boltoni (Trichoptera, Insecta). Sci Rep 2024; 14:4695. [PMID: 38409429 PMCID: PMC10897335 DOI: 10.1038/s41598-024-55211-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024] Open
Abstract
Insect feeding structures, such as mandibles, interact with the ingesta (food or/and substrate) and can be adapted in morphology, composition of material and mechanical properties. The foraging on abrasive ingesta, as on algae covering rocks, is particularly challenging because the mandibles will be prone to wear and structural failure, thus suggesting the presence of mandibular adaptations to accompany this feeding behavior. Adaptations to this are well studied in the mouthparts of molluscs and sea urchins, but for insects there are large gaps in our knowledge. In this study, we investigated the mandibles of a grazing insect, the larvae of the trichopteran Glossosoma boltoni. Using scanning electron microscopy, wear was documented on the mandibles. The highest degree was identified on the medial surface of the sharp mandible tip. Using nanoindentation, the mechanical properties, such as hardness and Young's modulus, of the medial and lateral mandible cuticles were tested. We found, that the medial cuticle of the tip was significantly softer and more flexible than the lateral one. These findings indicate that a self-sharpening mechanism is present in the mandibles of this species, since the softer medial cuticle is probably abraded faster than the harder lateral one, leading to sharp mandible tips. To investigate the origins of these properties, we visualized the degree of tanning by confocal laser scanning microscopy. The autofluorescence signal related to the mechanical property gradients. The presence of transition and alkaline earth metals by energy dispersive X-ray spectroscopy was also tested. We found Ca, Cl, Cu, Fe, K, Mg, Mn, P, S, Si, and Zn in the cuticle, but the content was very low and did not correlate with the mechanical property values.
Collapse
Affiliation(s)
- Wencke Krings
- Department of Electron Microscopy, Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.
- Department of Cariology, Endodontology and Periodontology, Universität Leipzig, Liebigstraße 12, 04103, Leipzig, Germany.
- Department of Mammalogy and Palaeoanthropology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.
- Department of Functional Morphology and Biomechanics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
| | - Patrick Below
- Department of Electron Microscopy, Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
- Department of Mammalogy and Palaeoanthropology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Stanislav N Gorb
- Department of Functional Morphology and Biomechanics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| |
Collapse
|
6
|
Qi H, Ding Y, Teng Y, Liang X, Chen L, Ma J, Yang Q, Liu T. A Core Structural Protein That Builds the Locust Mandible with a Mechanical Gradient. ACS NANO 2023; 17:25311-25321. [PMID: 38064446 DOI: 10.1021/acsnano.3c08715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Natural materials, such as locust mandibles and squid beaks, define significant mechanical gradients that have been attributed to the chemical gradients of their specialized structural proteins (SPs). However, the mechanism by which SPs form chemical gradients in these materials remains unknown. In this study, a highly abundant histidine-rich structural protein (LmMHSP) was identified in the mandible of a migratory locust (Locusta migratoria). LmMHSP was proven by both in vivo and in vitro evidence to act as a core building block of the mandible with a variety of synergistic functions including chitin binding, matrix formation via liquid-liquid phase separation, chemical cross-linking, and metal coordination. Furthermore, we found that the SP gradient in the locust mandible stems from the chitin-binding activity of LmMHSP and different microstructures of chitin scaffolds in different regions. These findings advance our understanding of the formation mechanisms of natural biomaterials and have implications for the fabrication of biomimetic materials.
Collapse
Affiliation(s)
- Huitang Qi
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yi Ding
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yingda Teng
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Xiangyu Liang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Lei Chen
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jianli Ma
- Department of Engineering Mechanics, Dalian University of Technology, Dalian 116024, China
| | - Qing Yang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tian Liu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| |
Collapse
|
7
|
Song J, Khare E, Rao L, Buehler MJ, Holten-Andersen N. Coordination Stoichiometry Effects on the Binding Hierarchy of Histamine and Imidazole-M 2+ Complexes. Macromol Rapid Commun 2023; 44:e2300077. [PMID: 37337912 DOI: 10.1002/marc.202300077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/14/2023] [Indexed: 06/21/2023]
Abstract
Histidine-M2+ coordination bonds are a recognized bond motif in biogenic materials with high hardness and extensibility, which has led to growing interest in their use in soft materials for mechanical function. However, the effect of different metal ions on the stability of the coordination complex remains poorly understood, complicating their implementation in metal-coordinated polymer materials. Herein, rheology experiments and density functional theory calculations are used to characterize the stability of coordination complexes and establish the binding hierarchy of histamine and imidazole with Ni2+ , Cu2+ , and Zn2+ . It is found that the binding hierarchy is driven by the specific affinity of the metal ions to different coordination states, which can be macroscopically tuned by changing the metal-to-ligand stoichiometry of the metal-coordinated network. These findings facilitate the rational selection of metal ions for optimizing the mechanical properties of metal-coordinated materials.
