1
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Weißheit S, Kuttich B, Vogel M, Thiele CM. Elastin-Like Peptide as a Model for Disordered Proteins: Diffusion Behaviour in Self-Crowding Conditions. Chemphyschem 2024; 25:e202400117. [PMID: 38511646 DOI: 10.1002/cphc.202400117] [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: 02/02/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 03/22/2024]
Abstract
Despite the current high interest, there is limited information on diffusion data for intrinsically disordered proteins (IDPs). This study investigates the effect of crowding on the diffusion behaviour of an elastin-like peptide (ELP), by combined pulse field gradient (PFG) and static field gradient (SFG) NMR techniques. We interpret our findings in terms of highly dynamic chain assemblies with weak interactions, resulting in ELP diffusion that is primarily governed by the viscous flow of the solvent. The diffusion behaviour of the peptide appears to resemble that of globular proteins rather than flexible linear polymers over a wide concentration range.
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Affiliation(s)
- Susann Weißheit
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Peter-Grünberg-Straße 16, 64287, Darmstadt, Germany
| | - Björn Kuttich
- Institut für Physik Kondensierter Materie, Technische Universität Darmstadt, Hochschulstr. 6, 64289, Darmstadt, Germany
| | - Michael Vogel
- Institut für Physik Kondensierter Materie, Technische Universität Darmstadt, Hochschulstr. 6, 64289, Darmstadt, Germany
| | - Christina Marie Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Peter-Grünberg-Straße 16, 64287, Darmstadt, Germany
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2
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Nawaz T, Gu L, Gibbons J, Hu Z, Zhou R. Bridging Nature and Engineering: Protein-Derived Materials for Bio-Inspired Applications. Biomimetics (Basel) 2024; 9:373. [PMID: 38921253 PMCID: PMC11201842 DOI: 10.3390/biomimetics9060373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
The sophisticated, elegant protein-polymers designed by nature can serve as inspiration to redesign and biomanufacture protein-based materials using synthetic biology. Historically, petro-based polymeric materials have dominated industrial activities, consequently transforming our way of living. While this benefits humans, the fabrication and disposal of these materials causes environmental sustainability challenges. Fortunately, protein-based biopolymers can compete with and potentially surpass the performance of petro-based polymers because they can be biologically produced and degraded in an environmentally friendly fashion. This paper reviews four groups of protein-based polymers, including fibrous proteins (collagen, silk fibroin, fibrillin, and keratin), elastomeric proteins (elastin, resilin, and wheat glutenin), adhesive/matrix proteins (spongin and conchiolin), and cyanophycin. We discuss the connection between protein sequence, structure, function, and biomimetic applications. Protein engineering techniques, such as directed evolution and rational design, can be used to improve the functionality of natural protein-based materials. For example, the inclusion of specific protein domains, particularly those observed in structural proteins, such as silk and collagen, enables the creation of novel biomimetic materials with exceptional mechanical properties and adaptability. This review also discusses recent advancements in the production and application of new protein-based materials through the approach of synthetic biology combined biomimetics, providing insight for future research and development of cutting-edge bio-inspired products. Protein-based polymers that utilize nature's designs as a base, then modified by advancements at the intersection of biology and engineering, may provide mankind with more sustainable products.
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Affiliation(s)
- Taufiq Nawaz
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA;
| | - Liping Gu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA;
| | | | - Zhong Hu
- Department of Mechanical Engineering, South Dakota State University, Brookings, SD 57007, USA;
| | - Ruanbao Zhou
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA;
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3
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Lau K, Reichheld S, Xian M, Sharpe SJ, Cerruti M. Directed Assembly of Elastic Fibers via Coacervate Droplet Deposition on Electrospun Templates. Biomacromolecules 2024; 25:3519-3531. [PMID: 38742604 DOI: 10.1021/acs.biomac.4c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Elastic fibers provide critical elasticity to the arteries, lungs, and other organs. Elastic fiber assembly is a process where soluble tropoelastin is coacervated into liquid droplets, cross-linked, and deposited onto and into microfibrils. While much progress has been made in understanding the biology of this process, questions remain regarding the timing of interactions during assembly. Furthermore, it is unclear to what extent fibrous templates are needed to guide coacervate droplets into the correct architecture. The organization and shaping of coacervate droplets onto a fiber template have never been previously modeled or employed as a strategy for shaping elastin fiber materials. Using an in vitro system consisting of elastin-like polypeptides (ELPs), genipin cross-linker, electrospun polylactic-co-glycolic acid (PLGA) fibers, and tannic acid surface coatings for fibers, we explored ELP coacervation, cross-linking, and deposition onto fiber templates. We demonstrate that integration of coacervate droplets into a fibrous template is primarily influenced by two factors: (1) the balance of coacervation and cross-linking and (2) the surface energy of the fiber templates. The success of this integration affects the mechanical properties of the final fiber network. Our resulting membrane materials exhibit highly tunable morphologies and a range of elastic moduli (0.8-1.6 MPa) comparable to native elastic fibers.
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Affiliation(s)
- Kirklann Lau
- Department of Mining and Materials Engineering, McGill University, 3610 University Street, Wong Building 2250, Montreal, Quebec H3A 0C5, Canada
| | - Sean Reichheld
- Molecular Medicine, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay Street, Room 20.9714, Toronto, Ontario M5G 1X8, Canada
| | - Mingqian Xian
- Department of Mining and Materials Engineering, McGill University, 3610 University Street, Wong Building 2250, Montreal, Quebec H3A 0C5, Canada
| | - Simon J Sharpe
- Molecular Medicine, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay Street, Room 20.9714, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 5207, Toronto, Ontario M5S 1A8, Canada
| | - Marta Cerruti
- Department of Mining and Materials Engineering, McGill University, 3610 University Street, Wong Building 2250, Montreal, Quebec H3A 0C5, Canada
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4
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Tang NC, Su JC, Shmidov Y, Kelly G, Deshpande S, Sirohi P, Peterson N, Chilkoti A. Synthetic intrinsically disordered protein fusion tags that enhance protein solubility. Nat Commun 2024; 15:3727. [PMID: 38697982 PMCID: PMC11066018 DOI: 10.1038/s41467-024-47519-7] [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: 08/22/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
We report the de novo design of small (<20 kDa) and highly soluble synthetic intrinsically disordered proteins (SynIDPs) that confer solubility to a fusion partner with minimal effect on the activity of the fused protein. To identify highly soluble SynIDPs, we create a pooled gene-library utilizing a one-pot gene synthesis technology to create a large library of repetitive genes that encode SynIDPs. We identify three small (<20 kDa) and highly soluble SynIDPs from this gene library that lack secondary structure and have high solvation. Recombinant fusion of these SynIDPs to three known inclusion body forming proteins rescue their soluble expression and do not impede the activity of the fusion partner, thereby eliminating the need for removal of the SynIDP tag. These findings highlight the utility of SynIDPs as solubility tags, as they promote the soluble expression of proteins in E. coli and are small, unstructured proteins that minimally interfere with the biological activity of the fused protein.
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Affiliation(s)
- Nicholas C Tang
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Jonathan C Su
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Yulia Shmidov
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Garrett Kelly
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Sonal Deshpande
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Parul Sirohi
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Nikhil Peterson
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
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5
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Chikunova A, Manley MP, Heijjer CN, Drenth CS, Cramer-Blok AJ, Ahmad MUD, Perrakis A, Ubbink M. Conserved proline residues prevent dimerization and aggregation in the β-lactamase BlaC. Protein Sci 2024; 33:e4972. [PMID: 38533527 DOI: 10.1002/pro.4972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Evolution leads to conservation of amino acid residues in protein families. Conserved proline residues are usually considered to ensure the correct folding and to stabilize the three-dimensional structure. Surprisingly, proline residues that are highly conserved in class A β-lactamases were found to tolerate various substitutions without large losses in enzyme activity. We investigated the roles of three conserved prolines at positions 107, 226, and 258 in the β-lactamase BlaC from Mycobacterium tuberculosis and found that mutations can lead to dimerization of the enzyme and an overall less stable protein that is prone to aggregate over time. For the variant Pro107Thr, the crystal structure shows dimer formation resembling domain swapping. It is concluded that the proline substitutions loosen the structure, enhancing multimerization. Even though the enzyme does not lose its properties without the conserved proline residues, the prolines ensure the long-term structural integrity of the enzyme.
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Affiliation(s)
- A Chikunova
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - M P Manley
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - C N Heijjer
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - C S Drenth
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - A J Cramer-Blok
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - M Ud Din Ahmad
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - A Perrakis
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - M Ubbink
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Department of Infectious Diseases, Imperial College, London, UK
- Zocdoc, New York City, New York, USA
- ZoBio BV, Leiden, The Netherlands
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6
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Depenveiller C, Baud S, Belloy N, Bochicchio B, Dandurand J, Dauchez M, Pepe A, Pomès R, Samouillan V, Debelle L. Structural and physical basis for the elasticity of elastin. Q Rev Biophys 2024; 57:e3. [PMID: 38501287 DOI: 10.1017/s0033583524000040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Elastin function is to endow vertebrate tissues with elasticity so that they can adapt to local mechanical constraints. The hydrophobicity and insolubility of the mature elastin polymer have hampered studies of its molecular organisation and structure-elasticity relationships. Nevertheless, a growing number of studies from a broad range of disciplines have provided invaluable insights, and several structural models of elastin have been proposed. However, many questions remain regarding how the primary sequence of elastin (and the soluble precursor tropoelastin) governs the molecular structure, its organisation into a polymeric network, and the mechanical properties of the resulting material. The elasticity of elastin is known to be largely entropic in origin, a property that is understood to arise from both its disordered molecular structure and its hydrophobic character. Despite a high degree of hydrophobicity, elastin does not form compact, water-excluding domains and remains highly disordered. However, elastin contains both stable and labile secondary structure elements. Current models of elastin structure and function are drawn from data collected on tropoelastin and on elastin-like peptides (ELPs) but at the tissue level, elasticity is only achieved after polymerisation of the mature elastin. In tissues, the reticulation of tropoelastin chains in water defines the polymer elastin that bears elasticity. Similarly, ELPs require polymerisation to become elastic. There is considerable interest in elastin especially in the biomaterials and cosmetic fields where ELPs are widely used. This review aims to provide an up-to-date survey of/perspective on current knowledge about the interplay between elastin structure, solvation, and entropic elasticity.
