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Kozak F, Brandis D, Pötzl C, Epasto LM, Reichinger D, Obrist D, Peterlik H, Polyansky A, Zagrovic B, Daus F, Geyer A, Becker CFW, Kurzbach D. An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401239. [PMID: 38874418 PMCID: PMC11321707 DOI: 10.1002/advs.202401239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/23/2024] [Indexed: 06/15/2024]
Abstract
Deciphering nature's remarkable way of encoding functions in its biominerals holds the potential to enable the rational development of nature-inspired materials with tailored properties. However, the complex processes that convert solution-state precursors into solid biomaterials remain largely unknown. In this study, an unconventional approach is presented to characterize these precursors for the diatom-derived peptides R5 and synthetic Silaffin-1A1 (synSil-1A1). These molecules can form defined supramolecular assemblies in solution, which act as templates for solid silica structures. Using a tailored structural biology toolbox, the structure-function relationships of these self-assemblies are unveiled. NMR-derived constraints are employed to enable a recently developed fractal-cluster formalism and then reveal the architecture of the peptide assemblies in atomistic detail. Finally, by monitoring the self-assembly activities during silica formation at simultaneous high temporal and residue resolution using real-time spectroscopy, the mechanism is elucidated underlying template-driven silica formation. Thus, it is demonstrated how to exercise morphology control over bioinorganic solids by manipulating the template architectures. It is found that the morphology of the templates is translated into the shape of bioinorganic particles via a mechanism that includes silica nucleation on the solution-state complexes' surfaces followed by complete surface coating and particle precipitation.
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Affiliation(s)
- Fanny Kozak
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Dörte Brandis
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Christopher Pötzl
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Ludovica M. Epasto
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Daniela Reichinger
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Dominik Obrist
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Herwig Peterlik
- Faculty of PhysicsUniversity of ViennaBoltzmanngasse 5Vienna1090Austria
| | - Anton Polyansky
- Department of Structural and Computational BiologyMax Perutz LabsUniversity of ViennaCampus Vienna Biocenter 5ViennaA‐1030Austria
| | - Bojan Zagrovic
- Department of Structural and Computational BiologyMax Perutz LabsUniversity of ViennaCampus Vienna Biocenter 5ViennaA‐1030Austria
| | - Fabian Daus
- Faculty of ChemistryPhilipps‐Universität Marburg35032MarburgGermany
| | - Armin Geyer
- Faculty of ChemistryPhilipps‐Universität Marburg35032MarburgGermany
| | - Christian FW Becker
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Dennis Kurzbach
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
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2
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Macchiagodena M, Fragai M, Gallo A, Pagliai M, Ravera E. The Role of Lysozyme in the Formation of Bioinspired Silicon Dioxide. Chemistry 2024; 30:e202401249. [PMID: 38722210 DOI: 10.1002/chem.202401249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Indexed: 06/19/2024]
Abstract
Several organisms are able to polycondensate tetraoxosilicic(IV) acid to form silicon(IV) dioxide using polycationic molecules. According to an earlier mechanistic proposal, these molecules undergo a phase separation and recent experimental evidence appears to confirm this model. At the same time, polycationic proteins like lysozyme can also promote polycondensation of silicon(IV) dioxide, and they do so under conditions that are not compatible with liquid-liquid phase separation. In this manuscript we investigate this conundrum by molecular simulations.
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Affiliation(s)
- Marina Macchiagodena
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Marco Fragai
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo-proteine (CIRMMP), via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Angelo Gallo
- Department of Chemistry, University of Turin, Via P. Giuria 7, 10125, Torino, Italy
| | - Marco Pagliai
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo-proteine (CIRMMP), via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Florence Data Science, University of Florence, Viale G.B. Morgagni 59, 50134, Florence, Italy
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Mao CM, Sampath J, Pfaendtner J. Molecular Driving Forces in the Self-Association of Silaffin Peptide R5 from MD Simulations. Chembiochem 2024:e202300788. [PMID: 38485668 DOI: 10.1002/cbic.202300788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/13/2024] [Indexed: 05/15/2024]
Abstract
The 19-residue silaffin-R5 peptide has been widely studied for its ability to precipitate uniform SiO2 particles through mild temperature and pH pathways, in the absence of any organic solvents. There is consensus that post-translational modification (PTM) of side chains has a large impact on the biomineralization process. Thus, it is imperative to understand the precise mechanisms that dictate the formation of SiO2 from R5 peptide, including the effects of PTM on peptide aggregation and peptide-surface adsorption. In this work, we use molecular dynamics (MD) simulations to study the aggregation of R5 dimer with multiple PTMs, with the presence of different ions in solution. Since this system has strong interactions with deep metastable states, we use parallel bias metadynamics with partitioned families to efficiently sample the different states of the system. We find that peptide aggregation is a prerequisite for biomineralization. We observe that the electrostatic interactions are essential in the R5 dimer aggregation; for wild type R5 that only has positively charged residues, phosphate ions HPO4 2- in the solution form a bridge between two peptides and are essential for peptide aggregation.
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Affiliation(s)
- Coco M Mao
- Department of Materials Science and Engineering, University of Washington, Seattle WA, 98195
| | - Janani Sampath
- Department of Chemical Engineering, University of Florida, Gainesville, FL, 32611
| | - Jim Pfaendtner
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695
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Ki MR, Kim SH, Park TI, Pack SP. Self-Entrapment of Antimicrobial Peptides in Silica Particles for Stable and Effective Antimicrobial Peptide Delivery System. Int J Mol Sci 2023; 24:16423. [PMID: 38003614 PMCID: PMC10671715 DOI: 10.3390/ijms242216423] [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: 10/07/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Antimicrobial peptides (AMPs) have emerged as a promising solution to tackle bacterial infections and combat antibiotic resistance. However, their vulnerability to protease degradation and toxicity towards mammalian cells has hindered their clinical application. To overcome these challenges, our study aims to develop a method to enhance the stability and safety of AMPs applicable to effective drug-device combination products. The KR12 antimicrobial peptide was chosen, and in order to further enhance its delivery and efficacy the human immunodeficiency virus TAT protein-derived cell-penetrating peptide (CPP) was fused to form CPP-KR12. A new product, CPP-KR12@Si, was developed by forming silica particles with self-entrapped CPP-KR12 peptide using biomimetic silica precipitability because of its cationic nature. Peptide delivery from CPP-KR12@Si to bacteria and cells was observed at a slightly delivered rate, with improved stability against trypsin treatment and a reduction in cytotoxicity compared to CPP-KR12. Finally, the antimicrobial potential of the CPP-KR12@Si/bone graft substitute (BGS) combination product was demonstrated. CPP-KR12 is coated in the form of submicron-sized particles on the surface of the BGS. Self-entrapped AMP in silica nanoparticles is a safe and effective AMP delivery method that will be useful for developing a drug-device combination product for tissue regeneration.
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Affiliation(s)
- Mi-Ran Ki
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea
- Institute of Industrial Technology, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea
| | - Sung Ho Kim
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea
| | - Tae In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea
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Strobl J, Kozak F, Kamalov M, Reichinger D, Kurzbach D, Becker CF. Understanding Self-Assembly of Silica-Precipitating Peptides to Control Silica Particle Morphology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207586. [PMID: 36509953 DOI: 10.1002/adma.202207586] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The most advanced materials are those found in nature. These evolutionary optimized substances provide highest efficiencies, e.g., in harvesting solar energy or providing extreme stability, and are intrinsically biocompatible. However, the mimicry of biological materials is limited to a few successful applications since there is still a lack of the tools to recreate natural materials. Herein, such means are provided based on a peptide library derived from the silaffin protein R5 that enables rational biomimetic materials design. It is now evident that biomaterials do not form via mechanisms observed in vitro. Instead, the material's function and morphology are predetermined by precursors that self-assemble in solution, often from a combination of protein and salts. These assemblies act as templates for biomaterials. The RRIL peptides used here are a small part of the silica-precipitation machinery in diatoms. By connecting RRIL motifs via varying central bi- or trifunctional residues, a library of stereoisomers is generated, which allows characterization of different template structures in the presence of phosphate ions by combining residue-resolved real-time NMR spectroscopy and molecular dynamics (MD) simulations. Understanding these templates in atomistic detail, the morphology of silica particles is controlled via manipulation of the template precursors.
