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Ma J, Jin B, Guye KN, Chowdhury ME, Naser NY, Chen CL, De Yoreo JJ, Baneyx F. Controlling Mineralization with Protein-Functionalized Peptoid Nanotubes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207543. [PMID: 36281797 DOI: 10.1002/adma.202207543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Sequence-defined foldamers that self-assemble into well-defined architectures are promising scaffolds to template inorganic mineralization. However, it has been challenging to achieve robust control of nucleation and growth without sequence redesign or extensive experimentation. Here, peptoid nanotubes functionalized with a panel of solid-binding proteins are used to mineralize homogeneously distributed and monodisperse anatase nanocrystals from the water-soluble TiBALDH precursor. Crystallite size is systematically tuned between 1.4 and 4.4 nm by changing protein coverage and the identity and valency of the genetically engineered solid-binding segments. The approach is extended to the synthesis of gold nanoparticles and, using a protein encoding both material-binding specificities, to the fabrication of titania/gold nanocomposites capable of photocatalysis under visible-light illumination. Beyond uncovering critical roles for hierarchical organization and denticity on solid-binding protein mineralization outcomes, the strategy described herein should prove valuable for the fabrication of hierarchical hybrid materials incorporating a broad range of inorganic components.
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Affiliation(s)
- Jinrong Ma
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, 98115, USA
| | - Biao Jin
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kathryn N Guye
- Department of Chemistry, University of Washington, Seattle, WA, 98115, USA
| | - Md Emtias Chowdhury
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Nada Y Naser
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98115, USA
| | - Chun-Long Chen
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98115, USA
| | - James J De Yoreo
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98115, USA
| | - François Baneyx
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, 98115, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98115, USA
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2
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Seo K, Hagino K, Ichihashi N. Progresses in Cell-Free In Vitro Evolution. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:121-140. [PMID: 37306699 DOI: 10.1007/10_2023_219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biopolymers, such as proteins and RNA, are integral components of living organisms and have evolved through a process of repeated mutation and selection. The technique of "cell-free in vitro evolution" is a powerful experimental approach for developing biopolymers with desired functions and structural properties. Since Spiegelman's pioneering work over 50 years ago, biopolymers with a wide range of functions have been developed using in vitro evolution in cell-free systems. The use of cell-free systems offers several advantages, including the ability to synthesize a wider range of proteins without the limitations imposed by cytotoxicity, and the capacity for higher throughput and larger library sizes than cell-based evolutionary experiments. In this chapter, we provide a comprehensive overview of the progress made in the field of cell-free in vitro evolution by categorizing evolution into directed and undirected. The biopolymers produced by these methods are valuable assets in medicine and industry, and as a means of exploring the potential of biopolymers.
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Affiliation(s)
- Kaito Seo
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan
| | - Katsumi Hagino
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan.
- Komaba Institute for Science, The University of Tokyo, Tokyo, Japan.
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan.
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3
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Strunge K, Hoinkis N, Lutz H, Alamdari S, Roeters SJ, Lu H, Pfaendtner J, Weidner T. Peptide Mimic of the Marine Sponge Protein Silicatein Fabricates Ultrathin Nanosheets of Silicon Dioxide and Titanium Dioxide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8087-8093. [PMID: 35727216 DOI: 10.1021/acs.langmuir.2c00918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Two-dimensional (2D) materials have attracted attention for potential applications in light harvesting, catalysis, and molecular electronics. Mineral proteins involved in hard tissue biogenesis can produce 2D structures with high fidelity by using sustainable production routes. This study shows that a peptide mimic based on the catalytic triad of the marine sponge protein silicatein catalyzes the formation of nanometer thin and stable sheets of silicon dioxide and titanium dioxide.