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Affiliation(s)
- Camille Depenveiller
- UMR URCA/CNRS 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UFR Sciences Exactes et Naturelles, SFR CAP Santé, Université de Reims Champagne-Ardenne, Reims, France
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, Amiens, France
| | - Stéphanie Baud
- UMR URCA/CNRS 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UFR Sciences Exactes et Naturelles, SFR CAP Santé, Université de Reims Champagne-Ardenne, Reims, France
| | - Nicolas Belloy
- UMR URCA/CNRS 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UFR Sciences Exactes et Naturelles, SFR CAP Santé, Université de Reims Champagne-Ardenne, Reims, France
| | - Brigida Bochicchio
- Laboratory of Bioinspired Materials, Department of Science, University of Basilicata, Potenza, Italy
| | - Jany Dandurand
- CIRIMAT UMR 5085, Université Paul Sabatier, Université de Toulouse, Toulouse, France
| | - Manuel Dauchez
- UMR URCA/CNRS 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UFR Sciences Exactes et Naturelles, SFR CAP Santé, Université de Reims Champagne-Ardenne, Reims, France
| | - Antonietta Pepe
- Laboratory of Bioinspired Materials, Department of Science, University of Basilicata, Potenza, Italy
| | - Régis Pomès
- Molecular Medicine, Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Valérie Samouillan
- CIRIMAT UMR 5085, Université Paul Sabatier, Université de Toulouse, Toulouse, France
| | - Laurent Debelle
- UMR URCA/CNRS 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UFR Sciences Exactes et Naturelles, SFR CAP Santé, Université de Reims Champagne-Ardenne, Reims, France
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7
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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8
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Basharat Z, Sattar S, Bahauddin AA, Al Mouslem AK, Alotaibi G. Screening Marine Microbial Metabolites as Promising Inhibitors of Borrelia garinii: A Structural Docking Approach towards Developing Novel Lyme Disease Treatment. BIOMED RESEARCH INTERNATIONAL 2024; 2024:9997082. [PMID: 38456098 PMCID: PMC10919988 DOI: 10.1155/2024/9997082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/26/2024] [Accepted: 02/13/2024] [Indexed: 03/09/2024]
Abstract
Lyme disease caused by the Borrelia species is a growing health concern in many parts of the world. Current treatments for the disease may have side effects, and there is also a need for new therapies that can selectively target the bacteria. Pathogens responsible for Lyme disease include B. burgdorferi, B. afzelii, and B. garinii. In this study, we employed structural docking-based screening to identify potential lead-like inhibitors against the bacterium. We first identified the core essential genome fraction of the bacterium, using 37 strains. Later, we screened a library of lead-like marine microbial metabolites (n = 4730) against the arginine deiminase (ADI) protein of Borrelia garinii. This protein plays a crucial role in the survival of the bacteria, and inhibiting it can kill the bacterium. The prioritized lead compounds demonstrating favorable binding energies and interactions with the active site of ADI were then evaluated for their drug-like and pharmacokinetic parameters to assess their suitability for development as drugs. Results from molecular dynamics simulation (100 ns) and other scoring parameters suggest that the compound CMNPD18759 (common name: aureobasidin; IUPAC name: 2-[(4R,6R)-4,6-dihydroxydecanoyl]oxypropan-2-yl (3S,5R)-3,5-dihydroxydecanoate) holds promise as a potential drug candidate for the treatment of Lyme disease, caused by B. garinii. However, further experimental studies are needed to validate the efficacy and safety of this compound in vivo.
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Affiliation(s)
| | - Sadia Sattar
- Molecular Virology Labs, Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Islamabad 45550, Pakistan
| | | | - Abdulaziz K. Al Mouslem
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al Ahsa 31982, Saudi Arabia
| | - Ghallab Alotaibi
- Department of Pharmacology, College of Pharmacy, Al-Dawadmi Campus, Shaqra University, Shaqra, Saudi Arabia
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9
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Zhang H, Lv S, Jin C, Ren F, Wang J. Wheat gluten amyloid fibrils: Conditions, mechanism, characterization, application, and future perspectives. Int J Biol Macromol 2023; 253:126435. [PMID: 37611682 DOI: 10.1016/j.ijbiomac.2023.126435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
Amyloid fibrils have excellent structural characteristics, such as a high aspect ratio, excellent stiffness, and a wide availability of functional groups on the surface. More studies are now focusing on the formation of amyloid fibrils using food proteins. Protein fibrillation is now becoming recognized as a promising strategy for enhancing the function of food proteins and expanding their range of applications. Wheat gluten is rich in glutamine (Q), hydrophobic amino acids, and the α-helix structure with high β-sheet tendency. These characteristics make it very easy for wheat gluten to form amyloid fibrils. The conditions, formation mechanism, characterization methods, and application of amyloid fibrils formed by wheat gluten are summarized in this review. Further exploration of amyloid fibrils formed by wheat gluten will reveal how they can play a significant role in food, biology, and other fields, especially in medicine.
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Affiliation(s)
- Huijuan Zhang
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Shihao Lv
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Chengming Jin
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Feiyue Ren
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Jing Wang
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China.
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10
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Mu X, Amouzandeh R, Vogts H, Luallen E, Arzani M. A brief review on the mechanisms and approaches of silk spinning-inspired biofabrication. Front Bioeng Biotechnol 2023; 11:1252499. [PMID: 37744248 PMCID: PMC10512026 DOI: 10.3389/fbioe.2023.1252499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Silk spinning, observed in spiders and insects, exhibits a remarkable biological source of inspiration for advanced polymer fabrications. Because of the systems design, silk spinning represents a holistic and circular approach to sustainable polymer fabrication, characterized by renewable resources, ambient and aqueous processing conditions, and fully recyclable "wastes." Also, silk spinning results in structures that are characterized by the combination of monolithic proteinaceous composition and mechanical strength, as well as demonstrate tunable degradation profiles and minimal immunogenicity, thus making it a viable alternative to most synthetic polymers for the development of advanced biomedical devices. However, the fundamental mechanisms of silk spinning remain incompletely understood, thus impeding the efforts to harness the advantageous properties of silk spinning. Here, we present a concise and timely review of several essential features of silk spinning, including the molecular designs of silk proteins and the solvent cues along the spinning apparatus. The solvent cues, including salt ions, pH, and water content, are suggested to direct the hierarchical assembly of silk proteins and thus play a central role in silk spinning. We also discuss several hypotheses on the roles of solvent cues to provide a relatively comprehensive analysis and to identify the current knowledge gap. We then review the state-of-the-art bioinspired fabrications with silk proteins, including fiber spinning and additive approaches/three-dimensional (3D) printing. An emphasis throughout the article is placed on the universal characteristics of silk spinning developed through millions of years of individual evolution pathways in spiders and silkworms. This review serves as a stepping stone for future research endeavors, facilitating the in vitro recapitulation of silk spinning and advancing the field of bioinspired polymer fabrication.
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Affiliation(s)
- Xuan Mu
- Roy J. Carver Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA, United States
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11
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Heckenhauer J, Stewart RJ, Ríos-Touma B, Powell A, Dorji T, Frandsen PB, Pauls SU. Characterization of the primary structure of the major silk gene, h-fibroin, across caddisfly (Trichoptera) suborders. iScience 2023; 26:107253. [PMID: 37529107 PMCID: PMC10387566 DOI: 10.1016/j.isci.2023.107253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/05/2023] [Accepted: 06/27/2023] [Indexed: 08/03/2023] Open
Abstract
Larvae of caddisflies (Trichoptera) produce silk to build various underwater structures allowing them to exploit a wide range of aquatic environments. The silk adheres to various substrates underwater and has high tensile strength, extensibility, and toughness and is of interest as a model for biomimetic adhesives. As a step toward understanding how the properties of underwater silk evolved in Trichoptera, we used genomic data to identify full-length sequences and characterize the primary structure of the major silk protein, h-fibroin, across the order. The h-fibroins have conserved termini and basic motif structure with high variation in repeating modules and variation in the percentage of amino acids, mainly proline. This finding might be linked to differences in mechanical properties related to the different silk usage and sets a starting point for future studies to screen and correlate amino acid motifs and other sequence features with quantifiable silk properties.
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Affiliation(s)
- Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Hesse 60325, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Hesse 60325, Germany
| | - Russell J. Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Blanca Ríos-Touma
- Facultad de Ingenierías y Ciencias Aplicadas, Ingeniería Ambiental, Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de Las Américas, Quito, EC 170124, Ecuador
| | - Ashlyn Powell
- Department of Plant and Wildlife Science, Brigham Young University, Provo, UT 84602, USA
| | - Tshering Dorji
- Department of Environment and Climate Studies, Royal University of Bhutan, Punakha 13001, Bhutan
| | - Paul B. Frandsen
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Hesse 60325, Germany
- Department of Plant and Wildlife Science, Brigham Young University, Provo, UT 84602, USA
- Data Science Lab, Smithsonian Institution, Washington, DC 20560, USA
| | - Steffen U. Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Hesse 60325, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Hesse 60325, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Gießen, Hesse 35392; Germany
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12
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Guo G, Wang X, Zhang Y, Li T. Sequence variations of phase-separating proteins and resources for studying biomolecular condensates. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1119-1132. [PMID: 37464880 PMCID: PMC10423696 DOI: 10.3724/abbs.2023131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/06/2023] [Indexed: 07/20/2023] Open
Abstract
Phase separation (PS) is an important mechanism underlying the formation of biomolecular condensates. Physiological condensates are associated with numerous biological processes, such as transcription, immunity, signaling, and synaptic transmission. Changes in particular amino acids or segments can disturb the protein's phase behavior and interactions with other biomolecules in condensates. It is thus presumed that variations in the phase-separating-prone domains can significantly impact the properties and functions of condensates. The dysfunction of condensates contributes to a number of pathological processes. Pharmacological perturbation of these condensates is proposed as a promising way to restore physiological states. In this review, we characterize the variations observed in PS proteins that lead to aberrant biomolecular compartmentalization. We also showcase recent advancements in bioinformatics of membraneless organelles (MLOs), focusing on available databases useful for screening PS proteins and describing endogenous condensates, guiding researchers to seek the underlying pathogenic mechanisms of biomolecular condensates.