Collapse
Affiliation(s)
- Jake Song
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Eesha Khare
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Li Rao
- Department of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Niels Holten-Andersen
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Bioengineering and Department of Materials Science and Engineering, Lehigh University, 27 Memorial Dr W, Bethlehem, PA, 18015, USA
| |
Collapse
|
8
|
Sugumaran M, Evans JJ. Catecholamine Derivatives as Novel Crosslinkers for the Synthesis of Versatile Biopolymers. J Funct Biomater 2023; 14:449. [PMID: 37754863 PMCID: PMC10531651 DOI: 10.3390/jfb14090449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Catecholamine metabolites are not only involved in primary metabolism, but also in secondary metabolism, serving a diverse array of physiologically and biochemically important functions. Melanin, which originates from dopa and dopamine, found in the hair, eye, and skin of all animals, is an important biopolymeric pigment. It provides protection against damaging solar radiation to animals. N-Acetyldopamine and N-β-alanyldopamine play a crucial role in the hardening of the exoskeletons of all insects. In addition, insects and other arthropods utilize the melanogenic process as a key component of their defense systems. Many marine organisms utilize dopyl peptides and proteins as bonding materials to adhere to various substrata. Moreover, the complex dopa derivatives that are precursors to the formation of the exoskeletons of numerous marine organisms also exhibit antibiotic properties. The biochemistry and mechanistic transformations of different catecholamine derivatives to produce various biomaterials with antioxidant, antibiotic, crosslinking, and gluing capabilities are highlighted. These reactivities are exhibited through the transient and highly reactive quinones, quinone methides, and quinone methide imine amide intermediates, as well as chelation to metal ions. A careful consideration of the reactivities summarized in this review will inspire numerous strategies for synthesizing novel biomaterials for future medical and industrial use.
Collapse
Affiliation(s)
- Manickam Sugumaran
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA;
| | - Jason J. Evans
- Department of Chemistry, University of Massachusetts Boston, Boston, MA 02125, USA
| |
Collapse
|
9
|
Miserez A, Yu J, Mohammadi P. Protein-Based Biological Materials: Molecular Design and Artificial Production. Chem Rev 2023; 123:2049-2111. [PMID: 36692900 PMCID: PMC9999432 DOI: 10.1021/acs.chemrev.2c00621] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Indexed: 01/25/2023]
Abstract
Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.
Collapse
Affiliation(s)
- Ali Miserez
- Center
for Sustainable Materials (SusMat), School of Materials Science and
Engineering, Nanyang Technological University
(NTU), Singapore637553
- School
of Biological Sciences, NTU, Singapore637551
| | - Jing Yu
- Center
for Sustainable Materials (SusMat), School of Materials Science and
Engineering, Nanyang Technological University
(NTU), Singapore637553
- Institute
for Digital Molecular Analytics and Science (IDMxS), NTU, 50 Nanyang Avenue, Singapore637553
| | - Pezhman Mohammadi
- VTT
Technical Research Centre of Finland Ltd., Espoo, UusimaaFI-02044, Finland
| |
Collapse
|
10
|
Lee J, Yang M, Song WJ. The expanded landscape of metalloproteins by genetic incorporation of noncanonical amino acids. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jaehee Lee
- Department of Chemistry Seoul National University Seoul South Korea
| | - Minwoo Yang
- Department of Chemistry Seoul National University Seoul South Korea
| | - Woon Ju Song
- Department of Chemistry Seoul National University Seoul South Korea
| |
Collapse
|
11
|
Bekele S, Singh K, Helton E, Farajollahi S, Naik RR, Dennis P, Kelley-Loughnane N, Berry R. Molecular Dynamics Investigation into pH Dependent Metal Binding of the Intrinsically Disordered Worm Jaw Protein, Nvjp-1. J Phys Chem B 2022; 126:6614-6623. [PMID: 36006408 PMCID: PMC9465683 DOI: 10.1021/acs.jpcb.2c02807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Sclerotization of the Nereis virens jaw
is mediated
by metal binding to the histidine-rich jaw protein, Nvjp-1. Previous
studies showed that the mechanical properties of Nvjp-1 hydrogels
could be modulated with zinc binding as well as the associated anion.
Here, we show that the mechanical properties of Nvjp-1 hydrogels can
be modulated by pH and that zinc binding to Nvjp-1 is stable at both
acidic and alkaline pH conditions. To probe the mechanism of Zn2+ binding to Nvjp-1 at different pH conditions, we utilized
all atom molecular dynamics simulations employing a polarizable force
field. At low pH conditions, polar residues predominantly interacted
with Zn2+, with at most two residues interacting with a
given zinc ion. Surprisingly, little to no Zn2+ binding
was observed with the abundant Nvjp-1 acidic residues, which form
salt-bridges with the protonated histidines to effectively block their
binding to Zn2+ ions. As the pH was shifted to alkaline
conditions, Zn2+ binding residues reconfigured to form
additional coordination bonds with histidine, resulting in a reduction
in the radius of gyration that correlated with hydrogel sclerotization.