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Affiliation(s)
- Johannes Strobl
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Fanny Kozak
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Meder Kamalov
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Daniela Reichinger
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Dennis Kurzbach
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Christian Fw Becker
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
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Qiu Y, Lin Y, Zeng B, Qin P, Yi Z, Zhang G. Revealing the role of tunable amino acid residues in elastin-like polypeptides (ELPs)-mediated biomimetic silicification. Int J Biol Macromol 2023; 227:105-112. [PMID: 36539170 DOI: 10.1016/j.ijbiomac.2022.12.152] [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: 11/16/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Elastin-like polypeptides (ELPs) are attractive materials for the green preparation of silica nanoparticles via biomimetic silicification. However, the critical factors affecting the ELP-mediated silicification remain unclear. Herein, the role of tunable amino acid residues of ELPs in silicification was studied using three ELPs (ELPs[V9F-40], ELPs[KV8F-40], and ELPs[K5V4F-40]) and their fusion proteins (ELPs[V9F-40]-SpyCatcher, ELPs[KV8F-40]-SpyCatcher, and ELPs[K5V4F-40]-SpyCatcher) with different contents of lysine residues. Bioinformatics methods were employed for the first time to reveal the key physicochemical parameters correlated with silicification. The specific activity of ELPs was increased with the promotion of lysine content with a high correlation coefficient (R = 0.899). Furthermore, exogenous acidic protein SpyCatcher would hinder the interactions between the silica precursors and ELPs, leading to the significantly decrease in specific activity. The isoelectric point (pI) of ELPs presented the highest correlation to silicification with a coefficient of 0.963. The charges of the ELPs [K5V4F-40] at different pH were calculated based on the sequence or structure. Interestingly, the excellent correlation between charges based on structure and specific activity was obtained. Collectively, the novel methods developed here may pave a new way for rational design of ELPs or other peptides for efficient and green preparation of silica nanomaterials for biomedicine, biocatalysis, and biosensor.
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Affiliation(s)
- Yue Qiu
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou 215008, Jiangsu, China; Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China
| | - Yuanqing Lin
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen 361024, Fujian, China.
| | - Bo Zeng
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Peiliang Qin
- Department of Science and Technology Industry Division, Suzhou Polytechnical Institute of Agriculture, Suzhou, Jiangsu 215008, China
| | - Zhiwei Yi
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China; Technology Innovation Center for Exploitation of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Guangya Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China.
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Reichinger D, Reithofer M, Hohagen M, Drinic M, Tobias J, Wiedermann U, Kleitz F, Jahn-Schmid B, Becker CFW. A Biomimetic, Silaffin R5-Based Antigen Delivery Platform. Pharmaceutics 2022; 15:pharmaceutics15010121. [PMID: 36678751 PMCID: PMC9866965 DOI: 10.3390/pharmaceutics15010121] [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: 11/28/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 01/01/2023] Open
Abstract
Nature offers a wide range of evolutionary optimized materials that combine unique properties with intrinsic biocompatibility and that can be exploited as biomimetic materials. The R5 and RRIL peptides employed here are derived from silaffin proteins that play a crucial role in the biomineralization of marine diatom silica shells and are also able to form silica materials in vitro. Here, we demonstrate the application of biomimetic silica particles as a vaccine delivery and adjuvant platform by linking the precipitating peptides R5 and the RRIL motif to a variety of peptide antigens. The resulting antigen-loaded silica particles combine the advantages of biomaterial-based vaccines with the proven intracellular uptake of silica particles. These particles induce NETosis in human neutrophils as well as IL-6 and TNF-α secretion in murine bone marrow-derived dendritic cells.
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Affiliation(s)
- Daniela Reichinger
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, 1090 Vienna, Austria
| | - Manuel Reithofer
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
- Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180 Vienna, Austria
| | - Mariam Hohagen
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, 1090 Vienna, Austria
- Department of Inorganic Chemistry–Functional Materials, Faculty of Chemistry, University of Vienna, Währinger Str. 42, 1090 Vienna, Austria
| | - Mirjana Drinic
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria
| | - Joshua Tobias
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria
| | - Ursula Wiedermann
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria
| | - Freddy Kleitz
- Department of Inorganic Chemistry–Functional Materials, Faculty of Chemistry, University of Vienna, Währinger Str. 42, 1090 Vienna, Austria
| | - Beatrice Jahn-Schmid
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Christian F. W. Becker
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Correspondence:
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Chen LL, Xu YC, Yang Y, Li N, Zou HX, Wen HH, Yan X. Prediction of peptide-induced silica formation under a wide pH range by molecular descriptors. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.130030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Seevaratnam D, Ansah F, Aniweh Y, Awandare GA, Hall EAH. Analysis and validation of silica-immobilised BST polymerase in loop-mediated isothermal amplification (LAMP) for malaria diagnosis. Anal Bioanal Chem 2022; 414:6309-6326. [PMID: 35657389 PMCID: PMC9163865 DOI: 10.1007/s00216-022-04131-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/04/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022]
Abstract
Bacillus stearothermophilus large fragment (BSTLF) DNA polymerase is reported, isolated on silica via a fused R5 silica-affinity peptide and used in nucleic acid diagnostics. mCherry (mCh), included in the fusion construct, was shown as an efficient fluorescent label to follow the workflow from gene to diagnostic. The R5 immobilisation on silica from cell lysate was consistent with cooperative R5-specific binding of R52-mCh-FL-BSTLF or R52-mCh-H10-BSTLF fusion proteins followed by non-specific protein binding (including E. coli native proteins). Higher R5-binding could be achieved in the presence of phosphate, but phosphate residue reduced loop-mediated isothermal amplification (LAMP) performance, possibly blocking sites on the BSTLF for binding of β- and γ-phosphates of the dNTPs. Quantitative assessment showed that cations (Mg2+ and Mn2+) that complex the PPi product optimised enzyme activity. In malaria testing, the limit of detection depended on Plasmodium species and primer set. For example, 1000 copies of P. knowlesi 18S rRNA could be detected with the P.KNO-LAU primer set with Si-R52-mCh-FL-BSTLF , but 10 copies of P. ovale 18S rRNA could be detected with the P.OVA-HAN primer set using the same enzyme. The Si-immobilised BSTLF outperformed the commercial enzyme for four of the nine Plasmodium LAMP primer sets tested. Si-R52-mCh-FL-BSTLF production was transferred from Cambridge to Accra and set up de novo for a trial with clinical samples. Different detection limits were found, targeting the mitochondrial DNA or the 18S rRNA gene for P. falciparum. The results are discussed in comparison with qPCR and sampling protocol and show that the Si-BSTLF polymerase can be optimised to meet the WHO recommended guidelines.