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Affiliation(s)
- Gaigai Guo
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Xinxin Wang
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Yi Zhang
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Tingting Li
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
- Key Laboratory for NeuroscienceMinistry of Education/National Health Commission of ChinaPeking UniversityBeijing100191China
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13
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Liang Y, Song J, Wang J, Liu H, Wu X, He B, Zhang X, Wang J. Investigating the Effects of NaCl on the Formation of AFs from Gluten in Cooked Wheat Noodles. Int J Mol Sci 2023; 24:9907. [PMID: 37373055 DOI: 10.3390/ijms24129907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/23/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
To clarify the effect of NaCl concentration (0-2.0%) on the formation of amyloid fibrils (AFs) in cooked wheat noodles, the morphology, surface hydrophobicity, secondary structure, molecular weight distribution, microstructure, and crystal structure of AFs were investigated in this paper. Fluorescence data and Congo red stain images confirmed the presence of AFs and revealed that the 0.4% NaCl concentration promoted the production of AFs. The surface hydrophobicity results showed that the hydrophobicity of AFs increased significantly from 3942.05 to 6117.57 when the salt concentration increased from 0 to 0.4%, indicating that hydrophobic interactions were critical for the formation of AFs. Size exclusion chromatography combined with gel electrophoresis plots showed that the effect of NaCl on the molecular weight of AFs was small and mainly distributed in the range of 5-7.1 KDa (equivalent to 40-56 amino acid residues). X-ray diffraction and AFM images showed that the 0.4% NaCl concentration promoted the formation and longitudinal growth of AFs, while higher NaCl concentrations inhibited the formation and expansion of AFs. This study contributes to the understanding of the mechanism of AF formation in wheat flour processing and provides new insight into wheat gluten aggregation behavior.
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Affiliation(s)
- Ying Liang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jiayang Song
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jiayi Wang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Hao Liu
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Xingquan Wu
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Baoshan He
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Xia Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jinshui Wang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
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14
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Dayani L, Aliomrani M, Hashempour H, Varshosaz J, Sadeghi Dinani M, Taheri A. Cyclotide Nanotubes as a Novel Potential Drug-Delivery System: Characterization and Biocompatibility. Int J Pharm 2023:123104. [PMID: 37277089 DOI: 10.1016/j.ijpharm.2023.123104] [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: 04/05/2023] [Revised: 05/29/2023] [Accepted: 06/01/2023] [Indexed: 06/07/2023]
Abstract
Cyclotides are a class of cyclic peptides that can be self-assembled. This study aimed to discover the properties of cyclotide nanotubes. We performed differential scanning calorimetric (DSC) to characterize their properties. Then, we incorporated the coumarin as a probe and identified the morphology of nanostructures. The stability of cyclotide nanotubes after 3 months of keeping at -20 °C was determined by field emission scanning electron microscopy (FESEM). The cytocompatibility of cyclotide nanotubes was evaluated on peripheral blood mononuclear cells. In vivo, studies were also conducted on female C57BL/6 mice by intraperitoneally administration of nanotubes at 5, 50, and 100 mg/kg doses. Blood sampling was done before and 24 h after nanotube administration and complete blood count tests were conducted. DSC thermogram showed that the cyclotide nanotubes were stable after heating until 200 °C. Fluorescence microscopy images proved that the self-assembled structures of cyclotide can encapsulate the coumarin. FESEM proved that these nanotubes were stable even after 3 months. The results of the cytotoxicity assay and in-vivo study confirmed that these novel prepared nanotubes were biocompatible. These results suggested that the cyclotide nanotubes could be considered as a new carrier in biological fields while they are biocompatible.
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Affiliation(s)
- Ladan Dayani
- Department of Pharmaceutics, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Mehdi Aliomrani
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Hossein Hashempour
- Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran.
| | - Jaleh Varshosaz
- Department of Pharmaceutics, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Pharmaceutics, Faculty of Pharmacy and Novel Drug Delivery Systems Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Masoud Sadeghi Dinani
- Department of Pharmacognosy, School of pharmacy and pharmaceutical sciences, Isfahan University of medical sciences, Isfahan, Iran.
| | - Azade Taheri
- Department of Pharmaceutics, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Pharmaceutics, Faculty of Pharmacy and Novel Drug Delivery Systems Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
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15
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Vendruscolo M, Fuxreiter M. Towards sequence-based principles for protein phase separation predictions. Curr Opin Chem Biol 2023; 75:102317. [PMID: 37207400 DOI: 10.1016/j.cbpa.2023.102317] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/21/2023]
Abstract
The phenomenon of protein phase separation, which underlies the formation of biomolecular condensates, has been associated with numerous cellular functions. Recent studies indicate that the amino acid sequences of most proteins may harbour not only the code for folding into the native state but also for condensing into the liquid-like droplet state and the solid-like amyloid state. Here we review the current understanding of the principles for sequence-based methods for predicting the propensity of proteins for phase separation. A guiding concept is that entropic contributions are generally more important to stabilise the droplet state than they are for the native and amyloid states. Although estimating these entropic contributions has proven difficult, we describe some progress that has been recently made in this direction. To conclude, we discuss the challenges ahead to extend sequence-based prediction methods of protein phase separation to include quantitative in vivo characterisations of this process.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, PD 35131, Italy; Department of Physics and Astronomy, University of Padova, PD 35131, Italy.
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16
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Dai Y, You L, Chilkoti A. Engineering synthetic biomolecular condensates. NATURE REVIEWS BIOENGINEERING 2023; 1:1-15. [PMID: 37359769 PMCID: PMC10107566 DOI: 10.1038/s44222-023-00052-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/06/2023] [Indexed: 06/28/2023]
Abstract
The concept of phase-separation-mediated formation of biomolecular condensates provides a new framework to understand cellular organization and cooperativity-dependent cellular functions. With growing understanding of how biological systems drive phase separation and how cellular functions are encoded by biomolecular condensates, opportunities have emerged for cellular control through engineering of synthetic biomolecular condensates. In this Review, we discuss how to construct synthetic biomolecular condensates and how they can regulate cellular functions. We first describe the fundamental principles by which biomolecular components can drive phase separation. Next, we discuss the relationship between the properties of condensates and their cellular functions, which informs the design of components to create programmable synthetic condensates. Finally, we describe recent applications of synthetic biomolecular condensates for cellular control and discuss some of the design considerations and prospective applications.
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Affiliation(s)
- Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC USA
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17
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Trębacz H, Barzycka A. Mechanical Properties and Functions of Elastin: An Overview. Biomolecules 2023; 13:biom13030574. [PMID: 36979509 PMCID: PMC10046833 DOI: 10.3390/biom13030574] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/08/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Human tissues must be elastic, much like other materials that work under continuous loads without losing functionality. The elasticity of tissues is provided by elastin, a unique protein of the extracellular matrix (ECM) of mammals. Its function is to endow soft tissues with low stiffness, high and fully reversible extensibility, and efficient elastic-energy storage. Depending on the mechanical functions, the amount and distribution of elastin-rich elastic fibers vary between and within tissues and organs. The article presents a concise overview of the mechanical properties of elastin and its role in the elasticity of soft tissues. Both the occurrence of elastin and the relationship between its spatial arrangement and mechanical functions in a given tissue or organ are overviewed. As elastin in tissues occurs only in the form of elastic fibers, the current state of knowledge about their mechanical characteristics, as well as certain aspects of degradation of these fibers and their mechanical performance, is presented. The overview also outlines the latest understanding of the molecular basis of unique physical characteristics of elastin and, in particular, the origin of the driving force of elastic recoil after stretching.
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Affiliation(s)
- Hanna Trębacz
- Department of Biophysics, Medical University of Lublin, Al. Racławickie 1, 20-059 Lublin, Poland
| | - Angelika Barzycka
- Department of Biophysics, Medical University of Lublin, Al. Racławickie 1, 20-059 Lublin, Poland
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18
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Miserez A, Yu J, Mohammadi P. Protein-Based Biological Materials: Molecular Design and Artificial Production. Chem Rev 2023; 123:2049-2111. [PMID: 36692900 PMCID: PMC9999432 DOI: 10.1021/acs.chemrev.2c00621] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [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.
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Affiliation(s)
- Ali Miserez
- Center
for Sustainable Materials (SusMat), School of Materials Science and
Engineering, Nanyang Technological University
(NTU), Singapore637553
- School
of Biological Sciences, NTU, Singapore637551
| | - Jing Yu
- Center
for Sustainable Materials (SusMat), School of Materials Science and
Engineering, Nanyang Technological University
(NTU), Singapore637553
- Institute
for Digital Molecular Analytics and Science (IDMxS), NTU, 50 Nanyang Avenue, Singapore637553
| | - Pezhman Mohammadi
- VTT
Technical Research Centre of Finland Ltd., Espoo, UusimaaFI-02044, Finland
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19
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Halsey G, Sinha D, Dhital S, Wang X, Vyavahare N. Role of elastic fiber degradation in disease pathogenesis. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166706. [PMID: 37001705 DOI: 10.1016/j.bbadis.2023.166706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023]
Abstract
Elastin is a crucial extracellular matrix protein that provides structural integrity to tissues. Crosslinked elastin and associated microfibrils, named elastic fiber, contribute to biomechanics by providing the elasticity required for proper function. During aging and disease, elastic fiber can be progressively degraded and since there is little elastin synthesis in adults, degraded elastic fiber is not regenerated. There is substantial evidence linking loss or damage of elastic fibers to the clinical manifestation and pathogenesis of a variety of diseases. Disruption of elastic fiber networks by hereditary mutations, aging, or pathogenic stimuli results in systemic ailments associated with the production of elastin degradation products, inflammatory responses, and abnormal physiology. Due to its longevity, unique mechanical properties, and widespread distribution in the body, elastic fiber plays a central role in homeostasis of various physiological systems. While pathogenesis related to elastic fiber degradation has been more thoroughly studied in elastic fiber rich tissues such as the vasculature and the lungs, even tissues containing relatively small quantities of elastic fibers such as the eyes or joints may be severely impacted by elastin degradation. Elastic fiber degradation is a common observation in certain hereditary, age, and specific risk factor exposure induced diseases representing a converging point of pathological clinical phenotypes which may also help explain the appearance of co-morbidities. In this review, we will first cover the role of elastic fiber degradation in the manifestation of hereditary diseases then individually explore the structural role and degradation effects of elastic fibers in various tissues and organ systems. Overall, stabilizing elastic fiber structures and repairing lost elastin may be effective strategies to reverse the effects of these diseases.
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Affiliation(s)
- Gregory Halsey
- Department of Bioengineering, Clemson University, SC 29634, United States of America
| | - Dipasha Sinha
- Department of Bioengineering, Clemson University, SC 29634, United States of America
| | - Saphala Dhital
- Department of Bioengineering, Clemson University, SC 29634, United States of America
| | - Xiaoying Wang
- Department of Bioengineering, Clemson University, SC 29634, United States of America
| | - Naren Vyavahare
- Department of Bioengineering, Clemson University, SC 29634, United States of America.