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Affiliation(s)
- Kris Strunge
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Nina Hoinkis
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Helmut Lutz
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sarah Alamdari
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
| | - Steven J Roeters
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Hao Lu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
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4
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Joshi N, Kocher GS, Kalia A, Banga HS. Bacillus circulans MTCC 7906 aided facile development of bioconjugate nano-silica alkaline protease formulation with superlative dehairing potential. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117181. [PMID: 33964559 DOI: 10.1016/j.envpol.2021.117181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/30/2021] [Accepted: 04/14/2021] [Indexed: 06/12/2023]
Abstract
The tannery industries utilize environmentally hazardous chemicals to achieve dehairing of animal hides, which causes enormous waterbed pollution & high TDS load. Alkaline protease enzyme for dehairing can be an effective solution to resolve the environmental problems of the tannery industry waste. However, stable, cost-efficient and eco-benign formulations of alkaline protease need to be developed for commercial applications in the tannery industry. This works aimed at development of a nano-formulation of the enzyme alkaline protease (AKP) as a bioconjugate nano silica-alkaline protease enzyme (BC-SiNP-AKP). This work reports one pot green synthesis of the BC-SiNP-AKP bionanoconjugate complex which included both biotemplating and immobilization of the AKP on to the synthesized silica nanoparticles from cell-free extracts of Bacillus circulans grown in potato peel based medium. Among the cell free crude, acetone concentrated and purified sols of the enzyme AKP, acetone precipitated enzyme sol was found to be best for the biological SiNP synthesis and formation of BC-SiNP-AKP conjugate. The BC-SiNP-AKP had size ranging from 100 to 200 nm with crystalline morphologies varying from spherical, tubular to laminated crystallites. The developed bioconjugate formulation displayed 1.7-fold increase in the enzyme activity post nano-conjugation with superlative dehairing potential on goat skin. The optimized parameters for dehairing were found to be as temperature 37 °C for 24 h of incubation and with enzyme to buffer ratio (2: 50 mL). Thereafter, the dehaired skin was assessed for its histopathological effects, which were found to be safe without any deteriorative changes. The developed formulation is environmentally congenial for its use as depilating agent for animal hides in terms of being green, single pot and cost effective synthesis.
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Affiliation(s)
- Nishu Joshi
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147001, India.
| | - Gurvinder Singh Kocher
- Department of Microbiology, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
| | - Anu Kalia
- Electron Microscopy and Nanoscience Laboratory, Department of Soil Science, College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
| | - Harmanjit Singh Banga
- Department of Veterinary Pathology, College of Veterinary Science, Guru Angad Dev Veterinary & Animal Sciences University, Ludhiana, 141 004, Punjab, India
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5
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Amalfitano E, Karlikow M, Norouzi M, Jaenes K, Cicek S, Masum F, Sadat Mousavi P, Guo Y, Tang L, Sydor A, Ma D, Pearson JD, Trcka D, Pinette M, Ambagala A, Babiuk S, Pickering B, Wrana J, Bremner R, Mazzulli T, Sinton D, Brumell JH, Green AA, Pardee K. A glucose meter interface for point-of-care gene circuit-based diagnostics. Nat Commun 2021; 12:724. [PMID: 33526784 PMCID: PMC7851131 DOI: 10.1038/s41467-020-20639-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 12/01/2020] [Indexed: 01/24/2023] Open
Abstract
Recent advances in cell-free synthetic biology have given rise to gene circuit-based sensors with the potential to provide decentralized and low-cost molecular diagnostics. However, it remains a challenge to deliver this sensing capacity into the hands of users in a practical manner. Here, we leverage the glucose meter, one of the most widely available point-of-care sensing devices, to serve as a universal reader for these decentralized diagnostics. We describe a molecular translator that can convert the activation of conventional gene circuit-based sensors into a glucose output that can be read by off-the-shelf glucose meters. We show the development of new glucogenic reporter systems, multiplexed reporter outputs and detection of nucleic acid targets down to the low attomolar range. Using this glucose-meter interface, we demonstrate the detection of a small-molecule analyte; sample-to-result diagnostics for typhoid, paratyphoid A/B; and show the potential for pandemic response with nucleic acid sensors for SARS-CoV-2. Getting synthetic biology circuit-based sensors into field applications is still a challenge. Here the authors combine a circuit sensor with a glucose meter for small analyte and nucleic acid detection.