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Tong X, Kim EJ, Lee JK. Sustainability of in vitro light-dependent NADPH generation by the thylakoid membrane of Synechocystis sp. PCC6803. Microb Cell Fact 2022; 21:94. [PMID: 35643504 PMCID: PMC9148488 DOI: 10.1186/s12934-022-01825-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/15/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND NADPH is used as a reductant in various biosynthetic reactions. Cell-free bio-systems have gained considerable attention owing to their high energy utilization and time efficiency. Efforts have been made to continuously supply reducing power to the reaction mixture in a cyclical manner. The thylakoid membrane (TM) is a promising molecular energy generator, producing NADPH under light. Thus, TM sustainability is of major relevance for its in vitro utilization. RESULTS Over 70% of TMs prepared from Synechocystis sp. PCC6803 existed in a sealed vesicular structure, with the F1 complex of ATP synthase facing outward (right-side-out), producing NADPH and ATP under light. The NADPH generation activity of TM increased approximately two-fold with the addition of carbonyl cyanide-p-(trifluoromethoxy) phenylhydrazone (FCCP) or removal of the F1 complex using EDTA. Thus, the uncoupling of proton translocation from the electron transport chain or proton leakage through the Fo complex resulted in greater NADPH generation. Biosilicified TM retained more than 80% of its NADPH generation activity after a week at 30°C in the dark. However, activity declined sharply to below 30% after two days in light. The introduction of engineered water-forming NADPH oxidase (Noxm) to keep the electron transport chain of TM working resulted in the improved sustainability of NADPH generation activity in a ratio (Noxm to TM)-dependent manner, which correlated with the decrease of singlet oxygen generation. Removal of reactive oxygen species (ROS) by catalase further highlighted the sustainable NADPH generation activity of up to 80% in two days under light. CONCLUSION Reducing power generated by light energy has to be consumed for TM sustainability. Otherwise, TM can generate singlet oxygen, causing oxidative damage. Thus, TMs should be kept in the dark when not in use. Although NADPH generation activity by TM can be extended via silica encapsulation, further removal of hydrogen peroxide results in an improvement of TM sustainability. Therefore, as long as ROS formation by TM in light is properly handled, it can be used as a promising source of reducing power for in vitro biochemical reactions.
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Affiliation(s)
- Xiaomeng Tong
- Department of Life Science, Sogang University, Mapo, Shinsu 1, Seoul, 121-742, Korea
| | - Eui-Jin Kim
- Microbial Research Department, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do, Sangju-si, 37242, Korea.
| | - Jeong K Lee
- Department of Life Science, Sogang University, Mapo, Shinsu 1, Seoul, 121-742, Korea.
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11
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Daus F, Xie X, Geyer A. The silica mineralisation properties of synthetic Silaffin-1A 1 ( synSil-1A 1). Org Biomol Chem 2022; 20:3387-3396. [PMID: 35362502 DOI: 10.1039/d2ob00390b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthetic monodisperse pentadecapeptide synSil-1A1 is a representative of the microdisperse mixture of the native silaffin natSil-1A1 produced by the diatom Cylindrotheca fusiformis. The octaphosphorylated zwitterionic synSil-1A1 is able to mineralise silica under slightly acidic conditions at pH 5.5, which is the physiologically relevant pH range assumed. Like the posttranslational modifications of the native silaffins, synSil-1A1 is functionalised on all four lysine and phosphorylated on all seven serine residues. We describe the synthesis of a trimethyl-δ-hydroxy-L-lysine building block, the incorporation of this choline-type amino acid in peptide synthesis and its phosphorylation, together with all further posttranslational modifications observed in the native silaffins. Quantitative structure-activity relationships from silicification experiments at high dilution reveal the unique mineralisation properties of the hyperphosphorylated peptide as a single substance and in interaction with long-chain polyamines (LCPA). Diffusion-ordered spectroscopy (DOSY) experiments reveal the formation of polyelectrolyte complexes (PEC) between synSil-1A1 and long-chain polyamines, which promotes the silicification process. The microdroplets have an overall balanced ratio of 100-150 cationic and the same number of anionic charges. The unique zwitterionic synSil-1A1 confirms the prevailing molecular model of biosilicification and validates it with quantitative data based on a single phosphopeptide species, avoiding the usual unphysiologically high concentrations of phosphate of many previous in vitro silicification experiments.
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Affiliation(s)
- Fabian Daus
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany.
| | - Xiulan Xie
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany.
| | - Armin Geyer
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany.
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12
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Hare SR, Pfaendtner J. Elucidating the role of catalytic amino acid residues in the peptide-mediated silica oligomerization reaction mechanism. Phys Chem Chem Phys 2022; 24:3664-3674. [PMID: 35080220 DOI: 10.1039/d1cp04542c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the detailed mechanism by which the proteins of marine diatoms such as silaffins are able to control the morphology of silica oligomers has eluded synthetic chemists and materials scientists for decades. In this study, we use DFT calculations to determine how individual amino acid residues of silaffin catalyze silica dimerization. The reaction network for formation of a silica dimer was explored using several different small molecules, including water, guanidinium ions, and methylammonium ions, the latter two molecules representing analogs of arginine and lysine, both of which are known to play critical roles in enabling the catalytic function of naturally occurring protein and synthetic analogs of silaffin. It was found that the lysine analog selectively lowers the energy of a direct water removal pathway for silicate dimerization. Comparing the energy landscapes and mechanisms for various catalysts for this reaction provides direct evidence for the role of lysine side chains of silaffins in the oligmerization of silica.
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Affiliation(s)
- Stephanie R Hare
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA. .,Physical Science Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, USA
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13
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Min KH, Shin JW, Ki MR, Kim SH, Kim KH, Pack SP. Bio-inspired formation of silica particles using the silica-forming peptides found by silica-binding motif sequence, RRSSGGRR. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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14
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Gascoigne L, Magana JR, Atkins DL, Sproncken CCM, Gumi-Audenis B, Schoenmakers SMC, Wakeham D, Wanless EJ, Voets IK. Fractal-like R5 assembly promote the condensation of silicic acid into silica particles. J Colloid Interface Sci 2021; 598:206-212. [PMID: 33905996 DOI: 10.1016/j.jcis.2021.04.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/29/2022]
Abstract
HYPOTHESIS Despite advances in understanding the R5 (SSKKSGSYSGKSGSKRRIL) peptide-driven bio-silica process, there remains significant discrepancies regarding the physicochemical characterization and the self-assembling mechanistic driving forces of the supramolecular R5 template. This paper investigates the self-assembly of R5 as a function of monovalent (sodium chloride) and multivalent salt (phosphate) to determine if assembly is phosphate ion concentration dependent. Additionally, we hypothesize that the assembled R5 aggregates do not resemble a micelle or unimer structure as proposed in current literature. EXPERIMENTS R5 peptides were synthesized, and aggregates evaluated for their size, morphology, and association state as a function of salt and ionic strength concentration via dynamic and static light scattering, small angle X-ray and neutron scattering and cryogenic transmission electron microscopy. Furthermore, we compare the proposed R5 template to precipitated silica by scanning electron microscopy. FINDINGS R5 peptides assemble into large aggregates due to multivalence bridging and the decrease in electrostatic repulsion due to ionic strength. We elucidate the structure of R5 aggregates as mass-fractals composed of small spherical aggregates. Moreover, we discover that phosphate ions not only have a significant role in driving the growth of the R5 scaffold, but additionally in driving the polycondensation of silicic acid during the bio-silification process via electrostatic interactions.
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Affiliation(s)
- Levena Gascoigne
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands; School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.
| | - Jose Rodrigo Magana
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands
| | - Dylan Luke Atkins
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands
| | - Christian C M Sproncken
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands
| | - Berta Gumi-Audenis
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands
| | - Sandra M C Schoenmakers
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands
| | - Deborah Wakeham
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW 2234, Australia
| | - Erica J Wanless
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Ilja Karina Voets
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands.
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15
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Bialas F, Becker CFW. Biomimetic Silica Encapsulation of Lipid Nanodiscs and β-Sheet-Stabilized Diacylglycerol Kinase. Bioconjug Chem 2021; 32:1742-1752. [PMID: 34288667 PMCID: PMC8382255 DOI: 10.1021/acs.bioconjchem.1c00260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/08/2021] [Indexed: 12/21/2022]
Abstract
Integral membrane proteins (IMPs) comprise highly important classes of proteins such as transporters, sensors, and channels, but their investigation and biotechnological application are complicated by the difficulty to stabilize them in solution. We set out to develop a biomimetic procedure to encapsulate functional integral membrane proteins in silica to facilitate their handling under otherwise detrimental conditions and thereby extend their applicability. To this end, we designed and expressed new fusion constructs of the membrane scaffold protein MSP with silica-precipitating peptides based on the R5 sequence from the diatom Cylindrotheca fusiformis. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) revealed that membrane lipid nanodiscs surrounded by our MSP variants fused to an R5 peptide, so-called nanodiscs, were formed. Exposing them to silicic acid led to silica-encapsulated nanodiscs, a new material for stabilizing membrane structures and a first step toward incorporating membrane proteins in such structures. In an alternative approach, four fusion constructs based on the amphiphilic β-sheet peptide BP-1 and the R5 peptide were generated and successfully employed toward silica encapsulation of functional diacylglycerol kinase (DGK). Silica-encapsulated DGK was significantly more stable against protease exposure and incubation with simulated gastric fluid (SGF) and intestinal fluid (SIF).