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20
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Mabuchi T, Kijima J, Yamashita Y, Miura E, Muraoka T. Coacervate Formation of Elastin-like Polypeptides in Explicit Aqueous Solution Using Coarse-Grained Molecular Dynamics Simulations. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c02195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Takuya Mabuchi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai, Miyagi980-8577, Japan
- Institute of Fluid Science, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai, Miyagi980-8577, Japan
| | - Junko Kijima
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai, Miyagi980-8577, Japan
| | - Yukino Yamashita
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho,
Koganei, Tokyo184-8588, Japan
| | - Erika Miura
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho,
Koganei, Tokyo184-8588, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho,
Koganei, Tokyo184-8588, Japan
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21
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Arguelles J, Baker RH, Perez-Rigueiro J, Guinea GV, Elices M, Hayashi CY. Relating spidroin motif prevalence and periodicity to the mechanical properties of major ampullate spider silks. J Comp Physiol B 2023; 193:25-36. [PMID: 36342510 PMCID: PMC9852138 DOI: 10.1007/s00360-022-01464-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 09/28/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]
Abstract
Spider dragline fibers exhibit incredible mechanical properties, outperforming many synthetic polymers in toughness assays, and possess desirable properties for medical and other human applications. These qualities make dragline fibers popular subjects for biomimetics research. The enormous diversity of spiders presents both an opportunity for the development of new bioinspired materials and a challenge for the identification of fundamental design principles, as the mechanical properties of dragline fibers show both intraspecific and interspecific variations. In this regard, the stress-strain curves of draglines from different species have been shown to be effectively compared by the α* parameter, a value derived from maximum-supercontracted silk fibers. To identify potential molecular mechanisms impacting α* values, here we analyze spider fibroin (spidroin) sequences of the Western black widow (Latrodectus hesperus) and the black and yellow garden spider (Argiope aurantia). This study serves as a primer for investigating the molecular properties of spidroins that underlie species-specific α* values. Initial findings are that while overall motif composition was similar between species, certain motifs and higher level periodicities of glycine-rich region lengths showed variation, notably greater distances between poly-A motifs in A. aurantia sequences. In addition to increased period lengths, A. aurantia spidroins tended to have an increased prevalence of charged and hydrophobic residues. These increases may impact the number and strength of hydrogen bond networks within fibers, which have been implicated in conformational changes and formation of nanocrystals, contributing to the greater extensibility of A. aurantia draglines compared to those of L. hesperus.
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Affiliation(s)
- Joseph Arguelles
- Division of Invertebrate Zoology and Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024 USA
| | - Richard H. Baker
- Division of Invertebrate Zoology and Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024 USA
| | - Jose Perez-Rigueiro
- Center for Biomedical Engineering (CTB), Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223 Madrid, Spain ,Centro de Investigatión Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain ,Departamento de Ciencia de Materiales, Universidad Politécnica de Madrid, ETSI Caminos, Canales y Peurtos, 28040 Madrid, Spain ,Biomaterials and Regenerative Medicine Group, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Calle Prof. Martín Lagos s/n, 28040 Madrid, Spain
| | - Gustavo V. Guinea
- Center for Biomedical Engineering (CTB), Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223 Madrid, Spain ,Centro de Investigatión Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain ,Departamento de Ciencia de Materiales, Universidad Politécnica de Madrid, ETSI Caminos, Canales y Peurtos, 28040 Madrid, Spain ,Biomaterials and Regenerative Medicine Group, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Calle Prof. Martín Lagos s/n, 28040 Madrid, Spain
| | - M. Elices
- Centro de Investigatión Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Cheryl Y. Hayashi
- Division of Invertebrate Zoology and Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024 USA
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22
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Otis JB, Sharpe S. Sequence Context and Complex Hofmeister Salt Interactions Dictate Phase Separation Propensity of Resilin-like Polypeptides. Biomacromolecules 2022; 23:5225-5238. [PMID: 36378745 DOI: 10.1021/acs.biomac.2c01027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Resilin is an elastic material found in insects with exceptional durability, resilience, and extensibility, making it a promising biomaterial for tissue engineering. The monomeric precursor, pro-resilin, undergoes thermo-responsive self-assembly through liquid-liquid phase separation (LLPS). Understanding the molecular details of this assembly process is critical to developing complex biomaterials. The present study investigates the interplay between the solvent, sequence syntax, structure, and dynamics in promoting LLPS of resilin-like-polypeptides (RLPs) derived from domains 1 and 3 of Drosophila melanogaster pro-resilin. NMR, UV-vis, and microscopy data demonstrate that while kosmotropic salts and low pH promote LLPS, the effects of chaotropic salts with increasing pH are more complex. Subtle variations between the repeating amino acid motifs of resilin domain 1 and domain 3 lead to significantly different salt and pH dependence of LLPS, with domain 3 sequence motifs more strongly favoring phase separation under most conditions. These findings provide new insight into the molecular drivers of RLP phase separation and the complex roles of both RLP sequence and solution composition in fine-tuning assembly conditions.
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Affiliation(s)
- James Brandt Otis
- Molecular Medicine, Hospital for Sick Children, 686 Bay St, Toronto, ONM5G 0A4, Canada.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ONM5S 1A8, Canada
| | - Simon Sharpe
- Molecular Medicine, Hospital for Sick Children, 686 Bay St, Toronto, ONM5G 0A4, Canada.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ONM5S 1A8, Canada
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23
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Rapid molecular diversification and homogenization of clustered major ampullate silk genes in Argiope garden spiders. PLoS Genet 2022; 18:e1010537. [PMID: 36508456 PMCID: PMC9779670 DOI: 10.1371/journal.pgen.1010537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/22/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022] Open
Abstract
The evolutionary diversification of orb-web weaving spiders is closely tied to the mechanical performance of dragline silk. This proteinaceous fiber provides the primary structural framework of orb web architecture, and its extraordinary toughness allows these structures to absorb the high energy of aerial prey impact. The dominant model of dragline silk molecular structure involves the combined function of two highly repetitive, spider-specific, silk genes (spidroins)-MaSp1 and MaSp2. Recent genomic studies, however, have suggested this framework is overly simplistic, and our understanding of how MaSp genes evolve is limited. Here we present a comprehensive analysis of MaSp structural and evolutionary diversity across species of Argiope (garden spiders). This genomic analysis reveals the largest catalog of MaSp genes found in any spider, driven largely by an expansion of MaSp2 genes. The rapid diversification of Argiope MaSp genes, located primarily in a single genomic cluster, is associated with profound changes in silk gene structure. MaSp2 genes, in particular, have evolved complex hierarchically organized repeat units (ensemble repeats) delineated by novel introns that exhibit remarkable evolutionary dynamics. These repetitive introns have arisen independently within the genus, are highly homogenized within a gene, but diverge rapidly between genes. In some cases, these iterated introns are organized in an alternating structure in which every other intron is nearly identical in sequence. We hypothesize that this intron structure has evolved to facilitate homogenization of the coding sequence. We also find evidence of intergenic gene conversion and identify a more diverse array of stereotypical amino acid repeats than previously recognized. Overall, the extreme diversification found among MaSp genes requires changes in the structure-function model of dragline silk performance that focuses on the differential use and interaction among various MaSp paralogs as well as the impact of ensemble repeat structure and different amino acid motifs on mechanical behavior.
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24
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Differences in the Elastomeric Behavior of Polyglycine-Rich Regions of Spidroin 1 and 2 Proteins. Polymers (Basel) 2022; 14:polym14235263. [PMID: 36501657 PMCID: PMC9738160 DOI: 10.3390/polym14235263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
Two different polyglycine-rich fragments were selected as representatives of major ampullate gland spidroins (MaSp) 1 and 2 types, and their behavior in a water-saturated environment was simulated within the framework of molecular dynamics (MD). The selected fragments are found in the sequences of the proteins MaSp1a and MaSp2.2a of Argiope aurantia with respective lengths of 36 amino acids (MaSp1a) and 50 amino acids (MaSp2.2s). The simulation took the fully extended β-pleated conformation as reference, and MD was used to determine the equilibrium configuration in the absence of external forces. Subsequently, MD were employed to calculate the variation in the distance between the ends of the fragments when subjected to an increasing force. Both fragments show an elastomeric behavior that can be modeled as a freely jointed chain with links of comparable length, and a larger number of links in the spidroin 2 fragment. It is found, however, that the maximum recovery force recorded from the spidroin 2 peptide (Fmax ≈ 400 pN) is found to be significantly larger than that of the spidroin 1 (Fmax ≈ 250 pN). The increase in the recovery force of the spidroin 2 polyglycine-rich fragment may be correlated with the larger values observed in the strain at breaking of major ampullate silk fibers spun by Araneoidea species, which contain spidroin 2 proteins, compared to the material produced by spider species that lack these spidroins (RTA-clade).
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25
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Sequence-Based Prediction of Protein Phase Separation: The Role of Beta-Pairing Propensity. Biomolecules 2022; 12:biom12121771. [PMID: 36551199 PMCID: PMC9775558 DOI: 10.3390/biom12121771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The formation of droplets of bio-molecular condensates through liquid-liquid phase separation (LLPS) of their component proteins is a key factor in the maintenance of cellular homeostasis. Different protein properties were shown to be important in LLPS onset, making it possible to develop predictors, which try to discriminate a positive set of proteins involved in LLPS against a negative set of proteins not involved in LLPS. On the other hand, the redundancy and multivalency of the interactions driving LLPS led to the suggestion that the large conformational entropy associated with non specific side-chain interactions is also a key factor in LLPS. In this work we build a LLPS predictor which combines the ability to form pi-pi interactions, with an unrelated feature, the propensity to stabilize the β-pairing interaction mode. The cross-β structure is formed in the amyloid aggregates, which are involved in degenerative diseases and may be the final thermodynamically stable state of protein condensates. Our results show that the combination of pi-pi and β-pairing propensity yields an improved performance. They also suggest that protein sequences are more likely to be involved in phase separation if the main chain conformational entropy of the β-pairing maintained droplet state is increased. This would stabilize the droplet state against the more ordered amyloid state. Interestingly, the entropic stabilization of the droplet state appears to proceed according to different mechanisms, depending on the fraction of "droplet-driving" proteins present in the positive set.