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Affiliation(s)
- Evan Amalfitano
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Margot Karlikow
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Masoud Norouzi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Katariina Jaenes
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Seray Cicek
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Fahim Masum
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | | | - Yuxiu Guo
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Laura Tang
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Andrew Sydor
- Program in Cell Biology, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, Toronto, ON, M5G 0A4, Canada
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and the School of Molecular Sciences, Arizona State University, AZ, 85287, USA
| | - Joel D Pearson
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada.,Department of Ophthalmology and Vision Science, University of Toronto, Toronto, M5T 3A9, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Daniel Trcka
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada
| | - Mathieu Pinette
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada
| | - Aruna Ambagala
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada
| | - Shawn Babiuk
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada
| | - Bradley Pickering
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, Faculty of Medicine, University of Manitoba, Winnipeg, R3E 0J9, MB, Canada.,Iowa State University, College of Veterinary Medicine, Department of Veterinary Microbiology and Preventive Medicine, Ames, IA, 50011, USA
| | - Jeff Wrana
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Rod Bremner
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada.,Department of Ophthalmology and Vision Science, University of Toronto, Toronto, M5T 3A9, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Tony Mazzulli
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Department of Microbiology, Sinai Health System/University Health Network, Toronto, M5G 1X5, ON, Canada
| | - David Sinton
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, M5S 3G8, ON, Canada
| | - John H Brumell
- Program in Cell Biology, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, M5S 1A8, ON, Canada.,SickKids IBD Centre, Hospital for Sick Children, Toronto, M5G 1X8, ON, Canada
| | - Alexander A Green
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and the School of Molecular Sciences, Arizona State University, AZ, 85287, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada. .,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, M5S 3G8, ON, Canada.
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6
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Yang D, Zhang Y, Zhang S, Cheng Y, Wu Y, Cai Z, Wang X, Shi J, Jiang Z. Coordination between Electron Transfer and Molecule Diffusion through a Bioinspired Amorphous Titania Nanoshell for Photocatalytic Nicotinamide Cofactor Regeneration. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03462] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Dong Yang
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, P. R. China
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, P. R. China
| | - Yishan Zhang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 92 Weijin Road,
Nankai District, Tianjin 300072, P. R. China
| | - Shaohua Zhang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 92 Weijin Road,
Nankai District, Tianjin 300072, P. R. China
| | - Yuqing Cheng
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 92 Weijin Road,
Nankai District, Tianjin 300072, P. R. China
| | - Yizhou Wu
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 92 Weijin Road,
Nankai District, Tianjin 300072, P. R. China
| | - Ziyi Cai
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 92 Weijin Road,
Nankai District, Tianjin 300072, P. R. China
| | - Xiaodong Wang
- Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3UE, Scotland, United Kingdom
| | - Jiafu Shi
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 92 Weijin Road,
Nankai District, Tianjin 300072, P. R. China
| | - Zhongyi Jiang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 92 Weijin Road,
Nankai District, Tianjin 300072, P. R. China
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North Second Street, Zhongguancun, Haidian District, Beijing 100190, P. R. China
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7
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Abstract
Cell-free systems (CFS) have recently evolved into key platforms for synthetic biology applications. Many synthetic biology tools have traditionally relied on cell-based systems, and while their adoption has shown great progress, the constraints inherent to the use of cellular hosts have limited their reach and scope. Cell-free systems, which can be thought of as programmable liquids, have removed many of these complexities and have brought about exciting opportunities for rational design and manipulation of biological systems. Here we review how these simple and accessible enzymatic systems are poised to accelerate the rate of advancement in synthetic biology and, more broadly, biotechnology.
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Affiliation(s)
- Aidan Tinafar
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, ON, M5S 3M2, Canada
| | - Katariina Jaenes
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, ON, M5S 3M2, Canada
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, ON, M5S 3M2, Canada.