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Affiliation(s)
- Friedrich Bialas
- Institute of Biological Chemistry,
Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| | - Christian F. W. Becker
- Institute of Biological Chemistry,
Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
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16
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Li K, Li Y, Wang X, Cui M, An B, Pu J, Liu J, Zhang B, Ma G, Zhong C. Diatom-inspired multiscale mineralization of patterned protein-polysaccharide complex structures. Natl Sci Rev 2021; 8:nwaa191. [PMID: 34691703 PMCID: PMC8363331 DOI: 10.1093/nsr/nwaa191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/27/2020] [Accepted: 08/02/2020] [Indexed: 01/11/2023] Open
Abstract
Marine diatoms construct their hierarchically ordered, three-dimensional (3D) external structures called frustules through precise biomineralization processes. Recapitulating the remarkable architectures and functions of diatom frustules in artificial materials is a major challenge that has important technological implications for hierarchically ordered composites. Here, we report the construction of highly ordered, mineralized composites based on fabrication of complex self-supporting porous structures-made of genetically engineered amyloid fusion proteins and the natural polysaccharide chitin-and performing in situ multiscale protein-mediated mineralization with diverse inorganic materials, including SiO2, TiO2 and Ga2O3. Subsequently, using sugar cubes as templates, we demonstrate that 3D fabricated porous structures can become colonized by engineered bacteria and can be functionalized with highly photoreactive minerals, thereby enabling co-localization of the photocatalytic units with a bacteria-based hydrogenase reaction for a successful semi-solid artificial photosynthesis system for hydrogen evolution. Our study thus highlights the power of coupling genetically engineered proteins and polysaccharides with biofabrication techniques to generate hierarchically organized mineralized porous structures inspired by nature.
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Affiliation(s)
- Ke Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yingfeng Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xinyu Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengkui Cui
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Bolin An
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jiahua Pu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jintao Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Boyang Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Guijun Ma
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chao Zhong
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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17
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Cassarino L, Curnow P, Hendry KR. A biomimetic peptide has no effect on the isotopic fractionation during in vitro silica precipitation. Sci Rep 2021; 11:9698. [PMID: 33958622 PMCID: PMC8102562 DOI: 10.1038/s41598-021-88881-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/14/2021] [Indexed: 11/25/2022] Open
Abstract
The stable isotopic composition of diatom silica is used as a proxy for nutrient utilisation in natural waters. This approach provides essential insight into the current and historic links between biological production, carbon cycling and climate. However, estimates of isotopic fractionation during diatom silica production from both laboratory and field studies are variable, and the biochemical pathways responsible remain unknown. Here, we investigate silicon isotopic fractionation through a series of chemical precipitation experiments that are analogous to the first stages of intracellular silica formation within the diatom silicon deposition vesicle. The novelty of our experiment is the inclusion of the R5 peptide, which is closely related to a natural biomolecule known to play a role in diatom silicification. Our results suggest that the presence of R5 induces a systematic but non-significant difference in fractionation behaviour. It thus appears that silicon isotopic fractionation in vitro is largely driven by an early kinetic fractionation during rapid precipitation that correlates with the initial amount of dissolved silica in the system. Our findings raise the question of how environmental changes might impact silicon isotopic fractionation in diatoms, and whether frustule archives record information in addition to silica consumption in surface water.
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Affiliation(s)
- Lucie Cassarino
- University of Bristol, School of Earth Sciences, Wills Memorial Building, Queen's Road, Brsitol, BS8 1RJ, UK.
| | - Paul Curnow
- University of Bristol, School of Biochemistry, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Katharine R Hendry
- University of Bristol, School of Earth Sciences, Wills Memorial Building, Queen's Road, Brsitol, BS8 1RJ, UK
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18
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Nakamura E, Ozaki N, Oaki Y, Imai H. Cellulose intrafibrillar mineralization of biological silica in a rice plant. Sci Rep 2021; 11:7886. [PMID: 33846494 PMCID: PMC8042044 DOI: 10.1038/s41598-021-87144-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/17/2021] [Indexed: 11/09/2022] Open
Abstract
The essence of morphological design has been a fascinating scientific problem with regard to understanding biological mineralization. Particularly shaped amorphous silicas (plant opals) play an important role in the vital activity in rice plants. Although various organic matters are associated with silica accumulation, their detailed functions in the shape-controlled mineralization process have not been sufficiently clarified. In the present study, cellulose nanofibers (CNFs) were found to be essential as a scaffold for silica accumulation in rice husks and leaf blades. Prior to silicification, CNFs ~ 10 nm wide are sparsely stacked in a space between the epidermal cell wall and the cuticle layer. Silica nanoparticles 20-50 nm in diameter are then deposited in the framework of the CNFs. The shape-controlled plant opals are formed through the intrafibrillar mineralization of silica nanoparticles on the CNF scaffold.
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Affiliation(s)
- Eri Nakamura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Noriaki Ozaki
- Department of Biotechnology, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita, 010-0195, Japan
| | - Yuya Oaki
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Hiroaki Imai
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan.
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19
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Lei Q, Guo J, Kong F, Cao J, Wang L, Zhu W, Brinker CJ. Bioinspired Cell Silicification: From Extracellular to Intracellular. J Am Chem Soc 2021; 143:6305-6322. [PMID: 33826324 DOI: 10.1021/jacs.1c00814] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In nature, biosilicification directs the formation of elaborate amorphous silica exoskeletons that provide diatoms mechanically strong, chemically inert, non-decomposable silica armor conferring chemical and thermal stability as well as resistance to microbial attack, without changing the optical transparency or adversely effecting nutrient and waste exchange required for growth. These extraordinary silica/cell biocomposites have inspired decades of biomimetic research aimed at replication of diatoms' hierarchically organized exoskeletons, immobilization of cells or living organisms within silica matrices and coatings to protect them against harmful external stresses, genetic re-programming of cellular functions by virtue of physico-chemical confinement within silica, cellular integration into devices, and endowment of cells with non-native, abiotic properties through facile silica functionalization. In this Perspective, we focus our discussions on the development and concomitant challenges of bioinspired cell silicification ranging from "cells encapsulated within 3D silica matrices" and "cells encapsulated within 2D silica shells" to extra- and intracellular silica replication, wherein all biomolecular interfaces are encased within nanoscopic layers of amorphous silica. We highlight notable examples of advances in the science and technology of biosilicification and consider challenges to advancing the field, where we propose cellular "mineralization" with arbitrary nanoparticle exoskeletons as a generalizable means to impart limitless abiotic properties and functions to cells, and, based on the interchangeability of water and silicic acid and analogies between amorphous ice and amorphous silica, we consider "freezing" cells within amorphous silica as an alternative to cryo-preservation.