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26
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Horvath A, Vendruscolo M, Fuxreiter M. Sequence-based Prediction of the Cellular Toxicity Associated with Amyloid Aggregation within Protein Condensates. Biochemistry 2022; 61:2461-2469. [DOI: 10.1021/acs.biochem.2c00499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Attila Horvath
- John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Canberra2600, Australia
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, UK
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Padova, PD35131Italy
- Department of Physics and Astronomy, University of Padova, Padova, PD35131Italy
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Lee B, Jaberi-Lashkari N, Calo E. A unified view of low complexity regions (LCRs) across species. eLife 2022; 11:e77058. [PMID: 36098382 PMCID: PMC9470157 DOI: 10.7554/elife.77058] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Low complexity regions (LCRs) play a role in a variety of important biological processes, yet we lack a unified view of their sequences, features, relationships, and functions. Here, we use dotplots and dimensionality reduction to systematically define LCR type/copy relationships and create a map of LCR sequence space capable of integrating LCR features and functions. By defining LCR relationships across the proteome, we provide insight into how LCR type and copy number contribute to higher order assemblies, such as the importance of K-rich LCR copy number for assembly of the nucleolar protein RPA43 in vivo and in vitro. With LCR maps, we reveal the underlying structure of LCR sequence space, and relate differential occupancy in this space to the conservation and emergence of higher order assemblies, including the metazoan extracellular matrix and plant cell wall. Together, LCR relationships and maps uncover and identify scaffold-client relationships among E-rich LCR-containing proteins in the nucleolus, and revealed previously undescribed regions of LCR sequence space with signatures of higher order assemblies, including a teleost-specific T/H-rich sequence space. Thus, this unified view of LCRs enables discovery of how LCRs encode higher order assemblies of organisms.
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Affiliation(s)
- Byron Lee
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Nima Jaberi-Lashkari
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
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Liu Y, Wang Y, Tong C, Wei G, Ding F, Sun Y. Molecular Insights into the Self-Assembly of Block Copolymer Suckerin Polypeptides into Nanoconfined β-Sheets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202642. [PMID: 35901284 PMCID: PMC9420834 DOI: 10.1002/smll.202202642] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Suckerin in squid sucker ring teeth is a block-copolymer peptide comprised of two repeating modules-the alanine and histidine-rich M1 and the glycine-rich M2. Suckerin self-assemblies display excellent thermo-plasticity and pH-responsive properties, along with the high biocompatibility, biodegradability, and sustainability. However, the self-assembly mechanism and the detailed role of each module are still elusive, limiting the capability of applying and manipulating such biomaterials. Here, the self-assembly dynamics of the two modules and two minimalist suckerin-mimetic block-copolymers, M1-M2-M1 and M2-M1-M2, in silico is investigated. The simulation results demonstrate that M2 has a stronger self-association but weaker β-sheet propensities than M1. The high self-assembly propensity of M2 allows the minimalist block-copolymer peptides to coalesce with microphase separation, enabling the formation of nanoconfined β-sheets in the matrix formed by M1-M2 contacts. Since these glycine-rich fragments with scatted hydrophobic and aromatic residues are building blocks of many other block-copolymer peptides, the study suggests that these modules function as the "molecular glue" in addition to the flexible linker or spacer to drive the self-assembly and microphase separation. The uncovered molecular insights may help understand the structure and function of suckerin and also aid in the design of functional block-copolymer peptides for nanotechnology and biomedicine applications.
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Affiliation(s)
- Yuying Liu
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Ying Wang
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Chaohui Tong
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Yunxiang Sun
- Department of Physics, Ningbo University, Ningbo 315211, China
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
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29
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Gandass N, Salvi P. Intrinsically disordered protein, DNA binding with one finger transcription factor ( OsDOF27) implicates thermotolerance in yeast and rice. FRONTIERS IN PLANT SCIENCE 2022; 13:956299. [PMID: 35968137 PMCID: PMC9372624 DOI: 10.3389/fpls.2022.956299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Intrinsically disorder regions or proteins (IDRs or IDPs) constitute a large subset of the eukaryotic proteome, which challenges the protein structure-function paradigm. These IDPs lack a stable tertiary structure, yet they play a crucial role in the diverse biological process of plants. This study represents the intrinsically disordered nature of a plant-specific DNA binding with one finger transcription factor (DOF-TF). Here, we have investigated the role of OsDOF27 and characterized it as an intrinsically disordered protein. Furthermore, the molecular role of OsDOF27 in thermal stress tolerance has been elucidated. The qRT-PCR analysis revealed that OsDOF27 was significantly upregulated under different abiotic stress treatments in rice, particularly under heat stress. The stress-responsive transcript induction of OsDOF27 was further correlated with enriched abiotic stress-related cis-regulatory elements present in its promoter region. The in vivo functional analysis of the potential role of OsDOF27 in thermotolerance was further studied in yeast and in planta. Ectopic expression of OsDOF27 in yeast implicates thermotolerance response. Furthermore, the rice transgenic lines with overexpressing OsDOF27 revealed a positive role in mitigating heat stress tolerance. Collectively, our results evidently show the intrinsically disorderedness in OsDOF27 and its role in thermal stress response in rice.
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Benson A, Steed J, Malloy M, Davis AJ. Quantitative Protein Analysis of ZPB2, ZPB1 and ZPC in the Germinal Disc and a Non-Germinal Disc Region of the Inner Perivitelline Layer in Two Genetic Lines of Turkey Hens That Differ in Fertility. Animals (Basel) 2022; 12:ani12131672. [PMID: 35804570 PMCID: PMC9265051 DOI: 10.3390/ani12131672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
The avian inner perivitelline layer (IPVL), containing the zona pellucida (ZP) family of proteins, surrounds the ovulated ovum. In mammalian species, ZP proteins serve as key component(s) in binding sperm and initiating the acrosome reaction. Sperm binding at the germinal disc (GD) region of the IPVL initiates fertilization in avian species, and the amount of sperm binding at the GD reflects female fertility. The current research determined whether reported differences in mRNA expression in two genetic lines of turkey hens (E, high fertility and F, low fertility) translated to the protein level. ZPB2 in the IPVL is greater in the GD region compared with the nongerminal disc (NGD) region, as indicated by both mRNA and protein expression. However, protein expressions of ZPB1 and ZPC in the IPVL of E- and F-line turkey hens was in contrast to previously reported mRNA expression. The results indicate that the mRNA expression of ZP proteins at their site of synthesis in E- and F-line hens often does not directly correlate with the IPVL abundance of these proteins. The greater protein concentration of ZPB2 in the GD region compared with the NGD regions suggests that this protein may be critical for sperm binding at the GD region.
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Taylor AIP, Staniforth RA. General Principles Underpinning Amyloid Structure. Front Neurosci 2022; 16:878869. [PMID: 35720732 PMCID: PMC9201691 DOI: 10.3389/fnins.2022.878869] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Amyloid fibrils are a pathologically and functionally relevant state of protein folding, which is generally accessible to polypeptide chains and differs fundamentally from the globular state in terms of molecular symmetry, long-range conformational order, and supramolecular scale. Although amyloid structures are challenging to study, recent developments in techniques such as cryo-EM, solid-state NMR, and AFM have led to an explosion of information about the molecular and supramolecular organization of these assemblies. With these rapid advances, it is now possible to assess the prevalence and significance of proposed general structural features in the context of a diverse body of high-resolution models, and develop a unified view of the principles that control amyloid formation and give rise to their unique properties. Here, we show that, despite system-specific differences, there is a remarkable degree of commonality in both the structural motifs that amyloids adopt and the underlying principles responsible for them. We argue that the inherent geometric differences between amyloids and globular proteins shift the balance of stabilizing forces, predisposing amyloids to distinct molecular interaction motifs with a particular tendency for massive, lattice-like networks of mutually supporting interactions. This general property unites previously characterized structural features such as steric and polar zippers, and contributes to the long-range molecular order that gives amyloids many of their unique properties. The shared features of amyloid structures support the existence of shared structure-activity principles that explain their self-assembly, function, and pathogenesis, and instill hope in efforts to develop broad-spectrum modifiers of amyloid function and pathology.
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Ezzat K, Sturchio A, Espay AJ. Proteins Do Not Replicate, They Precipitate: Phase Transition and Loss of Function Toxicity in Amyloid Pathologies. BIOLOGY 2022; 11:biology11040535. [PMID: 35453734 PMCID: PMC9031251 DOI: 10.3390/biology11040535] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 12/11/2022]
Abstract
Protein aggregation into amyloid fibrils affects many proteins in a variety of diseases, including neurodegenerative disorders, diabetes, and cancer. Physicochemically, amyloid formation is a phase transition process, where soluble proteins are transformed into solid fibrils with the characteristic cross-β conformation responsible for their fibrillar morphology. This phase transition proceeds via an initial, rate-limiting nucleation step followed by rapid growth. Several well-defined nucleation pathways exist, including homogenous nucleation (HON), which proceeds spontaneously; heterogeneous nucleation (HEN), which is catalyzed by surfaces; and seeding via preformed nuclei. It has been hypothesized that amyloid aggregation represents a protein-only (nucleic-acid free) replication mechanism that involves transmission of structural information via conformational templating (the prion hypothesis). While the prion hypothesis still lacks mechanistic support, it is also incompatible with the fact that proteins can be induced to form amyloids in the absence of a proteinaceous species acting as a conformational template as in the case of HEN, which can be induced by lipid membranes (including viral envelopes) or polysaccharides. Additionally, while amyloids can be formed from any protein sequence and via different nucleation pathways, they invariably adopt the universal cross-β conformation; suggesting that such conformational change is a spontaneous folding event that is thermodynamically favorable under the conditions of supersaturation and phase transition and not a templated replication process. Finally, as the high stability of amyloids renders them relatively inert, toxicity in some amyloid pathologies might be more dependent on the loss of function from protein sequestration in the amyloid state rather than direct toxicity from the amyloid plaques themselves.