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8
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Cuko A, Bromley ST, Calatayud M. Oxygen Vacancies in Oxide Nanoclusters: When Silica Is More Reducible Than Titania. Front Chem 2019; 7:37. [PMID: 30792977 PMCID: PMC6374336 DOI: 10.3389/fchem.2019.00037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/14/2019] [Indexed: 11/24/2022] Open
Abstract
Oxygen vacancies are related to specific optical, conductivity and magnetic properties in macroscopic SiO2 and TiO2 compounds. As such, the ease with which oxygen vacancies form often determines the application potential of these materials in many technological fields. However, little is known about the role of oxygen vacancies in nanosized materials. In this work we compute the energies to create oxygen vacancies in highly stable nanoclusters of (TiO2)N, (SiO2)N, and mixed (TixSi1-xO2)N for sizes between N = 2 and N = 24 units. Contrary to the results for bulk and surfaces, we predict that removing an oxygen atom from global minima silica clusters is energetically more favorable than from the respective titania species. This unexpected chemical behavior is clearly linked to the inherent presence of terminal unsaturated oxygens at these nanoscale systems. In order to fully characterize our findings, we provide an extensive set of descriptors (oxygen vacancy formation energy, electron localization, density of states, relaxation energy, and geometry) that can be used to compare our results with those for other compositions and sizes. Our results will help in the search of novel nanomaterials for technological and scientific applications such as heterogeneous catalysis, electronics, and cluster chemistry.
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Affiliation(s)
- Andi Cuko
- Departament de Ciència de Materials i Química Física, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain
- CNRS, Laboratoire de Chimie Théorique, LCT, Sorbonne Université, Paris, France
| | - Stefan T. Bromley
- Departament de Ciència de Materials i Química Física, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Monica Calatayud
- CNRS, Laboratoire de Chimie Théorique, LCT, Sorbonne Université, Paris, France
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9
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Shkryl YN, Semiletova IV, Nepomnyaschiy AV, Kovalchuk SN, Veremeichik GN, Avramenko TV, Bulgakov VP, Shchipunov YA, Voznesenskiy SS, Kozhemyako VB. Biomimetic Synthesis of Nanosized Silica Structures on a Substrate with Silicatein. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018040180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Bawazer LA, Ihli J, Levenstein MA, Jeuken LJC, Meldrum FC, McMillan DGG. Enzymatically-controlled biomimetic synthesis of titania/protein hybrid thin films. J Mater Chem B 2018; 6:3979-3988. [PMID: 32254326 DOI: 10.1039/c8tb00381e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Although it is widely recognised that enzymes play a significant role in sculpting complex silica skeletons in marine sponges, the potential for exploiting enzymes in materials synthesis has not yet been fully harnessed. In this work we show that the digestive enzyme papain can self-assemble into monolayers on oxide surfaces, where they then drive the formation of crystalline titanium dioxide nanoparticles. This dual functionality of thin film formation and mineralization promotion has the potential to enable the construction of hierarchical inorganic/organic structures in the form of continuous amorphous titania/protein films which can be refined to 93% anatase post annealing. Additional control over the film thickness is afforded by layer-by-layer processing using a simple dip-coating approach. Papain's TiO2-mineralizing activity displays complex kinetics that deviates from the native Michaelis-Menten kinetic activity, yet deactivation studies demonstrate that this activity relies upon residues that are essential for catalytic site function. These parameters provide unique insight into enzymatic biomineralization, allowing a flexible route to achieving bioengineered titania heterostructures, and potentially providing a green-chemistry solution to photovoltaic cell development.
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Affiliation(s)
- L A Bawazer
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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11
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Povarova NV, Markina NM, Baranov MS, Barinov NA, Klinov DV, Kozhemyako VB, Lukyanov KA. A water-soluble precursor for efficient silica polymerization by silicateins. Biochem Biophys Res Commun 2018; 495:2066-2070. [PMID: 29253563 DOI: 10.1016/j.bbrc.2017.12.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 12/14/2017] [Indexed: 11/18/2022]
Abstract
Silicateins, the spicule-forming proteins from marine demosponges capable to polymerize silica, are popular objects of biomineralization studies due to their ability to form particles varied in shape and composition under physiological conditions. Despite the occurrence of the many approaches to nanomaterial synthesis using silicateins, biochemical properties of this protein family are poorly characterized. The main reason for this is that tetraethyl orthosilicate (TEOS), the commonly used silica acid precursor, is almost insoluble in water and thus is poorly available for the protein. To solve this problem, we synthesized new water-soluble silica precursor, tetra(glycerol)orthosilicate (TGS), and characterized biochemical properties of the silicatein A1 from marine sponge Latrunculia oparinae. Compared to TEOS, TGS ensured much greater activity of silicatein and was less toxic for the mammalian cell culture. We evaluated optimum conditions for the enzyme - pH range, temperature and TGS concentration. We concluded that TGS is a useful silica acid precursor that can be used for silica particles synthesis and in vivo applications.