Furthermore, acetate ions were shown to facilitate the capture of
zinc ions through association with protonated histidines at low pH,
freeing acidic residues to interact with Zn2+ ions and
increasing the number of Zn2+ ions that diffuse into the
Nvjp-1 interior. Thus, these studies provide valuable molecular insights
into how amino acid residues in Nvjp-1 manage metal salt binding and
coordination in hydrogels as a function of the pH and ionic environments.
Collapse
Affiliation(s)
- Selemon Bekele
- Materials and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Ohio 45433-7131, United States.,UES Inc., Dayton, Ohio 45432, United States
| | - Kristi Singh
- Materials and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Ohio 45433-7131, United States.,UES Inc., Dayton, Ohio 45432, United States
| | - Evan Helton
- Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435, United States
| | - Sanaz Farajollahi
- Materials and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Ohio 45433-7131, United States.,UES Inc., Dayton, Ohio 45432, United States
| | - Rajesh R Naik
- 711th Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
| | - Patrick Dennis
- Materials and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Ohio 45433-7131, United States
| | - Nancy Kelley-Loughnane
- Materials and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Ohio 45433-7131, United States
| | - Rajiv Berry
- Materials and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Ohio 45433-7131, United States
| |
Collapse
|
12
|
Guo HB, Perminov A, Bekele S, Kedziora G, Farajollahi S, Varaljay V, Hinkle K, Molinero V, Meister K, Hung C, Dennis P, Kelley-Loughnane N, Berry R. AlphaFold2 models indicate that protein sequence determines both structure and dynamics. Sci Rep 2022; 12:10696. [PMID: 35739160 PMCID: PMC9226352 DOI: 10.1038/s41598-022-14382-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/06/2022] [Indexed: 12/29/2022] Open
Abstract
AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps. We show that PAE maps from AF2 are correlated with the distance variation (DV) matrices from molecular dynamics (MD) simulations, which reveals that the PAE maps can predict the dynamical nature of protein residues. Here, we introduce the AF2-scores, which are simply derived from pLDDT scores and are in the range of [0, 1]. We found that for most protein models, including large proteins and protein complexes, the AF2-scores are highly correlated with the root mean square fluctuations (RMSF) calculated from MD simulations. However, for an IDP and a randomized protein, the AF2-scores do not correlate with the RMSF from MD, especially for the IDP. Our results indicate that the protein structures predicted by AF2 also convey information of the residue flexibility, i.e., protein dynamics.
Collapse
Affiliation(s)
- Hao-Bo Guo
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Alexander Perminov
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- Computer Science Department, Miami University, Oxford, OH, USA
| | - Selemon Bekele
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Gary Kedziora
- General Dynamics Information Technology, Inc., Wright-Patterson Air Force Base, 45433, OH, USA
| | - Sanaz Farajollahi
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Vanessa Varaljay
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Kevin Hinkle
- Department of Chemical and Materials Engineering, Dayton University, Dayton, OH, USA
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, Salt Lake City, UT, USA
| | - Konrad Meister
- Department of Natural Sciences, University of Alaska Southeast, Juneau, AK, USA
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Chia Hung
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Patrick Dennis
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Nancy Kelley-Loughnane
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA.
| | - Rajiv Berry
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA.
| |
Collapse
|
13
|
Gorb SN, Krings W. Mechanical property gradients of taenioglossan radular teeth are associated with specific function and ecological niche in Paludomidae (Gastropoda: Mollusca). Acta Biomater 2021; 134:513-530. [PMID: 34329785 DOI: 10.1016/j.actbio.2021.07.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/16/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023]
Abstract
Biological tissues may exhibit graded heterogeneities in structure and mechanical properties that are crucial to their function. One biological structure that shows variation in both structure and function is the molluscan radula: the organ comprises a chitinous membrane with embedded teeth and serves to process and gather food. The tooth morphologies had been well studied in the last decades, but the mechanical properties of the teeth are not known for the vast majority of molluscs. This knowledge gap restricts our understanding of how the radula is able to act effectively on a target surface whilst simultaneously resisting structural failure. Here we employed nanoindentation technique to measure mechanical properties (hardness and Young's modulus) on distinct localities of individual radular teeth from 24 species of African paludomid gastropods. These species have distinct ecological niches as they forage on algae on different feeding substrates. A gradual distribution of measured properties along the teeth was found in species foraging on solid or mixed feeding substrates, but soft substrate feeders exhibit teeth almost homogeneous in their biomechanical properties. The presence or absence of large-scale gradients in these taenioglossan teeth could directly be linked with their specific function and in general with the species ecology, whereas the radular tooth morphologies do not always and fully reflect ecology. STATEMENT OF SIGNIFICANCE: African Lake Tanganyika is well known for harbouring endemic and morphologically distinct genera. Its paludomid gastropods form a flock of high interest because of its diversity. As they show distinct radular tooth morphologies hypotheses about potential trophic specializations had always been at hand. Here we evaluated the mechanical properties Young's modulus and hardness of 9027 individual teeth from 24 species along the tooth by nanoindentation and related them with the gastropods' specific feeding substrate. We find that hard substrate feeders have teeth that are hard at the tips but much less stiff at the base and thus heterogeneous with respect to material properties, whereas soft substrate feeders have teeth that are flexible and homogenous with respect to material properties.