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Affiliation(s)
- Qi Lei
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jimin Guo
- Center for Micro-Engineered Materials, Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, United States.,Department of Internal Medicine, Molecular Medicine, The University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Fanhui Kong
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jiangfan Cao
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Lu Wang
- Department of Biochemistry and Molecular Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Wei Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - C Jeffrey Brinker
- Center for Micro-Engineered Materials, Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, United States
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20
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Abdelhamid MAA, Pack SP. Biomimetic and bioinspired silicifications: Recent advances for biomaterial design and applications. Acta Biomater 2021; 120:38-56. [PMID: 32447061 DOI: 10.1016/j.actbio.2020.05.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022]
Abstract
The rational design and controllable synthesis of functional silica-based materials have gained increased interest in a variety of biomedical and biotechnological applications due to their unique properties. The current review shows that marine organisms, such as siliceous sponges and diatoms, could be the inspiration for the fabrication of advanced biohybrid materials. Several biomolecules were involved in the molecular mechanism of biosilicification in vivo. Mimicking their behavior, functional silica-based biomaterials have been generated via biomimetic and bioinspired silicification in vitro. Additionally, several advanced technologies were developed for in vitro and in vivo immobilization of biomolecules with potential applications in biocatalysis, biosensors, bioimaging, and immunoassays. A thin silica layer could coat a single living cell or virus as a protective shell offering new opportunities in biotechnology and nanomedicine fields. Promising nanotechnologies have been developed for drug encapsulation and delivery in a targeted and controlled manner, in particular for poorly soluble hydrophobic drugs. Moreover, biomimetic silica, as a morphogenetically active biocompatible material, has been utilized in the field of bone regeneration and in the development of biomedical implantable devices. STATEMENT OF SIGNIFICANCE: In nature, silica-based biomaterials, such as diatom frustules and sponge spicules, with high mechanical and physical properties were created under biocompatible conditions. The fundamental knowledge underlying the molecular mechanisms of biosilica formation could inspire engineers and chemists to design novel hybrid biomaterials using molecular biomimetic strategies. The production of such biohybrid materials brings the biosilicification field closer to practical applications. This review starts with the biosilicification process of sponges and diatoms with recently updated researches. Then, this article covers recent advances in the design of silica-based biomaterials and their potential applications in the fields of biotechnology and nanomedicine, highlighting several promising technologies for encapsulation of functional proteins and living cells, drug delivery and the preparation of scaffolds for bone regeneration.
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Affiliation(s)
- Mohamed A A Abdelhamid
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea; Department of Botany and Microbiology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea.
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21
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Gigli L, Ravera E, Calderone V, Luchinat C. On the Mechanism of Bioinspired Formation of Inorganic Oxides: Structural Evidence of the Electrostatic Nature of the Interaction between a Mononuclear Inorganic Precursor and Lysozyme. Biomolecules 2020; 11:43. [PMID: 33396930 PMCID: PMC7823628 DOI: 10.3390/biom11010043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/31/2022] Open
Abstract
Nature has evolved several molecular machineries to promote the formation at physiological conditions of inorganic materials, which would otherwise be formed in extreme conditions. The molecular determinants of this process have been established over the last decade, identifying a strong role of electrostatics in the first steps of the precipitation. However, no conclusive, structure-based evidence has been provided so far. In this manuscript, we test the binding of lysozyme with silica and titania potential precursors. In contrast with the absence of structural information about the interaction with the silica precursor, we observe the interaction with a mononuclear titanium(IV) species, which is found to occur in a region rich of positive charges.
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Affiliation(s)
- Lucia Gigli
- Magnetic Resonance Center (CERM)/Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (L.G.); (C.L.)
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, 50019 Florence, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM)/Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (L.G.); (C.L.)
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, 50019 Florence, Italy
| | - Vito Calderone
- Magnetic Resonance Center (CERM)/Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (L.G.); (C.L.)
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, 50019 Florence, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM)/Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (L.G.); (C.L.)
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, 50019 Florence, Italy
- CNR ICCOM, Sesto Fiorentino, 50019 Florence, Italy
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22
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Buckle EL, Sampath J, Michael N, Whedon SD, Leonen CJA, Pfaendtner J, Drobny GP, Chatterjee C. Trimethylation of the R5 Silica-Precipitating Peptide Increases Silica Particle Size by Redirecting Orthosilicate Binding. Chembiochem 2020; 21:3208-3211. [PMID: 32596917 PMCID: PMC8604655 DOI: 10.1002/cbic.202000264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/27/2020] [Indexed: 12/29/2022]
Abstract
The unmodified R5 peptide from silaffin in the diatom Cylindrotheca fusiformis rapidly precipitates silica particles from neutral aqueous solutions of orthosilicic acid. A range of post-translational modifications found in R5 contribute toward tailoring silica morphologies in a species-specific manner. We investigated the specific effect of R5 lysine side-chain trimethylation, which adds permanent positive charges, on silica particle formation. Our studies revealed that a doubly trimethylated R5K3,4me3 peptide has reduced maximum activity yet, surprisingly, generates larger silica particles. Molecular dynamics simulations of R5K3,4me3 binding by the precursor orthosilicate anion revealed that orthosilicate preferentially associates with unmodified lysine side-chain amines and the peptide N terminus. Thus, larger silica particles arise from reduced orthosilicate association with trimethylated lysine side chains and their redirection to the N terminus of the R5 peptide.
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Affiliation(s)
- Erika L Buckle
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Janani Sampath
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Nina Michael
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Samuel D Whedon
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Calvin J A Leonen
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Gary P Drobny
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
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23
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Levin A, Hakala TA, Schnaider L, Bernardes GJL, Gazit E, Knowles TPJ. Biomimetic peptide self-assembly for functional materials. Nat Rev Chem 2020. [DOI: 10.1038/s41570-020-0215-y] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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24
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Peptides from diatoms and grasses harness phosphate ion binding to silica to help regulate biomaterial structure. Acta Biomater 2020; 112:286-297. [PMID: 32434074 DOI: 10.1016/j.actbio.2020.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 05/01/2020] [Accepted: 05/05/2020] [Indexed: 01/08/2023]
Abstract
Many life forms generate intricate submicron biosilica structures with various important biological functions. The formation of such structures, from the silicic acid in the waters and in the soil, is thought to be regulated by unique proteins with high repeats of specific amino acids and unusual sidechain modifications. Some silicifying proteins are characterized by high prevalence of basic amino acids in their primary structures. Lysine-rich domains are found, for instance, in diatom silaffin proteins and in the sorghum grass siliplant1 protein. These domains exhibit catalytic activity in silica chain condensation, owing to molecular interactions of the lysine amine groups with the forming mineral. The use of amine chemistry by two very remote organisms has motivated us to seek other molecular biosilicification processes that may be common to the two life forms. In diatom silaffins, domains rich in phosphoserine residues are thought to assist the assembly of silaffin molecules into an organic supra-structure which serves as a template for the silica to precipitate on. This mold, held by salt bridges between serine phosphates and lysine amines, dictates the shape of the silica particles formed. Yet, silica synthesized with the dephosphorylated silaffin in phosphate buffer showed similar morphology to the one prepared with the native protein, suggesting that a defined spatial arrangement of serine phosphates is not required to generate silica with the desired shape. Concurrently, free phosphates enhanced the activity of siliplant1 in silica formation. It is therefore beneficial to characterize the involvement of these anions as co-factors in regulated silicification by functional peptides from the two proteins and to understand whether they play similar molecular role in the mechanism of mineralization. Here we analyze the molecular interactions of free phosphate ions with silica and the silaffin peptide PL12 and separately with silica and siliplant1 peptide SLP1 in the two biomimetic silica products generated by the two peptides. MAS NMR measurements show that the phosphate ions interact with the peptides and at the same time may be forming bonds with the silica mineral. This bridging capability may add another avenue by which the structure of the silica material is influenced. A model for the molecular/ionic interactions at the bio-inorganic interface is described, which may have bearings for the role of phosphorylated residues beyond the function as intermolecular cross linkers or free phosphate ions as co-factors in regulation of silicification. STATEMENT OF SIGNIFICANCE: The manuscript addresses the question how proteins in diatoms and plants regulate the biosilica materials that are produced for various purposes in organisms. It uses preparation of silica in vitro with functional peptide derivatives from a sorghum grass protein and from a diatom silaffin protein separately to show that phosphate ions are important for the control that is achieved by these proteins on the final shape of the silica material produced. It portrays via magnetic resonance spectroscopic measurements, in atomic detail, the interface between atoms in the peptide, atoms on the surface of the silica formed and the phosphate ions that form chemical bonds with atoms on the silica as part of the mechanism of action of these peptides.