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Affiliation(s)
- Natalia V Povarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia.
| | - Nadezda M Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | - Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435 Moscow, Russia.
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435 Moscow, Russia.
| | - Valery B Kozhemyako
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia.
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia.
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12
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Tang L, Shi J, Wu H, Zhang S, Liu H, Zou H, Wu Y, Zhao J, Jiang Z. In situ biosynthesis of ultrafine metal nanoparticles within a metal-organic framework for efficient heterogeneous catalysis. NANOTECHNOLOGY 2017; 28:365604. [PMID: 28617249 DOI: 10.1088/1361-6528/aa79e1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The synthesis of ultrafine, uniform, well-dispersed functional nanoparticles (NPs) under mild conditions in a controlled manner remains a great challenge. In biological systems, a well-defined biomineralization process is exploited, in which the control over NPs' size, shape and distribution is temporally and spatially regulated by a variety of biomolecules in a confined space. Inspired by this, we embedded proteins into metal-organic frameworks (MOFs) and explored a novel approach to synthesize metallic NPs by taking the synergy of protein-induced biomineralization process and space-confined effect of MOFs. The generation and growth of ultrafine metal NPs (Ag or Au) was induced by the entrapped lysozyme molecules and confined by the ZIF-8 pores. Due to the narrow size distribution and homogeneous spatial distribution of metal NPs, the as-synthesized NPs exhibit remarkably elevated catalytic activity. These findings demonstrate that MOFs can be loaded with specific proteins to selectively deposit inorganic NPs via biomimetic mineralization and these novel kinds of nanohybrid materials may find applications in catalysis, sensing and optics.
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Affiliation(s)
- Lei Tang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
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Curran CD, Lu L, Jia Y, Kiely CJ, Berger BW, McIntosh S. Direct Single-Enzyme Biomineralization of Catalytically Active Ceria and Ceria-Zirconia Nanocrystals. ACS NANO 2017; 11:3337-3346. [PMID: 28212489 DOI: 10.1021/acsnano.7b00696] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Biomineralization is an intriguing approach to the synthesis of functional inorganic materials for energy applications whereby biological systems are engineered to mineralize inorganic materials and control their structure over multiple length scales under mild reaction conditions. Herein we demonstrate a single-enzyme-mediated biomineralization route to synthesize crystalline, catalytically active, quantum-confined ceria (CeO2-x) and ceria-zirconia (Ce1-yZryO2-x) nanocrystals for application as environmental catalysts. In contrast to typical anthropogenic synthesis routes, the crystalline oxide nanoparticles are formed at room temperature from an otherwise inert aqueous solution without the addition of a precipitant or additional reactant. An engineered form of silicatein, rCeSi, as a single enzyme not only catalyzes the direct biomineralization of the nanocrystalline oxides but also serves as a templating agent to control their morphological structure. The biomineralized nanocrystals of less than 3 nm in diameter are catalytically active toward carbon monoxide oxidation following an oxidative annealing step to remove carbonaceous residue. The introduction of zirconia into the nanocrystals leads to an increase in Ce(III) concentration, associated catalytic activity, and the thermal stability of the nanocrystals.