Collapse
|
14
|
Zechel S, Hager MD, Priemel T, Harrington MJ. Healing through Histidine: Bioinspired Pathways to Self-Healing Polymers via Imidazole⁻Metal Coordination. Biomimetics (Basel) 2019; 4:E20. [PMID: 31105205 PMCID: PMC6477608 DOI: 10.3390/biomimetics4010020] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 12/03/2022] Open
Abstract
Biology offers a valuable inspiration toward the development of self-healing engineering composites and polymers. In particular, chemical level design principles extracted from proteinaceous biopolymers, especially the mussel byssus, provide inspiration for design of autonomous and intrinsic healing in synthetic polymers. The mussel byssus is an acellular tissue comprised of extremely tough protein-based fibers, produced by mussels to secure attachment on rocky surfaces. Threads exhibit self-healing response following an apparent plastic yield event, recovering initial material properties in a time-dependent fashion. Recent biochemical analysis of the structure-function relationships defining this response reveal a key role of sacrificial cross-links based on metal coordination bonds between Zn2+ ions and histidine amino acid residues. Inspired by this example, many research groups have developed self-healing polymeric materials based on histidine (imidazole)-metal chemistry. In this review, we provide a detailed overview of the current understanding of the self-healing mechanism in byssal threads, and an overview of the current state of the art in histidine- and imidazole-based synthetic polymers.
Collapse
Affiliation(s)
- Stefan Zechel
- Laboratory for Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany.
- Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany.
| | - Martin D Hager
- Laboratory for Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany.
- Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany.
| | - Tobias Priemel
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada.
| | - Matthew J Harrington
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada.
| |
Collapse
|
15
|
Gupta MK, Becknell KA, Crosby MG, Bedford NM, Wright J, Dennis PB, Naik RR. Programmable Mechanical Properties from a Worm Jaw-Derived Biopolymer through Hierarchical Ion Exposure. ACS APPLIED MATERIALS & INTERFACES 2018; 10:31928-31937. [PMID: 30165014 DOI: 10.1021/acsami.8b10107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mechanisms of biomaterial sclerotization in natural systems promise new insights into how the mechanical properties of engineered materials may be dynamically modulated. One such example involves the proteinaceous jaw of the marine sandworm, Nereis virens. Previously, the mechanical properties of the N. virens jaw were shown to be modulated by Zn binding, a property that was proposed to be enabled by the presence of the histidine-rich jaw protein, Nvjp-1. Here we demonstrate the creation of Nvjp-1-based hydrogels and show that progressive sclerotization of these hydrogels can be accomplished with hierarchical exposure to metal cations and anions. Divalent Zn cations are capable of reversibly sclerotizing the hydrogels through the formation of coordinate cross-links, an effect that is shown to be remarkably specific for Zn. Additionally, the degree of Zn-induced sclerotization is strongly influenced by the identity of the anion present in the hydrogel. Thus, the viscoelastic properties of Nvjp-1 hydrogels can be modulated through programmed, hierarchical exposure to specific cations and anions present in the sclerotizing salts. These observations have resulted in new hydrogel capabilities, such as the creation of anion-controlled shape-memory polymers, and will add to the number of control parameters that can be used to tune the properties of functional hydrogels in a dynamic manner.
Collapse
Affiliation(s)
- Maneesh K Gupta
- Materials and Manufacturing Directorate, Air Force Research Laboratory , Wright-Patterson Air Force Base , Ohio 45433 , United States
| | - Kellie A Becknell
- Materials and Manufacturing Directorate, Air Force Research Laboratory , Wright-Patterson Air Force Base , Ohio 45433 , United States
| | - Marquise G Crosby
- Materials and Manufacturing Directorate, Air Force Research Laboratory , Wright-Patterson Air Force Base , Ohio 45433 , United States
| | - Nicholas M Bedford
- Materials and Manufacturing Directorate, Air Force Research Laboratory , Wright-Patterson Air Force Base , Ohio 45433 , United States
| | - Joshua Wright
- Department of Physics , Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Patrick B Dennis
- Materials and Manufacturing Directorate, Air Force Research Laboratory , Wright-Patterson Air Force Base , Ohio 45433 , United States
| | - Rajesh R Naik
- 711th Human Performance Wing , Air Force Research Laboratory , Wright-Patterson Air Force Base , Ohio 45433 , United States
| |
Collapse
|
16
|
Liu Z, Zhang Z, Ritchie RO. On the Materials Science of Nature's Arms Race. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1705220. [PMID: 29870573 DOI: 10.1002/adma.201705220] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/14/2017] [Indexed: 05/05/2023]
Abstract
Biological material systems have evolved unique combinations of mechanical properties to fulfill their specific function through a series of ingenious designs. Seeking lessons from Nature by replicating the underlying principles of such biological materials offers new promise for creating unique combinations of properties in man-made systems. One case in point is Nature's means of attack and defense. During the long-term evolutionary "arms race," naturally evolved weapons have achieved exceptional mechanical efficiency with a synergy of effective offense and persistence-two characteristics that often tend to be mutually exclusive in many synthetic systems-which may present a notable source of new materials science knowledge and inspiration. This review categorizes Nature's weapons into ten distinct groups, and discusses the unique structural and mechanical designs of each group by taking representative systems as examples. The approach described is to extract the common principles underlying such designs that could be translated into man-made materials. Further, recent advances in replicating the design principles of natural weapons at differing lengthscales in artificial materials, devices and tools to tackle practical problems are revisited, and the challenges associated with biological and bioinspired materials research in terms of both processing and properties are discussed.