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25
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Qiu Y, Lin Y, Zhang G. Unique silica biomimetic mineralization of acidic elastin-like polypeptides without hydroxyl and charged residues. Int J Biol Macromol 2020; 153:224-231. [PMID: 32142846 DOI: 10.1016/j.ijbiomac.2020.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/18/2020] [Accepted: 03/02/2020] [Indexed: 11/26/2022]
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26
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Hellner B, Alamdari S, Pyles H, Zhang S, Prakash A, Sprenger KG, De Yoreo JJ, Baker D, Pfaendtner J, Baneyx F. Sequence–Structure–Binding Relationships Reveal Adhesion Behavior of the Car9 Solid-Binding Peptide: An Integrated Experimental and Simulation Study. J Am Chem Soc 2020; 142:2355-2363. [DOI: 10.1021/jacs.9b11617] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | | | | | - Shuai Zhang
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | | | | | - James J. De Yoreo
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Daus F, Pfeifer E, Seipp K, Hampp N, Geyer A. The role of phosphopeptides in the mineralisation of silica. Org Biomol Chem 2020; 18:700-706. [DOI: 10.1039/c9ob02438g] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the synthesis of hyperphosphorylated peptides and the investigation of theirin vitrosilicification activity in combination with long-chain polyamines (LCPA) at high dilution and mildly acidic conditions.
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Affiliation(s)
- Fabian Daus
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Erik Pfeifer
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Kevin Seipp
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Norbert Hampp
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Armin Geyer
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
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28
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Novel silica forming peptide, RSGH, from Equus caballus: Its unique biosilica formation under acidic conditions. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107389] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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29
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Sampath J, Pfaendtner J. Amphiphilic peptide binding on crystalline vs. amorphous silica from molecular dynamics simulations. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1657192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Janani Sampath
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
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Lin Y, Jin W, Qiu Y, Zhang G. Programmable stimuli-responsive polypeptides for biomimetic synthesis of silica nanocomposites and enzyme self-immobilization. Int J Biol Macromol 2019; 134:1156-1169. [PMID: 31128196 DOI: 10.1016/j.ijbiomac.2019.05.159] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 12/26/2022]
Abstract
Bioinspired silicification is an attractive route for achieving unique silica nanocomposites. Herein, a novel, facile and inexpensive route for biosilica synthesis is developed using the stimuli-responsive elastin-like polypeptide (ELP). The ELP is precisely tailored to a silica-mineralizing peptide by programming it with lysine residues. The resulting cationic ELP[KV8F-40] is purified in ultrahigh yield using a chromatography-free ITC purification technique based on thermal-responsive property. Excitingly, the specific activity of ELP is 40-fold higher than that of silaffin. Besides, efficient and strong entrapment of ELP is achieved with over 98% of immobilization yield and less than 2% of leakage. These imply that cationic ELP may be used as a bifunctional tag (purification and immobilization) for fusion protein. An enzyme (xylanase) is therefore chosen to genetically fuse to ELP. The ELP-fused xylanase is purified by ELP with high purity (~98%) and enables the rapid (within minutes) self-immobilization. The immobilization yield was greater than 95%, and the immobilized xylanases hardly leaked from the silica matrix, demonstrating high efficiency of the self-immobilization process. The strategy developed here may provide a new opportunity for fabricating functional silica nanocomposites in a feasible and inexpensive pathway, which will have great potentials in the field of biotechnology.
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Affiliation(s)
- Yuanqing Lin
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China
| | - Wenhui Jin
- Third Institute of Oceanography, Ministry of Nature Resources, Xiamen 361005, Fujian, China
| | - Yue Qiu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China
| | - Guangya Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China.
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31
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Mao CM, Sampath J, Sprenger KG, Drobny G, Pfaendtner J. Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5911-5920. [PMID: 30955325 DOI: 10.1021/acs.langmuir.8b01392] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Molecular recognition between peptides and metal oxide surfaces is a fundamental process in biomineralization, self-assembly, and biocompatibility. Yet, the underlying driving forces and dominant mechanisms remain unclear, bringing obstacles to understand and control this process. To elucidate the mechanism of peptide/surface recognition, specifically the role of serine phosphorylation, we employed molecular dynamics simulation and metadynamics-enhanced sampling to study five artificial peptides, DDD, DSS, DpSpS, DpSpSGKK, and DpSKGpSK, interacting with two surfaces: rutile TiO2 and quartz SiO2. On both surfaces, we observe that phosphorylation increases the binding energy. However, the interfacial peptide conformation reveals a distinct binding mechanism on each surface. We also study the impact of peptide sequence to binding free energy and interfacial conformation on both surfaces, specifically the impact on the behavior of phosphorylated serine. Finally, the results are discussed in context of prior studies investigating the role of serine phosphorylation in peptide binding to silica.
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32
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Hellner B, Lee SB, Subramaniam A, Subramanian VR, Baneyx F. Modeling the Cooperative Adsorption of Solid-Binding Proteins on Silica: Molecular Insights from Surface Plasmon Resonance Measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5013-5020. [PMID: 30869906 DOI: 10.1021/acs.langmuir.9b00283] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Combinatorially selected solid-binding peptides (SBPs) provide a versatile route for synthesizing advanced materials and devices, especially when they are installed within structurally or functionally useful protein scaffolds. However, their promise has not been fully realized because we lack a predictive understanding of SBP-material interactions. Thermodynamic and kinetic binding parameters obtained by fitting quartz crystal microbalance and surface plasmon resonance (SPR) data with the Langmuir model whose assumptions are rarely satisfied provide limited information on underpinning molecular interactions. Using SPR, we show here that a technologically useful SBP called Car9 confers proteins to which is fused a sigmoidal adsorption behavior modulated by partner identity, quaternary structure, and ionic strength. We develop a two-step cooperative model that accurately captures the kinetics of silica binding and provides insights into how SBP-SBP interactions, fused scaffold, and solution conditions modulate adsorption. Because cooperative binding can be converted to Langmuir adhesion by mutagenesis, our approach offers a path to identify and to better understand and design practically useful SBPs.
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Affiliation(s)
- Brittney Hellner
- Department of Chemical Engineering , University of Washington , Box 351750 Seattle , 98195 Washington , United States
| | - Seong Beom Lee
- Department of Chemical Engineering , University of Washington , Box 351750 Seattle , 98195 Washington , United States
| | - Akshay Subramaniam
- Department of Chemical Engineering , University of Washington , Box 351750 Seattle , 98195 Washington , United States
| | - Venkat R Subramanian
- Department of Chemical Engineering , University of Washington , Box 351750 Seattle , 98195 Washington , United States
| | - François Baneyx
- Department of Chemical Engineering , University of Washington , Box 351750 Seattle , 98195 Washington , United States
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Del Favero G, Bialas F, Grabher S, Wittig A, Bräuer B, Gerthsen D, Echalier C, Kamalov M, Marko D, Becker CFW. Silica particles with a quercetin–R5 peptide conjugate are taken up into HT-29 cells and translocate into the nucleus. Chem Commun (Camb) 2019; 55:9649-9652. [DOI: 10.1039/c9cc02215e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Particles generated by biomimetic silica precipitation with a quercetin–R5 peptide enter the nucleus of HT-29 cells without inducing toxicity.
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34
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Abdelhamid MAA, Yeo KB, Ki MR, Pack SP. Self-encapsulation and controlled release of recombinant proteins using novel silica-forming peptides as fusion linkers. Int J Biol Macromol 2018; 125:1175-1183. [PMID: 30576734 DOI: 10.1016/j.ijbiomac.2018.12.160] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 01/25/2023]
Abstract
Recently, the potential use of biomimetic silica as smart matrices for the auto-encapsulation and controlled release of functional proteins has gained increased interest because of the mild synthesis conditions. Inspired by biological silicification, in this study, we studied novel silica-forming peptides (SFPs), Volp1 and Salp1, to mediate the generation of silica hybrids in vitro. The fusion of SFPs to model fluorescent proteins directed their auto-encapsulation in wet sol-gel silica materials. Furthermore, the SFPs served as affinity linkers for the immobilization of recombinant proteins in silica. Interestingly, the SFP fusion proteins modulated silicic acid polycondensation and allowed for the self-immobilization of SFP fusion proteins in two distinct silica formulations depending on the ionic strength-precipitated silica particles or wet silica gel. The controlled release of Salp1/Volp1 fusion proteins from silica matrices was significantly greater than that of the silaffin R5 fusion proteins. Subsequently, we showed that multiple SFP-tagged proteins homogenously entrapped within a silica matrix could be separately released following pre-incubation with different concentrations of l-arginine solution. These new findings provide a simple and reproducible route for silica hybrid formation for in situ stable auto-encapsulation and the sustained release of recombinant proteins with potential applications in biotechnology.