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Affiliation(s)
| | - Li Lu
- Department of Materials Science and Engineering, Lehigh University , 5 East Packer Avenue, Bethlehem, Pennsylvania 18015, United States
| | | | - Christopher J Kiely
- Department of Materials Science and Engineering, Lehigh University , 5 East Packer Avenue, Bethlehem, Pennsylvania 18015, United States
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Bawazer LA, McNally CS, Empson CJ, Marchant WJ, Comyn TP, Niu X, Cho S, McPherson MJ, Binks BP, deMello A, Meldrum FC. Combinatorial microfluidic droplet engineering for biomimetic material synthesis. SCIENCE ADVANCES 2016; 2:e1600567. [PMID: 27730209 PMCID: PMC5055387 DOI: 10.1126/sciadv.1600567] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/31/2016] [Indexed: 05/19/2023]
Abstract
Although droplet-based systems are used in a wide range of technologies, opportunities for systematically customizing their interface chemistries remain relatively unexplored. This article describes a new microfluidic strategy for rapidly tailoring emulsion droplet compositions and properties. The approach uses a simple platform for screening arrays of droplet-based microfluidic devices and couples this with combinatorial selection of the droplet compositions. Through the application of genetic algorithms over multiple screening rounds, droplets with target properties can be rapidly generated. The potential of this method is demonstrated by creating droplets with enhanced stability, where this is achieved by selecting carrier fluid chemistries that promote titanium dioxide formation at the droplet interfaces. The interface is a mixture of amorphous and crystalline phases, and the resulting composite droplets are biocompatible, supporting in vitro protein expression in their interiors. This general strategy will find widespread application in advancing emulsion properties for use in chemistry, biology, materials, and medicine.
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Affiliation(s)
- Lukmaan A. Bawazer
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, U.K
- Corresponding author. (F.C.M.); (L.A.B.)
| | | | | | | | - Tim P. Comyn
- Institute for Materials Research, School of Process, Environmental and Materials Engineering, University of Leeds, Leeds LS2 9JT, U.K
| | - Xize Niu
- Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, U.K
| | - Soongwon Cho
- Samsung Display, 465, Beonyeong-ro, Seobuk-gu, Cheonan-si, Chungcheongnam-do, Republic of Korea
| | - Michael J. McPherson
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Bernard P. Binks
- Surfactant & Colloid Group, Department of Chemistry, University of Hull, Hull HU6 7RX, U.K
| | - Andrew deMello
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Fiona C. Meldrum
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, U.K
- Corresponding author. (F.C.M.); (L.A.B.)
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Shkryl YN, Bulgakov VP, Veremeichik GN, Kovalchuk SN, Kozhemyako VB, Kamenev DG, Semiletova IV, Timofeeva YO, Shchipunov YA, Kulchin YN. Bioinspired enzymatic synthesis of silica nanocrystals provided by recombinant silicatein from the marine sponge Latrunculia oparinae. Bioprocess Biosyst Eng 2016; 39:53-8. [PMID: 26494639 DOI: 10.1007/s00449-015-1488-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/08/2015] [Accepted: 10/12/2015] [Indexed: 11/24/2022]
Abstract
The process of silica formation in marine sponges is thought to be mediated by a family of catalytically active structure-directing enzymes called silicateins. It has been demonstrated in biomimicking syntheses that silicateins facilitated the formation of amorphous SiO2. Here, we present evidence that the silicatein LoSiLA1 from the marine sponge Latrunculia oparinae catalyzes the in vitro synthesis of hexa-tetrahedral SiO2 crystals of 200–300 nm. This was possible in the presence of the silica precursor tetrakis-(2-hydroxyethyl)-orthosilicate that is completely soluble in water and biocompatible, experiences hydrolysis–condensation at neutral pH and ambient conditions.
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16
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Schröder HC, Grebenjuk VA, Wang X, Müller WEG. Hierarchical architecture of sponge spicules: biocatalytic and structure-directing activity of silicatein proteins as model for bioinspired applications. BIOINSPIRATION & BIOMIMETICS 2016; 11:041002. [PMID: 27452043 DOI: 10.1088/1748-3190/11/4/041002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Since the first description of the silicateins, a group of enzymes that mediate the formation of the amorphous, hydrated biosilica of the skeleton of the siliceous sponges, much progress has been achieved in the understanding of this biomineralization process. These discoveries include, beside the proof of the enzymatic nature of the sponge biosilica formation, the dual property of the enzyme, to act both as a structure-forming and structure-guiding protein, and the demonstration that the initial product of silicatein is a soft, gel-like material that has to undergo a maturation process during which it achieves its favorable physical-chemical properties allowing the development of various technological or medical applications. This process comprises the hardening of the material by the removal of water and ions, its cast-molding to specific morphologies, as well as the fusion of the biosilica nanoparticles through a biosintering mechanism. The discovery that the enzymatically formed biosilica is morphogenetically active and printable also opens new applications in rapid prototyping and three-dimensional bioprinting of customized scaffolds/implants for biomedical use.