Collapse
Affiliation(s)
- Zengqian Liu
- Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, Shenyang, 110016, China
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Zhefeng Zhang
- Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Robert O Ritchie
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| |
Collapse
|
17
|
Smith AM, Papaleo C, Reid CW, Bliss JM. RNA-Seq reveals a central role for lectin, C1q and von Willebrand factor A domains in the defensive glue of a terrestrial slug. BIOFOULING 2017; 33:741-754. [PMID: 28899232 PMCID: PMC6124484 DOI: 10.1080/08927014.2017.1361413] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/25/2017] [Indexed: 06/07/2023]
Abstract
The tough, hydrogel glue produced by the slug Arion subfuscus achieves impressive performance through metal-based, protein cross-links. The primary sequence of these proteins was determined through transcriptome sequencing and proteome analysis by tandem mass spectrometry. The main proteins that correlate with adhesive function are a group of 11 small, highly abundant lectin-like proteins. These proteins matched the ligand-binding C-lectin, C1q or H-lectin domains. The variety of different lectin-like proteins and their potential for oligomerization suggests that they function as versatile and potent cross-linkers. In addition, the glue contains five matrilin-like proteins that are rich in von Willebrand factor A (VWA) and EGF domains. Both C-lectins and VWA domains are known to bind to ligands using divalent cations. These findings are consistent with the double network mechanism proposed for slug glue, with divalent ions serving as sacrificial bonds to dissipate energy.
Collapse
Affiliation(s)
- Andrew M. Smith
- Ithaca College, Department of Biology, 953 Danby Road, Ithaca, NY 14850 607-274-3975, ,
| | - Cassandra Papaleo
- Ithaca College, Department of Biology, 953 Danby Road, Ithaca, NY 14850 607-274-3975, ,
| | - Christopher W. Reid
- Bryant University, Science and Technology Department, 1150 Douglas Pike, Smithfield, RI 02917 401-232-6000,
| | - Joseph M. Bliss
- Women & Infants Hospital of Rhode Island, Warren Alpert Medical School of Brown University 100 Dudley Street, Providence, RI 02905, 401-274-1100,
| |
Collapse
|
18
|
Conde-Vela VM. The troglomorphic adaptations of Namanereidinae (Annelida, Nereididae) revisited, including a redescription of Namanereis cavernicola (Solís-Weiss & Espinasa, 1991), and a new Caribbean species of Namanereis Chamberlin, 1919. SUBTERRANEAN BIOLOGY 2017. [DOI: 10.3897/subtbiol.23.13701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
|
19
|
Chou CC, Martin-Martinez FJ, Qin Z, Dennis PB, Gupta MK, Naik RR, Buehler MJ. Ion Effect and Metal-Coordinated Cross-Linking for Multiscale Design of Nereis Jaw Inspired Mechanomutable Materials. ACS NANO 2017; 11:1858-1868. [PMID: 28165707 DOI: 10.1021/acsnano.6b07878] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The Nvjp-1 protein is a key component in the jaws of Nereis virens, a species of marine worm. It contains over 25 mol % of histidine, which is believed to play a key role in the metal-coordinated cross-linking responsible for the structural stability and exceptional mechanical performance of the worm jaw. Understanding the nanoscale mechanism behind this cross-linking and its pathway in affecting the macroscopic mechanical behavior of the material is crucial to develop bioinspired mechanomutable materials based on Nvjp-1. Here, we use a combination of multiscale modeling and experimental synthesis to understand the behavior of this heterologous-expressed protein from the nano- to the macroscale. We have built a bottom-up molecular-based model, which includes electronic-based density functional theory calculations, atomistic simulation of the nanoscale properties with replica exchange molecular dynamics, and an elastic network model for describing the macroscale behavior at different pHs. This multiscale modeling supports the experimental synthesis of a photo-cross-linked Nvjp-1 hydrogel by proving both the nanoscale mechanisms and mechanical behavior predictions. Our theoretical results agree well with the experimental observations, showing that Nvjp-1 forms a more compact structure in the presence of Zn2+ ions with a suitable pH environment, leading to the formation of more stable intramolecular metal-coordinated cross-links. These metal-coordinated cross-links induce nanoscale aggregation of Nvjp-1, which is responsible for the hydrogel contraction observed in experiments and predicted by the model.