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Affiliation(s)
- Kariem Ezzat
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, 141 57 Stockholm, Sweden
- Correspondence:
| | - Andrea Sturchio
- Department of Clinical Neuroscience, Neuro Svenningsson, Karolinska Institutet, 171 76 Stockholm, Sweden;
- James J. and Joan A. Gardner Family Center for Parkinson’s Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH 45221, USA;
| | - Alberto J. Espay
- James J. and Joan A. Gardner Family Center for Parkinson’s Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH 45221, USA;
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Gonzalez-Obeso C, Rodriguez-Cabello JC, Kaplan DL. Fast and reversible crosslinking of a silk elastin-like polymer. Acta Biomater 2022; 141:14-23. [PMID: 34971785 PMCID: PMC8898266 DOI: 10.1016/j.actbio.2021.12.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022]
Abstract
Elastin-like polymers (ELPs) and their chimeric subfamily the silk elastin-like polymers (SELPs) exhibit a lower critical solvation temperature (LCST) behavior in water which has been extensively studied from theoretical, computational and experimental perspectives. The inclusion of silk domains in the backbone of the ELPs effects the molecular dynamics of the elastin-like domains in response to increased temperature above its transition temperature and confers gelation ability. This response has been studied in terms of initial and long-term changes in structures, however, intermediate transition states have been less investigated. Moreover, little is known about the effects of reversible hydration on the elastin versus silk domains in the physical crosslinks. We used spectroscopic techniques to analyze initial, intermediate and long-term states of the crosslinks in SELPs. A combination of thermoanalytical and rheological measurements demonstrated that the fast reversible rehydration of the elastin motifs adjacent to the relatively small silk domains was capable of breaking the silk physical crosslinks. This feature can be exploited to tailor the dynamics of these types of crosslinks in SELPs. STATEMENT OF SIGNIFICANCE: The combination of silk and elastin in a single molecule results in synergy via their interactions to impact the protein polymer properties. The ability of the silk domains to crosslink affects the thermoresponsive properties of the elastin domains. These interactions have been studied at early and late states of the physical crosslinking, while the intermediate states were the focus of the present study to understand the reversible phase-transitions of the elastin domains over the silk physical crosslinking. The thermoresponsive properties of the elastin domains at the initial, intermediate and late states of silk crosslinking were characterized to demonstrate that reversible hydration of the elastin domains influenced the reversibility of the silk crosslinks.
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Affiliation(s)
- Constancio Gonzalez-Obeso
- Department of Biomedical Engineering Tufts University, 4, Colby St., Medford, MA, 02155, USA; BIOFORGE (Group for Advanced Materials and Nanobiotechnology), University of Valladolid-CIBER-BBN, Paseo de Belén 19, 47011, Valladolid, Spain.
| | - J C Rodriguez-Cabello
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology), University of Valladolid-CIBER-BBN, Paseo de Belén 19, 47011, Valladolid, Spain.
| | - David L Kaplan
- Department of Biomedical Engineering Tufts University, 4, Colby St., Medford, MA, 02155, USA.
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Glyakina AV, Balabaev NK, Galzitskaya OV. Determination of the Most Stable Packing of Peptides from Ribosomal S1 Protein, Protein Bgl2p, and Aβ peptide in β-layers During Molecular Dynamics Simulations. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2340:221-233. [PMID: 35167077 DOI: 10.1007/978-1-0716-1546-1_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Our task was to determine the most stable packing of peptides in β-layers to construct an oligomer structure for fibril growth. The β-layers consisting of eight short peptides with the amino acid sequences IVRGVVVAID, VDSWNVLVAG (VESWNVLVAG), KLVFFAEDVG, and IIGLMVGGVV were built. These sequences correspond to the amyloidogenic regions of ribosomal S1 protein from E. coli, protein glucantransferase Bgl2p from the yeast cell wall, and Aβ peptide. First, the amyloidogenic regions were predicted theoretically, and then were confirmed experimentally. Four β-layers with different orientation of the peptides in the layers and the layers relative to each other were constructed. To determine the most stable packing of β-strands, the molecular dynamic (MD) simulations in explicit water were carried out. Two charge states (pH3 and pH5) for each β-layer were considered. The fraction of the secondary structure was a measure of stability for β-layers. β-Layers, in which β-strands are antiparallel relative to each other, were the most stable. Using this packing for β-strands, we constructed the oligomer structures and also checked their stability by using MD simulations.
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Affiliation(s)
- Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
| | - Nikolai K Balabaev
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia. .,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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35
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Isaacson KJ, Van Devener BR, Steinhauff DB, Jensen MM, Cappello J, Ghandehari H. Liquid-cell transmission electron microscopy for imaging of thermosensitive recombinant polymers. J Control Release 2022; 344:39-49. [PMID: 35182613 PMCID: PMC9121634 DOI: 10.1016/j.jconrel.2022.02.019] [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: 09/07/2021] [Revised: 02/09/2022] [Accepted: 02/13/2022] [Indexed: 11/19/2022]
Abstract
Various polymers used in controlled release applications exhibit solution-based thermal responses. Unfortunately, very few characterization and imaging techniques permit resolution of individual polymers during their thermally-triggered phase transitions. Here, we demonstrate the use of temperature-ramp liquid-cell transmission electron microscopy (LCTEM) for real-time evaluation of the solution and interfacial behavior of elastinlike polypeptides (ELPs) and their self-assembled nanostructures over a temperature range incorporating their intrinsic lower critical solution temperatures (LCSTs). Individual polymers and supramolecular assemblies were discriminated dependent upon solubility states. The recombinant polymers were shown to adsorb to the silicon-nitride chip window from the buffered saline solution and desorb in a temperature-dependent manner. Silk-elastinlike protein block copolymers (SELPs) (composed of repeat peptide motifs of silk and elastin) differed from ELPs in thermal behavior. While both polymers were shown to cluster, only SELPs formed robust amyloid-like fibers upon heating.
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Affiliation(s)
- Kyle J Isaacson
- Utah Center for Nanomedicine, University of Utah, Salt Lake City, UT, USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Brian R Van Devener
- Utah Nanofab - Nano Scale Imaging and Surface Analysis Lab, University of Utah, Salt Lake City, UT, USA
| | - Douglas B Steinhauff
- Utah Center for Nanomedicine, University of Utah, Salt Lake City, UT, USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - M Martin Jensen
- Utah Center for Nanomedicine, University of Utah, Salt Lake City, UT, USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Joseph Cappello
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Hamidreza Ghandehari
- Utah Center for Nanomedicine, University of Utah, Salt Lake City, UT, USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA; Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT, USA.
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36
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Thermodynamic insights on the liquid-liquid fractionation of gluten proteins in aqueous ethanol. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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37
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Li J, Li S, Huang J, Khan AQ, An B, Zhou X, Liu Z, Zhu M. Spider Silk-Inspired Artificial Fibers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103965. [PMID: 34927397 PMCID: PMC8844500 DOI: 10.1002/advs.202103965] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/19/2021] [Indexed: 05/14/2023]
Abstract
Spider silk is a natural polymeric fiber with high tensile strength, toughness, and has distinct thermal, optical, and biocompatible properties. The mechanical properties of spider silk are ascribed to its hierarchical structure, including primary and secondary structures of the spidroins (spider silk proteins), the nanofibril, the "core-shell", and the "nano-fishnet" structures. In addition, spider silk also exhibits remarkable properties regarding humidity/water response, water collection, light transmission, thermal conductance, and shape-memory effect. This motivates researchers to prepare artificial functional fibers mimicking spider silk. In this review, the authors summarize the study of the structure and properties of natural spider silk, and the biomimetic preparation of artificial fibers from different types of molecules and polymers by taking some examples of artificial fibers exhibiting these interesting properties. In conclusion, biomimetic studies have yielded several noteworthy findings in artificial fibers with different functions, and this review aims to provide indications for biomimetic studies of functional fibers that approach and exceed the properties of natural spider silk.
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Affiliation(s)
- Jiatian Li
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and College of ChemistryKey Laboratory of Functional Polymer MaterialsFrontiers Science Center for New Organic MatterNankai UniversityTianjin300071China
| | - Sitong Li
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and College of ChemistryKey Laboratory of Functional Polymer MaterialsFrontiers Science Center for New Organic MatterNankai UniversityTianjin300071China
| | - Jiayi Huang
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and College of ChemistryKey Laboratory of Functional Polymer MaterialsFrontiers Science Center for New Organic MatterNankai UniversityTianjin300071China
| | - Abdul Qadeer Khan
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and College of ChemistryKey Laboratory of Functional Polymer MaterialsFrontiers Science Center for New Organic MatterNankai UniversityTianjin300071China
| | - Baigang An
- School of Chemical EngineeringUniversity of Science and Technology LiaoningAnshan114051China
| | - Xiang Zhou
- Department of ScienceChina Pharmaceutical UniversityNanjing211198China
| | - Zunfeng Liu
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and College of ChemistryKey Laboratory of Functional Polymer MaterialsFrontiers Science Center for New Organic MatterNankai UniversityTianjin300071China
- School of Chemical EngineeringUniversity of Science and Technology LiaoningAnshan114051China
| | - Meifang Zhu
- State Key Laboratory for Modification of Chemical Fibers and Polymer MaterialsCollege of Materials Science and EngineeringDonghua UniversityShanghai201620China
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38
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Mu X, Yuen JSK, Choi J, Zhang Y, Cebe P, Jiang X, Zhang YS, Kaplan DL. Conformation-driven strategy for resilient and functional protein materials. Proc Natl Acad Sci U S A 2022; 119:e2115523119. [PMID: 35074913 PMCID: PMC8795527 DOI: 10.1073/pnas.2115523119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/17/2021] [Indexed: 01/08/2023] Open
Abstract
The exceptional elastic resilience of some protein materials underlies essential biomechanical functions with broad interest in biomedical fields. However, molecular design of elastic resilience is restricted to amino acid sequences of a handful of naturally occurring resilient proteins such as resilin and elastin. Here, we exploit non-resilin/elastin sequences that adopt kinetically stabilized, random coil-dominated conformations to achieve near-perfect resilience comparable with that of resilin and elastin. We also show a direct correlation between resilience and Raman-characterized protein conformations. Furthermore, we demonstrate that metastable conformation of proteins enables the construction of mechanically graded protein materials that exhibit spatially controlled conformations and resilience. These results offer insights into molecular mechanisms of protein elastomers and outline a general conformation-driven strategy for developing resilient and functional protein materials.
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Affiliation(s)
- Xuan Mu
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139
| | - John S K Yuen
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Jaewon Choi
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Yixin Zhang
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Peggy Cebe
- Department of Physics and Astronomy, Tufts University, Medford, MA 02155
| | - Xiaocheng Jiang
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139;
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155;
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39
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Kucharska I, Hossain L, Ivanochko D, Yang Q, Rubinstein JL, Pomès R, Julien JP. Structural basis of Plasmodium vivax inhibition by antibodies binding to the circumsporozoite protein repeats. eLife 2022; 11:e72908. [PMID: 35023832 PMCID: PMC8809896 DOI: 10.7554/elife.72908] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/12/2022] [Indexed: 11/24/2022] Open
Abstract
Malaria is a global health burden, with Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) responsible for the majority of infections worldwide. Circumsporozoite protein (CSP) is the most abundant protein on the surface of Plasmodium sporozoites, and antibodies targeting the central repeat region of CSP can prevent parasite infection. Although much has been uncovered about the molecular basis of antibody recognition of the PfCSP repeats, data remains scarce for PvCSP. Here, we performed molecular dynamics simulations for peptides comprising the PvCSP repeats from strains VK210 and VK247 to reveal how the PvCSP central repeats are highly disordered, with minor propensities to adopt turn conformations. Next, we solved eight crystal structures to unveil the interactions of two inhibitory monoclonal antibodies (mAbs), 2F2 and 2E10.E9, with PvCSP repeats. Both antibodies can accommodate subtle sequence variances in the repeat motifs and recognize largely coiled peptide conformations that also contain isolated turns. Our structural studies uncover various degrees of Fab-Fab homotypic interactions upon recognition of the PvCSP central repeats by these two inhibitory mAbs, similar to potent mAbs against PfCSP. These findings augment our understanding of host-Plasmodium interactions and contribute molecular details of Pv inhibition by mAbs to unlock structure-based engineering of PvCSP-based vaccines.