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Affiliation(s)
- Heinz C Schröder
- Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, D-55128 Mainz, Germany
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17
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Single-enzyme biomineralization of cadmium sulfide nanocrystals with controlled optical properties. Proc Natl Acad Sci U S A 2016; 113:5275-80. [PMID: 27118834 DOI: 10.1073/pnas.1523633113] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nature has evolved several unique biomineralization strategies to direct the synthesis and growth of inorganic materials. These natural systems are complex, involving the interaction of multiple biomolecules to catalyze biomineralization and template growth. Herein we describe the first report to our knowledge of a single enzyme capable of both catalyzing mineralization in otherwise unreactive solution and of templating nanocrystal growth. A recombinant putative cystathionine γ-lyase (smCSE) mineralizes CdS from an aqueous cadmium acetate solution via reactive H2S generation from l-cysteine and controls nanocrystal growth within the quantum confined size range. The role of enzymatic nanocrystal templating is demonstrated by substituting reactive Na2S as the sulfur source. Whereas bulk CdS is formed in the absence of the enzyme or other capping agents, nanocrystal formation is observed when smCSE is present to control the growth. This dual-function, single-enzyme, aerobic, and aqueous route to functional material synthesis demonstrates the powerful potential of engineered functional material biomineralization.
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18
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Molina-Espeja P, Viña-Gonzalez J, Gomez-Fernandez BJ, Martin-Diaz J, Garcia-Ruiz E, Alcalde M. Beyond the outer limits of nature by directed evolution. Biotechnol Adv 2016; 34:754-767. [PMID: 27064127 DOI: 10.1016/j.biotechadv.2016.03.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/22/2016] [Accepted: 03/27/2016] [Indexed: 01/19/2023]
Abstract
For more than thirty years, biotechnology has borne witness to the power of directed evolution in designing molecules of industrial relevance. While scientists all over the world discuss the future of molecular evolution, dozens of laboratory-designed products are being released with improved characteristics in terms of turnover rates, substrate scope, catalytic promiscuity or stability. In this review we aim to present the most recent advances in this fascinating research field that are allowing us to surpass the limits of nature and apply newly gained attributes to a range of applications, from gene therapy to novel green processes. The use of directed evolution in non-natural environments, the generation of catalytic promiscuity for non-natural reactions, the insertion of unnatural amino acids into proteins or the creation of unnatural DNA, is described comprehensively, together with the potential applications in bioremediation, biomedicine and in the generation of new bionanomaterials. These successful case studies show us that the limits of directed evolution will be defined by our own imagination, and in some cases, stretching beyond that.
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Affiliation(s)
- Patricia Molina-Espeja
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Javier Viña-Gonzalez
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | | | - Javier Martin-Diaz
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61801, USA
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain.
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19
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Green DW, Goto TK, Kim KS, Jung HS. Calcifying tissue regeneration via biomimetic materials chemistry. J R Soc Interface 2015; 11:20140537. [PMID: 25320063 DOI: 10.1098/rsif.2014.0537] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Materials chemistry is making a fundamental impact in regenerative sciences providing many platforms for tissue development. However, there is a surprising paucity of replacements that accurately mimic the structure and function of the structural fabric of tissues or promote faithful tissue reconstruction. Methodologies in biomimetic materials chemistry have shown promise in replicating morphologies, architectures and functional building blocks of acellular mineralized tissues dentine, enamel and bone or that can be used to fully regenerate them with integrated cell populations. Biomimetic materials chemistry encompasses the two processes of crystal formation and mineralization of crystals into inorganic formations on organic templates. This review will revisit the successes of biomimetics materials chemistry in regenerative medicine, including coccolithophore simulants able to promote in vivo bone formation. In-depth knowledge of biomineralization throughout evolution informs the biomimetic materials chemist of the most effective techniques for regenerative framework construction exemplified via exploitation of liquid crystals (LCs) and complex self-organizing media. Therefore, a new innovative direction would be to create chemical environments that perform reaction-diffusion exchanges as the basis for building complex biomimetic inorganic structures. This has evolved widely in biology, as have LCs, serving as self-organizing templates in pattern formation of structural biomaterials. For instance, a study is highlighted in which artificially fabricated chiral LCs, made from bacteriophages are transformed into a faithful copy of enamel. While chemical-based strategies are highly promising at creating new biomimetic structures there are limits to the degree of complexity that can be generated. Thus, there may be good reason to implement living or artificial cells in 'morphosynthesis' of complex inorganic constructs. In the future, cellular construction is probably key to instruct building of ultimate biomimetic hierarchies with a totality of functions.