Collapse
Affiliation(s)
- Chia-Ching Chou
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Francisco J Martin-Martinez
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Zhao Qin
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Patrick B Dennis
- Air Force Research Laboratory, Materials and Manufacturing Directorate , Wright-Patterson AFB, Ohio 45433, United States
| | - Maneesh K Gupta
- Air Force Research Laboratory, Materials and Manufacturing Directorate , Wright-Patterson AFB, Ohio 45433, United States
| | - Rajesh R Naik
- Air Force Research Laboratory, Materials and Manufacturing Directorate , Wright-Patterson AFB, Ohio 45433, United States
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
20
|
Hiew SH, Guerette PA, Zvarec OJ, Phillips M, Zhou F, Su H, Pervushin K, Orner BP, Miserez A. Modular peptides from the thermoplastic squid sucker ring teeth form amyloid-like cross-β supramolecular networks. Acta Biomater 2016; 46:41-54. [PMID: 27693688 DOI: 10.1016/j.actbio.2016.09.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 09/23/2016] [Accepted: 09/28/2016] [Indexed: 12/22/2022]
Abstract
The hard sucker ring teeth (SRT) from decapodiforme cephalopods, which are located inside the sucker cups lining the arms and tentacles of these species, have recently emerged as a unique model structure for biomimetic structural biopolymers. SRT are entirely composed of modular, block co-polymer-like proteins that self-assemble into a large supramolecular network. In order to unveil the molecular principles behind SRT's self-assembly and robustness, we describe a combinatorial screening assay that maps the molecular-scale interactions between the most abundant modular peptide blocks of suckerin proteins. By selecting prominent interaction hotspots from this assay, we identified four peptides that exhibited the strongest homo-peptidic interactions, and conducted further in-depth biophysical characterizations complemented by molecular dynamic (MD) simulations to investigate the nature of these interactions. Circular Dichroism (CD) revealed conformations that transitioned from semi-extended poly-proline II (PII) towards β-sheet structure. The peptides spontaneously self-assembled into microfibers enriched with cross β-structures, as evidenced by Fourier-Transform Infrared Spectroscopy (FTIR) and Congo red staining. Nuclear Magnetic Resonance (NMR) experiments identified the residues involved in the hydrogen-bonded network and demonstrated that these self-assembled β-sheet-based fibers exhibit high protection factors that bear resemblance to amyloids. The high stability of the β-sheet network and an amyloid-like model of fibril assembly were supported by MD simulations. The work sheds light on how Nature has evolved modular sequence design for the self-assembly of mechanically robust functional materials, and expands our biomolecular toolkit to prepare load-bearing biomaterials from protein-based block co-polymers and self-assembled peptides. STATEMENT OF SIGNIFICANCE The sucker ring teeth (SRT) located on the arms and tentacles of cephalopods represent as a very promising protein-based biopolymer with the potential to rival silk in biomedical and engineering applications. SRT are made of modular, block co-polymer like proteins (suckerins), which assemble into a semicrystalline polymer reinforced by nano-confined β-sheets, resulting in a supramolecular network with mechanical properties that match those of the strongest engineering polymers. In this study, we aimed to understand the molecular mechanisms behind SRT's self-assembly and robustness. The most abundant modular peptidic blocks of suckerin proteins were studied by various spectroscopic methods, which demonstrate that SRT peptides form amyloid-like cross-β structures.
Collapse
|
21
|
Liu C, Xie L, Zhang R. Ca2+ Mediates the Self-Assembly of the Foot Proteins of Pinctada fucata from the Nanoscale to the Microscale. Biomacromolecules 2016; 17:3347-3355. [DOI: 10.1021/acs.biomac.6b01125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chuang Liu
- Institute
of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084 China
- Tsinghua-Peking
Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084 China
| | - Liping Xie
- Institute
of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084 China
| | - Rongqing Zhang
- Institute
of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084 China
- Department
of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang Province 314006, China
| |
Collapse
|
22
|
Mozhdehi D, Neal JA, Grindy SC, Cordeau Y, Ayala S, Holten-Andersen N, Guan Z. Tuning Dynamic Mechanical Response in Metallopolymer Networks through Simultaneous Control of Structural and Temporal Properties of the Networks. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01626] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Davoud Mozhdehi
- Department
of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - James A. Neal
- Department
of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Scott C. Grindy
- Department
of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yves Cordeau
- Department
of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Sergio Ayala
- Department
of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Niels Holten-Andersen
- Department
of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Zhibin Guan
- Department
of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| |
Collapse
|
23
|
Hiew SH, Miserez A. Squid Sucker Ring Teeth: Multiscale Structure-Property Relationships, Sequencing, and Protein Engineering of a Thermoplastic Biopolymer. ACS Biomater Sci Eng 2016; 3:680-693. [PMID: 33440495 DOI: 10.1021/acsbiomaterials.6b00284] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The arms and tentacles of Decapodiform cephalopods (squids and cuttlefish) are lined with suckers, each of which contains embedded sucker ring teeth (SRT), which are used by the animal for prey capture and handling. SRT exhibit intriguing physicochemical and thermomechanical characteristics that have so far not been observed in other protein-based biomaterials. Notably, despite their comparatively high mechanical properties, SRT are almost fully soluble in chaotropic solvents and can be readily reconstituted after solvent evaporation into three-dimensional structures. SRT also exhibit thermoplastic characteristics: they can be melted and reshaped multiple times with no-or only minimal-loss of mechanical performance postprocessing. Intrigued by these unusual material characteristics, in recent years, we have conducted in-depth fundamental studies to unveil structure/property relationships of SRT from the molecular (genetic) level to the macroscopic scale. These investigations have demonstrated that SRT are entirely assembled from a protein family called "suckerins" that self-assemble into semicrystalline polymer infinite networks. Suckerins are block copolymers at the molecular level, whose closest analogy appears to be silk fibroins, although significant differences exist between these two protein families. Parallel to these studies, there have been efforts to mimic and engineer suckerins by protein engineering and to demonstrate potential applications through proof-of-concept studies, with a focus on the biomedical field. Both fundamental aspects and emerging applications are presented in this short review. Given the rather unusual source of this model structure, we start by a brief historical account of SRT and suckerin discovery.