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Affiliation(s)
- Iga Kucharska
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
| | - Lamia Hossain
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
| | - Danton Ivanochko
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
| | - Qiren Yang
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
| | - John L Rubinstein
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
- Department of Medical Biophysics, University of TorontoTorontoCanada
| | - Régis Pomès
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
- Department of Immunology, University of TorontoTorontoCanada
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40
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Schultz CJ, Wu Y, Baumann U. A targeted bioinformatics approach identifies highly variable cell surface proteins that are unique to Glomeromycotina. MYCORRHIZA 2022; 32:45-66. [PMID: 35031894 PMCID: PMC8786786 DOI: 10.1007/s00572-021-01066-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Diversity in arbuscular mycorrhizal fungi (AMF) contributes to biodiversity and resilience in natural environments and healthy agricultural systems. Functional complementarity exists among species of AMF in symbiosis with their plant hosts, but the molecular basis of this is not known. We hypothesise this is in part due to the difficulties that current sequence assembly methodologies have assembling sequences for intrinsically disordered proteins (IDPs) due to their low sequence complexity. IDPs are potential candidates for functional complementarity because they often exist as extended (non-globular) proteins providing additional amino acids for molecular interactions. Rhizophagus irregularis arabinogalactan-protein-like proteins (AGLs) are small secreted IDPs with no known orthologues in AMF or other fungi. We developed a targeted bioinformatics approach to identify highly variable AGLs/IDPs in RNA-sequence datasets. The approach includes a modified multiple k-mer assembly approach (Oases) to identify candidate sequences, followed by targeted sequence capture and assembly (mirabait-mira). All AMF species analysed, including the ancestral family Paraglomeraceae, have small families of proteins rich in disorder promoting amino acids such as proline and glycine, or glycine and asparagine. Glycine- and asparagine-rich proteins also were found in Geosiphon pyriformis (an obligate symbiont of a cyanobacterium), from the same subphylum (Glomeromycotina) as AMF. The sequence diversity of AGLs likely translates to functional diversity, based on predicted physical properties of tandem repeats (elastic, amyloid, or interchangeable) and their broad pI ranges. We envisage that AGLs/IDPs could contribute to functional complementarity in AMF through processes such as self-recognition, retention of nutrients, soil stability, and water movement.
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Affiliation(s)
- Carolyn J Schultz
- School of Agriculture, Food, and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.
| | - Yue Wu
- School of Agriculture, Food, and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Ute Baumann
- School of Agriculture, Food, and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
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Destabilization of the Alzheimer's amyloid-β peptide by a proline-rich β-sheet breaker peptide: a molecular dynamics simulation study. J Mol Model 2021; 27:356. [PMID: 34796404 DOI: 10.1007/s00894-021-04968-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/25/2021] [Indexed: 11/27/2022]
Abstract
The amyloid-β peptide exists in the form of fibrils in the plaques found in the brains of patients with Alzheimer's disease. One of the therapeutic strategies is the design of molecules which can destabilize these fibrils. We present a designed peptide KLVFFP5 with two segments: the self-recognition sequence KLVFF and a β-sheet breaker proline pentamer. Molecular dynamics simulations and docking results showed that this peptide could bind to the protofibrils and destabilize them by establishing hydrophobic contacts and hydrogen bonds with a higher affinity than the KLVFF peptide. In the presence of the KLVFFP5 peptide, the β-sheet content of the protofibrils was reduced significantly; the hydrogen bonding network and the salt bridges were disrupted to a greater extent than the KLVFF peptide. Our results indicate that the KLVFFP5 peptide is an effective β-sheet disruptor which can be considered in the therapy of Alzheimer's disease.
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42
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Kar M, Posey AE, Dar F, Hyman AA, Pappu RV. Glycine-Rich Peptides from FUS Have an Intrinsic Ability to Self-Assemble into Fibers and Networked Fibrils. Biochemistry 2021; 60:3213-3222. [PMID: 34648275 PMCID: PMC10715152 DOI: 10.1021/acs.biochem.1c00501] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Glycine-rich regions feature prominently in intrinsically disordered regions (IDRs) of proteins that drive phase separation and the regulated formation of membraneless biomolecular condensates. Interestingly, the Gly-rich IDRs seldom feature poly-Gly tracts. The protein fused in sarcoma (FUS) is an exception. This protein includes two 10-residue poly-Gly tracts within the prion-like domain (PLD) and at the interface between the PLD and the RNA binding domain. Poly-Gly tracts are known to be highly insoluble, being potent drivers of self-assembly into solid-like fibrils. Given that the internal concentrations of FUS and FUS-like molecules cross the high micromolar and even millimolar range within condensates, we reasoned that the intrinsic insolubility of poly-Gly tracts might be germane to emergent fluid-to-solid transitions within condensates. To assess this possibility, we characterized the concentration-dependent self-assembly for three non-overlapping 25-residue Gly-rich peptides derived from FUS. Two of the three peptides feature 10-residue poly-Gly tracts. These peptides form either long fibrils based on twisted ribbon-like structures or self-supporting gels based on physical cross-links of fibrils. Conversely, the peptide with similar Gly contents but lacking a poly-Gly tract does not form fibrils or gels. Instead, it remains soluble across a wide range of concentrations. Our findings highlight the ability of poly-Gly tracts within IDRs that drive phase separation to undergo self-assembly. We propose that these tracts are likely to contribute to nucleation of fibrillar solids within dense condensates formed by FUS.
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Affiliation(s)
- Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), 01307 Dresden, Germany
| | - Ammon E. Posey
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Furqan Dar
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Anthony A. Hyman
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), 01307 Dresden, Germany
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
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43
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Tang X, Ye X, Wang X, Zhao S, Wu M, Ruan J, Zhong B. High mechanical property silk produced by transgenic silkworms expressing the spidroins PySp1 and ASG1. Sci Rep 2021; 11:20980. [PMID: 34697320 PMCID: PMC8546084 DOI: 10.1038/s41598-021-00029-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 09/30/2021] [Indexed: 11/08/2022] Open
Abstract
Spider silk is one of the best natural fibers with excellent mechanical properties; however, due to the visual awareness, biting behavior and territory consciousness of spiders, we cannot obtain spider silk by large-scale breeding. Silkworms have a spinning system similar to that of spiders, and the use of transgenic technology in Bombyx mori, which is an ideal reactor for producing spider silk, is routine. In this study, the piggyBac transposon technique was used to achieve specific expression of two putative spider silk genes in the posterior silk glands of silkworms: aggregate spider glue 1 (ASG1) of Trichonephila clavipes (approximately 1.2 kb) and two repetitive units of pyriform spidroin 1 (PySp1) of Argiope argentata (approximately 1.4 kb). Then, two reconstituted spider silk-producing strains, the AG and PA strains, were obtained. Finally, the toughness of the silk fiber was increased by up to 91.5% and the maximum stress was enhanced by 36.9% in PA, and the respective properties in AG were increased by 21.0% and 34.2%. In summary, these two spider genes significantly enhanced the mechanical properties of silk fiber, which can provide a basis for spidroin silk production.
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Affiliation(s)
- Xiaoli Tang
- College of Animal Science, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiaogang Ye
- College of Animal Science, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiaoxiao Wang
- College of Animal Science, Zhejiang University, Hangzhou, People's Republic of China
| | - Shuo Zhao
- College of Animal Science, Zhejiang University, Hangzhou, People's Republic of China
| | - Meiyu Wu
- College of Animal Science, Zhejiang University, Hangzhou, People's Republic of China
| | - Jinghua Ruan
- College of Animal Science, Zhejiang University, Hangzhou, People's Republic of China
| | - Boxiong Zhong
- College of Animal Science, Zhejiang University, Hangzhou, People's Republic of China.
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44
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Chang MP, Huang W, Mai DJ. Monomer‐scale design of functional protein polymers using consensus repeat sequences. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Marina P. Chang
- Department of Materials Science and Engineering Stanford University Stanford California USA
| | - Winnie Huang
- Department of Chemical Engineering Stanford University Stanford California USA
| | - Danielle J. Mai
- Department of Chemical Engineering Stanford University Stanford California USA
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45
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Juanes-Gusano D, Santos M, Reboto V, Alonso M, Rodríguez-Cabello JC. Self-assembling systems comprising intrinsically disordered protein polymers like elastin-like recombinamers. J Pept Sci 2021; 28:e3362. [PMID: 34545666 DOI: 10.1002/psc.3362] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/02/2021] [Accepted: 07/13/2021] [Indexed: 12/19/2022]
Abstract
Despite lacking cooperatively folded structures under native conditions, numerous intrinsically disordered proteins (IDPs) nevertheless have great functional importance. These IDPs are hybrids containing both ordered and intrinsically disordered protein regions (IDPRs), the structure of which is highly flexible in this unfolded state. The conformational flexibility of these disordered systems favors transitions between disordered and ordered states triggered by intrinsic and extrinsic factors, folding into different dynamic molecular assemblies to enable proper protein functions. Indeed, prokaryotic enzymes present less disorder than eukaryotic enzymes, thus showing that this disorder is related to functional and structural complexity. Protein-based polymers that mimic these IDPs include the so-called elastin-like polypeptides (ELPs), which are inspired by the composition of natural elastin. Elastin-like recombinamers (ELRs) are ELPs produced using recombinant techniques and which can therefore be tailored for a specific application. One of the most widely used and studied characteristic structures in this field is the pentapeptide (VPGXG)n . The structural disorder in ELRs probably arises due to the high content of proline and glycine in the ELR backbone, because both these amino acids help to keep the polypeptide structure of elastomers disordered and hydrated. Moreover, the recombinant nature of these systems means that different sequences can be designed, including bioactive domains, to obtain specific structures for each application. Some of these structures, along with their applications as IDPs that self-assemble into functional vesicles or micelles from diblock copolymer ELRs, will be studied in the following sections. The incorporation of additional order- and disorder-promoting peptide/protein domains, such as α-helical coils or β-strands, in the ELR sequence, and their influence on self-assembly, will also be reviewed. In addition, chemically cross-linked systems with controllable order-disorder balance, and their role in biomineralization, will be discussed. Finally, we will review different multivalent IDPs-based coatings and films for different biomedical applications, such as spatially controlled cell adhesion, osseointegration, or biomaterial-associated infection (BAI).