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Affiliation(s)
- Mohamed A A Abdelhamid
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong, 30019, Republic of Korea; Department of Botany and Microbiology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Ki Baek Yeo
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong, 30019, Republic of Korea
| | - Mi-Ran Ki
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong, 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong, 30019, Republic of Korea.
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35
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Escobar S, Bernal C, Bolivar JM, Nidetzky B, López-Gallego F, Mesa M. Understanding the silica-based sol-gel encapsulation mechanism of Thermomyces lanuginosus lipase: The role of polyethylenimine. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2018.02.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Sprenger KG, Prakash A, Drobny G, Pfaendtner J. Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1199-1207. [PMID: 28981294 DOI: 10.1021/acs.langmuir.7b02868] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biomimetic silica formation, a process that is largely driven by proteins, has garnered considerable interest in recent years due to its role in the development of new biotechnologies. However, much remains unknown of the molecular-scale mechanisms underlying the binding of proteins to biomineral surfaces such as silica, or even of the key residue-level interactions between such proteins and surfaces. In this study, we employ molecular dynamics (MD) simulations to study the binding of R5-a 19-residue segment of a native silaffin peptide used for in vitro silica formation-to a silica surface. The metadynamics enhanced sampling method is used to converge the binding behavior of R5 on silica at both neutral (pH 7.5) and acidic (pH 5) conditions. The results show fundamental differences in the mechanism of binding between the two cases, providing unique insight into the pH-dependent ability of R5 and native silaffin to precipitate silica. We also study the effect of phosphorylation of serine residues in R5 on both the binding free energy to silica and the interfacial conformation of the peptide. Results indicate that phosphorylation drastically decreases the binding free energy and changes the structure of silica-adsorbed R5 through the introduction of charge and steric repulsion. New mechanistic insights from this work could inform rational design of new biomaterials and biotechnologies.
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Affiliation(s)
- K G Sprenger
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Arushi Prakash
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Gary Drobny
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
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38
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Iline-Vul T, Adiram-Filiba N, Matlahov I, Geiger Y, Abayev M, Keinan-Adamsky K, Akbey U, Oschkinat H, Goobes G. Understanding the roles of functional peptides in designing apatite and silica nanomaterials biomimetically using NMR techniques. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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39
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Song IW, Park H, Park JH, Kim H, Kim SH, Yi S, Jaworski J, Sang BI. Silica formation with nanofiber morphology via helical display of the silaffin R5 peptide on a filamentous bacteriophage. Sci Rep 2017; 7:16212. [PMID: 29176625 PMCID: PMC5701198 DOI: 10.1038/s41598-017-16278-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/09/2017] [Indexed: 11/17/2022] Open
Abstract
Biological systems often generate unique and useful structures, which can have industrial relevance either as direct components or as an inspiration for biomimetic materials. For fabrication of nanoscale silica structures, we explored the use of the silaffin R5 peptide from Cylindrotheca fusiformis expressed on the surface of the fd bacteriophage. By utilizing the biomineralizing peptide component displayed on the bacteriophage surface, we found that low concentrations (0.09 mg/mL of the R5 bacteriophage, below the concentration range used in other studies) could be used to create silica nanofibers. An additional benefit of this approach is the ability of our R5-displaying phage to form silica materials without the need for supplementary components, such as aminopropyl triethoxysilane, that are typically used in such processes. Because this method for silica formation can occur under mild conditions when implementing our R5 displaying phage system, we may provide a relatively simple, economical, and environmentally friendly process for creating silica nanomaterials.
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Affiliation(s)
- In-Wong Song
- Department of Fuel Cell and Hydrogen Technology, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Hyojung Park
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Jung Han Park
- Science&Technology Policy Coordination Division, Ministry of Science, ICT and Future Planning, 47 Gwanmun-ro, Gwacheon-si, Gyeonggi-do, 13809, Republic of Korea
| | - Hyunook Kim
- Department of Environmental Engineering, 163 Seoulsiripdaero, Dongdaemun-gu, The University of Seoul, Seoul, 02504, Republic of Korea
| | - Seong Hun Kim
- Department of Organic and Nano Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Sung Yi
- Department of Fuel Cell and Hydrogen Technology, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Justyn Jaworski
- Department of Bioengineering, University of Texas at Arlington, 500 UTA Blvd., Arlington, TX, 76019, USA.
| | - Byoung-In Sang
- Department of Fuel Cell and Hydrogen Technology, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
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40
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Guo J, Li C, Ling S, Huang W, Chen Y, Kaplan DL. Multiscale design and synthesis of biomimetic gradient protein/biosilica composites for interfacial tissue engineering. Biomaterials 2017; 145:44-55. [PMID: 28843732 PMCID: PMC5610098 DOI: 10.1016/j.biomaterials.2017.08.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/16/2017] [Accepted: 08/14/2017] [Indexed: 01/13/2023]
Abstract
Continuous gradients present at tissue interfaces such as osteochondral systems, reflect complex tissue functions and involve changes in extracellular matrix compositions, cell types and mechanical properties. New and versatile biomaterial strategies are needed to create suitable biomimetic engineered grafts for interfacial tissue engineering. Silk protein-based composites, coupled with selective peptides with mineralization domains, were utilized to mimic the soft-to-hard transition in osteochondral interfaces. The gradient composites supported tunable mineralization and mechanical properties corresponding to the spatial concentration gradient of the mineralization domains (R5 peptide). The composite system exhibited continuous transitions in terms of composition, structure and mechanical properties, as well as cytocompatibility and biodegradability. The gradient silicified silk/R5 composites promoted and regulated osteogenic differentiation of human mesenchymal stem cells in an osteoinductive environment in vitro. The cells differentiated along the composites in a manner consistent with the R5-gradient profile. This novel biomimetic gradient biomaterial design offers a useful approach to meet a broad range of needs in regenerative medicine.
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Affiliation(s)
- Jin Guo
- Department of Chemical and Biological Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA; Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Chunmei Li
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Shengjie Ling
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wenwen Huang
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Ying Chen
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA.
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41
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Buckle EL, Roehrich A, Vandermoon B, Drobny GP. Comparative Study of Secondary Structure and Interactions of the R5 Peptide in Silicon Oxide and Titanium Oxide Coprecipitates Using Solid-State NMR Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10517-10524. [PMID: 28898103 PMCID: PMC6786483 DOI: 10.1021/acs.langmuir.7b01048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A biomimetic, peptide-mediated approach to inorganic nanostructure formation is of great interest as an alternative to industrial production methods. To investigate the role of peptide structure on silica (SiO2) and titania (TiO2) morphologies, we use the R5 peptide domain derived from the silaffin protein to produce uniform SiO2 and TiO2 nanostructures from the precursor silicic acid and titanium bis(ammonium lactato)dihydroxide, respectively. The resulting biosilica and biotitania nanostructures are characterized using scanning electron microscopy. To investigate the process of R5-mediated SiO2 and TiO2 formation, we carry out 1D and 2D solid-state NMR (ssNMR) studies on R5 samples with uniformly 13C- and 15N-labeled residues to determine the backbone and side-chain chemical shifts. 13C chemical shift data are in turn used to determine peptide backbone torsion angles and secondary structure for the R5 peptide neat, in silica, and in titania. We are thus able to assess the impact of the different mineral environments on peptide structure, and we can further elucidate from 13C chemical shifts change the degree to which various side chains are in close proximity to the mineral phases. These comparisons add to the understanding of the role of R5 and its structure in both SiO2 and TiO2 formation.