Collapse
Affiliation(s)
- Shu Hui Hiew
- School of Material Science and Engineering and ‡Center for Biomimetic Sensor Science, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 639798
| | - Ali Miserez
- School of Material Science and Engineering and Center for Biomimetic Sensor Science, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 639798
| |
Collapse
|
24
|
Degtyar E, Mlynarczyk B, Fratzl P, Harrington MJ. Recombinant engineering of reversible cross-links into a resilient biopolymer. POLYMER 2015. [DOI: 10.1016/j.polymer.2015.03.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
25
|
Uyeno TA, Kier WM. The structure and function of a muscle articulation-type jaw joint of a polychaete worm. J Morphol 2014; 276:403-14. [PMID: 25503370 DOI: 10.1002/jmor.20349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 10/21/2014] [Accepted: 11/18/2014] [Indexed: 11/08/2022]
Abstract
The arrangement of the musculature and the fibers of the extracellular matrix (ECM) in the flexible jaw joint of the sandworm Alitta virens (Annelida, Polychaeta) was studied using dissection and histology. The jaws are capable of a wide range of motions principally related to defense and feeding. The left and right jaws are embedded in and moved by a compact pharyngeal bulb of muscle and ECM that also forms the mouth and esophagus. Eight pharyngeal bulbs were removed and dissected to document gross anatomical features or preserved and embedded in plastic for sectioning in multiple planes. The sections were stained with toluidine blue and basic fuchsin to differentiate muscle and ECM. The sections were then digitized and used to develop a three-dimensional computer illustration. We hypothesize that the muscle and fibers in the ECM are arranged as a muscular hydrostat to support the movement of the jaws. Four specimens were recorded using a digital video camera and a tank with an angled mirror to record lateral and ventral views of jaw movements during locomotion and biting associated with burrow guarding and feeding. Frame by frame kinematic analysis of this video showed that the jaws move symmetrically in a roughly horizontal plane. Although the angle between the jaws increases and then decreases after maximum gape has been reached, the jaws also translate relative to each other such that the axis of rotation is not fixed. Together, these functional morphological and behavioral data identify the jaw mechanism as a flexible joint known as a muscle articulation. As muscle articulations have been previously described only in the beaks of cephalopods and flatworms, this study implies that this type of joint is more common and important than previously recognized.
Collapse
Affiliation(s)
- Theodore A Uyeno
- Department of Biology, University of North Carolina at Chapel Hill, CB #3280, Coker Hall, Chapel Hill, North Carolina, 27599 3280
| | | |
Collapse
|
26
|
Degtyar E, Harrington MJ, Politi Y, Fratzl P. Die Bedeutung von Metallionen für die mechanischen Eigenschaften von Biomaterialien auf Proteinbasis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
27
|
Degtyar E, Harrington MJ, Politi Y, Fratzl P. The Mechanical Role of Metal Ions in Biogenic Protein-Based Materials. Angew Chem Int Ed Engl 2014; 53:12026-44. [DOI: 10.1002/anie.201404272] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Indexed: 12/23/2022]
|
28
|
Hwang DS, Masic A, Prajatelistia E, Iordachescu M, Waite JH. Marine hydroid perisarc: a chitin- and melanin-reinforced composite with DOPA-iron(III) complexes. Acta Biomater 2013; 9:8110-7. [PMID: 23791678 DOI: 10.1016/j.actbio.2013.06.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 06/07/2013] [Accepted: 06/10/2013] [Indexed: 10/26/2022]
Abstract
Many marine invertebrates utilize biomacromolecules as building blocks to form their load-bearing tissues. These polymeric tissues are appealing for their unusual physical and mechanical properties, including high hardness and stiffness, toughness and low density. Here, a marine hydroid perisarc of Aglaophenia latirostris was investigated to understand how nature designs a stiff, tough and lightweight sheathing structure. Chitin, protein and a melanin-like pigment, were found to represent 10, 17 and 60 wt.% of the perisarc, respectively. Interestingly, similar to the adhesive and coating of marine mussel byssus, a DOPA (3,4-dihydroxyphenylalanine) containing protein and iron were detected in the perisarc. Resonance Raman microprobe analysis of perisarc indicates the presence of catechol-iron(III) complexes in situ, but it remains to be determined whether the DOPA-iron(III) interaction plays a cohesive role in holding the protein, chitin and melanin networks together.