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Affiliation(s)
- Diana Juanes-Gusano
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology) CIBER-BBN, Edificio Lucía, University of Valladolid, Valladolid, Spain
| | - Mercedes Santos
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology) CIBER-BBN, Edificio Lucía, University of Valladolid, Valladolid, Spain
| | - Virginia Reboto
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology) CIBER-BBN, Edificio Lucía, University of Valladolid, Valladolid, Spain
| | - Matilde Alonso
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology) CIBER-BBN, Edificio Lucía, University of Valladolid, Valladolid, Spain
| | - José Carlos Rodríguez-Cabello
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology) CIBER-BBN, Edificio Lucía, University of Valladolid, Valladolid, Spain
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46
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Vendruscolo M, Fuxreiter M. Sequence Determinants of the Aggregation of Proteins Within Condensates Generated by Liquid-liquid Phase Separation. J Mol Biol 2021; 434:167201. [PMID: 34391803 DOI: 10.1016/j.jmb.2021.167201] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/08/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022]
Abstract
The transition between the native and amyloid states of proteins can proceed via a deposition pathway via oligomeric intermediates or via a condensation pathway involving liquid droplet intermediates generated through liquid-liquid phase separation. While several computational methods are available to perform sequence-based predictions of the propensity of proteins to aggregate via the deposition pathway, much less is known about the physico-chemical principles that underlie aggregation within condensates. Here we investigate the sequence determinants of aggregation via the condensation pathway, and identify three relevant features: droplet-promoting propensity, aggregation-promoting propensity and multimodal interactions quantified by the binding mode entropy. By using this approach, we show that it is possible to predict aggregation-promoting mutations in droplet-forming proteins associated with amyotrophic lateral sclerosis (ALS). This analysis provides insights into the amino acid code for the conversion of proteins between liquid-like and solid-like condensates.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, UK.
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Italy; Department of Biochemistry and Molecular Biology, University of Debrecen, Hungary.
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47
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López Barreiro D, Minten IJ, Thies JC, Sagt CMJ. Structure-Property Relationships of Elastin-like Polypeptides: A Review of Experimental and Computational Studies. ACS Biomater Sci Eng 2021. [PMID: 34251181 DOI: 10.1021/acsbiomaterials.1c00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Elastin is a structural protein with outstanding mechanical properties (e.g., elasticity and resilience) and biologically relevant functions (e.g., triggering responses like cell adhesion or chemotaxis). It is formed from its precursor tropoelastin, a 60-72 kDa water-soluble and temperature-responsive protein that coacervates at physiological temperature, undergoing a phenomenon termed lower critical solution temperature (LCST). Inspired by this behavior, many scientists and engineers are developing recombinantly produced elastin-inspired biopolymers, usually termed elastin-like polypeptides (ELPs). These ELPs are generally comprised of repetitive motifs with the sequence VPGXG, which corresponds to repeats of a small part of the tropoelastin sequence, X being any amino acid except proline. ELPs display LCST and mechanical properties similar to tropoelastin, which renders them promising candidates for the development of elastic and stimuli-responsive protein-based materials. Unveiling the structure-property relationships of ELPs can aid in the development of these materials by establishing the connections between the ELP amino acid sequence and the macroscopic properties of the materials. Here we present a review of the structure-property relationships of ELPs and ELP-based materials, with a focus on LCST and mechanical properties and how experimental and computational studies have aided in their understanding.
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Affiliation(s)
- Diego López Barreiro
- DSM Biotechnology Center, DSM, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Inge J Minten
- DSM Materials Science Center - Applied Science Center, DSM, Urmonderbaan 22, 6160 BB, Geleen, The Netherlands
| | - Jens C Thies
- DSM Biomedical, DSM, Koestraat 1, 6167 RA, Geleen, The Netherlands
| | - Cees M J Sagt
- DSM Biotechnology Center, DSM, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
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48
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Htut KZ, Alicea-Serrano AM, Singla S, Agnarsson I, Garb JE, Kuntner M, Gregorič M, Haney RA, Marhabaie M, Blackledge TA, Dhinojwala A. Correlation between protein secondary structure and mechanical performance for the ultra-tough dragline silk of Darwin's bark spider. J R Soc Interface 2021; 18:20210320. [PMID: 34129788 PMCID: PMC8205537 DOI: 10.1098/rsif.2021.0320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/24/2021] [Indexed: 11/12/2022] Open
Abstract
The spider major ampullate (MA) silk exhibits high tensile strength and extensibility and is typically a blend of MaSp1 and MaSp2 proteins with the latter comprising glycine-proline-glycine-glycine-X repeating motifs that promote extensibility and supercontraction. The MA silk from Darwin's bark spider (Caerostris darwini) is estimated to be two to three times tougher than the MA silk from other spider species. Previous research suggests that a unique MaSp4 protein incorporates proline into a novel glycine-proline-glycine-proline motif and may explain C. darwini MA silk's extraordinary toughness. However, no direct correlation has been made between the silk's molecular structure and its mechanical properties for C. darwini. Here, we correlate the relative protein secondary structure composition of MA silk from C. darwini and four other spider species with mechanical properties before and after supercontraction to understand the effect of the additional MaSp4 protein. Our results demonstrate that C. darwini MA silk possesses a unique protein composition with a lower ratio of helices (31%) and β-sheets (20%) than other species. Before supercontraction, toughness, modulus and tensile strength correlate with percentages of β-sheets, unordered or random coiled regions and β-turns. However, after supercontraction, only modulus and strain at break correlate with percentages of β-sheets and β-turns. Our study highlights that additional information including crystal size and crystal and chain orientation is necessary to build a complete structure-property correlation model.
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Affiliation(s)
- K Zin Htut
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, OH 44325, USA
| | - Angela M. Alicea-Serrano
- Department of Biology, Integrated Bioscience Program, The University of Akron, Akron, OH 44325, USA
| | - Saranshu Singla
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, OH 44325, USA
| | - Ingi Agnarsson
- Department of Biology, University of Vermont, Burlington, VT 05405, USA
| | - Jessica E. Garb
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Matjaž Kuntner
- Jovan Hadži Institute of Biology ZRC SAZU, Novi trg 2, 1000 Ljubljana, Slovenia
- Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Matjaž Gregorič
- Jovan Hadži Institute of Biology ZRC SAZU, Novi trg 2, 1000 Ljubljana, Slovenia
| | - Robert A. Haney
- Department of Biology, Ball State University, Muncie, IN 47306, USA
| | - Mohammad Marhabaie
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43215, USA
| | - Todd A. Blackledge
- Department of Biology, Integrated Bioscience Program, The University of Akron, Akron, OH 44325, USA
| | - Ali Dhinojwala
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, OH 44325, USA
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Abstract
Snails can provide a considerable variety of bioactive compounds for cosmetic and pharmaceutical industries, useful for the development of new formulations with less toxicity and post effects compared to regular compounds used for the purpose. Compounds from crude extract, mucus, slime consist of glycans, polypeptides, proteins, etc., and can be used for curing diseases like viral lesions, warts, and different dermal problems. Some particular uses of snails involve treating post-traumatic stress. Micro RNA of Lymnaea stagnalis, was known to be responsible for the development of long-term memory and treatment of Alzheimer's and Dementia like diseases. This review explores the application of various bioactive compounds from snails with its potential as new translational medicinal and cosmetic applications. Snail bioactive compounds like ω-MVIIA, μ-SIIIA, μO-MrVIB, Xen2174, δ-EVIA, α-Vc1.1, σ-GVIIA, Conantokin-G, and Contulakin-G, conopeptides can be used for the development of anti-cancer drugs. These compounds target the innate immunity and improve the defense system of humans and provide protection against these life-threatening health concerns.AbbreviationsFDA: Food and Drug Administration; UTI: urinal tract infection; nAChRs: nicotinic acetylcholine receptors; NMDA: N-methyl-D-aspartate; CNS: central nervous system; CAR T: chimeric antigen receptors therapy; Micro RNA: micro ribonucleic acid.
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Affiliation(s)
- Varun Dhiman
- Department of Environmental Sciences, Central University of Himachal Pradesh, DharamshalaDharamshala, India
| | - Deepak Pant
- School of Chemical Sciences, Central University of Haryana, Mahendragarh, Haryana, India
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50
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Schmelzer CEH, Duca L. Elastic fibers: formation, function, and fate during aging and disease. FEBS J 2021; 289:3704-3730. [PMID: 33896108 DOI: 10.1111/febs.15899] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 01/09/2023]
Abstract
Elastic fibers are extracellular components of higher vertebrates and confer elasticity and resilience to numerous tissues and organs such as large blood vessels, lungs, and skin. Their formation and maturation take place in a complex multistage process called elastogenesis. It requires interactions between very different proteins but also other molecules and leads to the deposition and crosslinking of elastin's precursor on a scaffold of fibrillin-rich microfibrils. Mature fibers are exceptionally resistant to most influences and, under healthy conditions, retain their biomechanical function over the life of the organism. However, due to their longevity, they accumulate damages during aging. These are caused by proteolytic degradation, formation of advanced glycation end products, calcification, oxidative damage, aspartic acid racemization, lipid accumulation, carbamylation, and mechanical fatigue. The resulting changes can lead to diminution or complete loss of elastic fiber function and ultimately affect morbidity and mortality. Particularly, the production of elastokines has been clearly shown to influence several life-threatening diseases. Moreover, the structure, distribution, and abundance of elastic fibers are directly or indirectly influenced by a variety of inherited pathological conditions, which mainly affect organs and tissues such as skin, lungs, or the cardiovascular system. A distinction can be made between microfibril-related inherited diseases that are the result of mutations in diverse microfibril genes and indirectly affect elastogenesis, and elastinopathies that are linked to changes in the elastin gene. This review gives an overview on the formation, structure, and function of elastic fibers and their fate over the human lifespan in health and disease.
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Affiliation(s)
- Christian E H Schmelzer
- Fraunhofer Institute for Microstructure of Materials and Systems IMWS, Halle (Saale), Germany.,Institute of Pharmacy, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Laurent Duca
- UMR CNRS 7369 MEDyC, SFR CAP-Sante, Université de Reims Champagne-Ardenne, France
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