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Affiliation(s)
- Erika L Buckle
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | - Adrienne Roehrich
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | - Branden Vandermoon
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | - Gary P Drobny
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
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42
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Lutz H, Jaeger V, Schmüser L, Bonn M, Pfaendtner J, Weidner T. The Structure of the Diatom Silaffin Peptide R5 within Freestanding Two-Dimensional Biosilica Sheets. Angew Chem Int Ed Engl 2017; 56:8277-8280. [DOI: 10.1002/anie.201702707] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Helmut Lutz
- Department of Molecular Spectroscopy; Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Vance Jaeger
- Department of Chemical Engineering; University of Washington; 105 Benson Hall Seattle WA 98195-1750 USA
| | - Lars Schmüser
- Department of Molecular Spectroscopy; Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Mischa Bonn
- Department of Molecular Spectroscopy; Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Jim Pfaendtner
- Department of Chemical Engineering; University of Washington; 105 Benson Hall Seattle WA 98195-1750 USA
| | - Tobias Weidner
- Department of Molecular Spectroscopy; Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Denmark
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43
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Lutz H, Jaeger V, Schmüser L, Bonn M, Pfaendtner J, Weidner T. Die Struktur des Silaffin-Peptids R5 aus Diatomeen in freistehenden zweidimensionalen Biosilikatwänden. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Helmut Lutz
- Arbeitskreis Molekulare Spektroskopie; Max-Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Vance Jaeger
- Department of Chemical Engineering; University of Washington; 105 Benson Hall Seattle WA 98195-1750 USA
| | - Lars Schmüser
- Arbeitskreis Molekulare Spektroskopie; Max-Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Mischa Bonn
- Arbeitskreis Molekulare Spektroskopie; Max-Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Jim Pfaendtner
- Department of Chemical Engineering; University of Washington; 105 Benson Hall Seattle WA 98195-1750 USA
| | - Tobias Weidner
- Arbeitskreis Molekulare Spektroskopie; Max-Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Dänemark
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44
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Han W, Chilkoti A, López GP. Self-assembled hybrid elastin-like polypeptide/silica nanoparticles enable triggered drug release. NANOSCALE 2017; 9:6178-6186. [PMID: 28447683 DOI: 10.1039/c7nr00172j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The discovery of biomimetic polypeptides that enable the biomineralization of synthetic and biosynthetic materials has resulted in the development of hybrid materials that incorporate inorganic components for potential application in drug delivery, enzyme immobilization, and surface modification. Here, we describe an approach that uses micellar assemblies of an elastin-like polypeptide (ELP) modified with silica-promoting sequences and drug conjugates that are subsequently encapsulated within a silica matrix. Incorporation of a lysine-rich tag derived from the silaffin R5 peptide into the N-terminus of a hydrophilic ELP that self-assembles upon conjugation of hydrophobic molecules at the C-terminus results in the formation of spherical micelles with a conjugated drug embedded in the core and a corona that is decorated with the silaffin peptide. These micelles serve as the building blocks for the polycondensation of silica into uniform, hybrid polypeptide-silica nanoparticles. We demonstrate proof-of-concept examples using a model hydrophobic small molecule and doxorobucin, a small molecule chemotherapeutic, and further show pH-dependent doxorubicin release from the hybrid nanoparticles.
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Affiliation(s)
- Wei Han
- Research Triangle Materials Science and Engineering Center, Durham, North Carolina 27708, USA.
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Yang W, Hellner B, Baneyx F. Self-Immobilization of Car9 Fusion Proteins within High Surface Area Silica Sol–Gels and Dynamic Control of Protein Release. Bioconjug Chem 2016; 27:2450-2459. [DOI: 10.1021/acs.bioconjchem.6b00406] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Wenlan Yang
- Department of Chemical Engineering, Box
351750, University of Washington, Seattle, Washington 98195, United States
| | - Brittney Hellner
- Department of Chemical Engineering, Box
351750, University of Washington, Seattle, Washington 98195, United States
| | - François Baneyx
- Department of Chemical Engineering, Box
351750, University of Washington, Seattle, Washington 98195, United States
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Hall EA, Chen S, Chun J, Du Y, Zhao Z. A molecular biology approach to protein coupling at a biosensor interface. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.01.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Geiger Y, Gottlieb HE, Akbey Ü, Oschkinat H, Goobes G. Studying the Conformation of a Silaffin-Derived Pentalysine Peptide Embedded in Bioinspired Silica using Solution and Dynamic Nuclear Polarization Magic-Angle Spinning NMR. J Am Chem Soc 2016; 138:5561-7. [DOI: 10.1021/jacs.5b07809] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yasmin Geiger
- Department
of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Hugo E. Gottlieb
- Department
of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Ümit Akbey
- Leibniz Institute für Molekulare Pharmakologie (FMP), NMR Supported Structural Biology, Robert-Roessle-Str.
10, Berlin 13125, Germany
| | - Hartmut Oschkinat
- Leibniz Institute für Molekulare Pharmakologie (FMP), NMR Supported Structural Biology, Robert-Roessle-Str.
10, Berlin 13125, Germany
| | - Gil Goobes
- Department
of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
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Kotzsch A, Pawolski D, Milentyev A, Shevchenko A, Scheffel A, Poulsen N, Shevchenko A, Kröger N. Biochemical Composition and Assembly of Biosilica-associated Insoluble Organic Matrices from the Diatom Thalassiosira pseudonana. J Biol Chem 2016; 291:4982-97. [PMID: 26710847 PMCID: PMC4777836 DOI: 10.1074/jbc.m115.706440] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/23/2015] [Indexed: 11/06/2022] Open
Abstract
The nano- and micropatterned biosilica cell walls of diatoms are remarkable examples of biological morphogenesis and possess highly interesting material properties. Only recently has it been demonstrated that biosilica-associated organic structures with specific nanopatterns (termed insoluble organic matrices) are general components of diatom biosilica. The model diatom Thalassiosira pseudonana contains three types of insoluble organic matrices: chitin meshworks, organic microrings, and organic microplates, the latter being described in the present study for the first time. To date, little is known about the molecular composition, intracellular assembly, and biological functions of organic matrices. Here we have performed structural and functional analyses of the organic microrings and organic microplates from T. pseudonana. Proteomics analysis yielded seven proteins of unknown function (termed SiMat proteins) together with five known silica biomineralization proteins (four cingulins and one silaffin). The location of SiMat1-GFP in the insoluble organic microrings and the similarity of tyrosine- and lysine-rich functional domains identifies this protein as a new member of the cingulin protein family. Mass spectrometric analysis indicates that most of the lysine residues of cingulins and the other insoluble organic matrix proteins are post-translationally modified by short polyamine groups, which are known to enhance the silica formation activity of proteins. Studies with recombinant cingulins (rCinY2 and rCinW2) demonstrate that acidic conditions (pH 5.5) trigger the assembly of mixed cingulin aggregates that have silica formation activity. Our results suggest an important role for cingulins in the biogenesis of organic microrings and support the hypothesis that this type of insoluble organic matrix functions in biosilica morphogenesis.
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Affiliation(s)
| | | | - Alexander Milentyev
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - Anna Shevchenko
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - André Scheffel
- the Max-Planck-Institute of Plant Physiology, 14476 Potsdam, Germany
| | | | - Andrej Shevchenko
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - Nils Kröger
- From the B CUBE Center for Molecular Bioengineering and the Department of Chemistry and Food Chemistry, Technische Universität Dresden, 01307 Dresden, Germany,
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Improved stability and reusability of endoglucanase from Clostridium thermocellum by a biosilica-based auto-encapsulation method. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Martelli T, Ravera E, Louka A, Cerofolini L, Hafner M, Fragai M, Becker CFW, Luchinat C. Atomic-Level Quality Assessment of Enzymes Encapsulated in Bioinspired Silica. Chemistry 2015; 22:425-32. [DOI: 10.1002/chem.201503613] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Indexed: 12/23/2022]
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