Collapse
|
29
|
Lapidot S, Meirovitch S, Sharon S, Heyman A, Kaplan DL, Shoseyov O. Clues for biomimetics from natural composite materials. Nanomedicine (Lond) 2012; 7:1409-23. [PMID: 22994958 PMCID: PMC3567446 DOI: 10.2217/nnm.12.107] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bio-inspired material systems are derived from different living organisms such as plants, arthropods, mammals and marine organisms. These biomaterial systems from nature are always present in the form of composites, with molecular-scale interactions optimized to direct functional features. With interest in replacing synthetic materials with natural materials due to biocompatibility, sustainability and green chemistry issues, it is important to understand the molecular structure and chemistry of the raw component materials to also learn from their natural engineering, interfaces and interactions leading to durable and highly functional material architectures. This review will focus on applications of biomaterials in single material forms, as well as biomimetic composites inspired by natural organizational features. Examples of different natural composite systems will be described, followed by implementation of the principles underlying their composite organization into artificial bio-inspired systems for materials with new functional features for future medicine.
Collapse
Affiliation(s)
- Shaul Lapidot
- The Robert H. Smith Faculty of Agriculture, Food & Environment, the Hebrew University of Jerusalem, Israel
| | - Sigal Meirovitch
- The Robert H. Smith Faculty of Agriculture, Food & Environment, the Hebrew University of Jerusalem, Israel
| | - Sigal Sharon
- The Robert H. Smith Faculty of Agriculture, Food & Environment, the Hebrew University of Jerusalem, Israel
| | - Arnon Heyman
- The Robert H. Smith Faculty of Agriculture, Food & Environment, the Hebrew University of Jerusalem, Israel
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Oded Shoseyov
- The Robert H. Smith Faculty of Agriculture, Food & Environment, the Hebrew University of Jerusalem, Israel
| |
Collapse
|
30
|
Hardness in arthropod exoskeletons in the absence of transition metals. Acta Biomater 2010; 6:3152-6. [PMID: 20152944 DOI: 10.1016/j.actbio.2010.02.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 01/27/2010] [Accepted: 02/03/2010] [Indexed: 11/24/2022]
Abstract
The arthropod cuticle is a remarkable and versatile biological material commonly composed of chitin and proteins. Lessons can be learned from the way it is adapted to fit its functions. The larval jewel beetle, Pseudotaenia frenchi, demonstrates hardness in the cutting edge of the mandibles in excess of the mineralized carapace of stone crabs and compares favourably with some stainless steels. Yet this is a form of cuticle which is devoid of transition metals or mineralization. In seeming contradiction, the similarly dark coloured adult beetle mandibles contain the transition metal manganese, but are significantly softer. Energy dispersive X-ray analysis and infrared spectroscopy have been used to investigate the differences in composition of mandible cuticle of the adult and larval beetles.
Collapse
|
31
|
On computational approaches for size-and-shape distributions from sedimentation velocity analytical ultracentrifugation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:1261-75. [PMID: 19806353 PMCID: PMC2892069 DOI: 10.1007/s00249-009-0545-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 09/08/2009] [Accepted: 09/14/2009] [Indexed: 11/06/2022]
Abstract
Sedimentation velocity analytical ultracentrifugation has become a very popular technique to study size distributions and interactions of macromolecules. Recently, a method termed two-dimensional spectrum analysis (2DSA) for the determination of size-and-shape distributions was described by Demeler and colleagues (Eur Biophys J 2009). It is based on novel ideas conceived for fitting the integral equations of the size-and-shape distribution to experimental data, illustrated with an example but provided without proof of the principle of the algorithm. In the present work, we examine the 2DSA algorithm by comparison with the mathematical reference frame and simple well-known numerical concepts for solving Fredholm integral equations, and test the key assumptions underlying the 2DSA method in an example application. While the 2DSA appears computationally excessively wasteful, key elements also appear to be in conflict with mathematical results. This raises doubts about the correctness of the results from 2DSA analysis.
Collapse
|
32
|
Srivastava A, Holten-Andersen N, Stucky GD, Waite JH. Ragworm Jaw-Inspired Metal Ion Cross-Linking for Improved Mechanical Properties of Polymer Blends. Biomacromolecules 2008; 9:2873-80. [DOI: 10.1021/bm8006659] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aasheesh Srivastava
- Materials Research Laboratory and Graduate Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106
| | - Niels Holten-Andersen
- Materials Research Laboratory and Graduate Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106
| | - Galen D. Stucky
- Materials Research Laboratory and Graduate Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106
| | - J. Herbert Waite
- Materials Research Laboratory and Graduate Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106
| |
Collapse
|