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Affiliation(s)
- David W Green
- Department of Oral Biosciences, The University of Hong Kong, Sai Ying Pun, Hong Kong SAR, People's Republic of China
| | - Tazuko K Goto
- Oral Diagnosis and Polyclinics, Faculty of Dentistry, The University of Hong Kong, Sai Ying Pun, Hong Kong SAR, People's Republic of China
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, College of Medicine, Hanyang University, Seoul, Korea
| | - Han-Sung Jung
- Department of Oral Biosciences, The University of Hong Kong, Sai Ying Pun, Hong Kong SAR, People's Republic of China Division in Anatomy and Developmental Biology, Department of Oral Biology, Oral Science Research Center, BK21 PLUS Project, Yonsei University College of Dentistry, Seoul, Korea
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20
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Bawazer LA, Ihli J, Comyn TP, Critchley K, Empson CJ, Meldrum FC. Genetic algorithm-guided discovery of additive combinations that direct quantum dot assembly. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:223-227. [PMID: 25420626 DOI: 10.1002/adma.201403185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/12/2014] [Indexed: 06/04/2023]
Abstract
The use of combinations of organic additives to control crystallization, as occurs in biomineralization, is rarely investigated due to the vast potential reaction space. It is demonstrated here that combinatorial approaches led by genetic algorithm heuristics can enable identification of active additive combinations, and four key organic molecules are rapidly identified, which generate highly fluorescent CdS quantum dot superstructures.
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Bawazer LA, Newman AM, Gu Q, Ibish A, Arcila M, Cooper JB, Meldrum FC, Morse DE. Efficient selection of biomineralizing DNA aptamers using deep sequencing and population clustering. ACS NANO 2014; 8:387-395. [PMID: 24341560 DOI: 10.1021/nn404448s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
DNA-based information systems drive the combinatorial optimization processes of natural evolution, including the evolution of biominerals. Advances in high-throughput DNA sequencing expand the power of DNA as a potential information platform for combinatorial engineering, but many applications remain to be developed due in part to the challenge of handling large amounts of sequence data. Here we employ high-throughput sequencing and a recently developed clustering method (AutoSOME) to identify single-stranded DNA sequence families that bind specifically to ZnO semiconductor mineral surfaces. These sequences were enriched from a diverse DNA library after a single round of screening, whereas previous screening approaches typically require 5-15 rounds of enrichment for effective sequence identification. The consensus sequence of the largest cluster was poly d(T)30. This consensus sequence exhibited clear aptamer behavior and was shown to promote the synthesis of crystalline ZnO from aqueous solution at near-neutral pH. This activity is significant, as the crystalline form of this wide-bandgap semiconductor is not typically amenable to solution synthesis in this pH range. High-resolution TEM revealed that this DNA synthesis route yields ZnO nanoparticles with an amorphous-crystalline core-shell structure, suggesting that the mechanism of mineralization involves nanoscale coacervation around the DNA template. We thus demonstrate that our new method, termed Single round Enrichment of Ligands by deep Sequencing (SEL-Seq), can facilitate biomimetic synthesis of technological nanomaterials by accelerating combinatorial selection of biomolecular-mineral interactions. Moreover, by enabling direct characterization of sequence family demographics, we anticipate that SEL-Seq will enhance aptamer discovery in applications employing additional rounds of screening.
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Affiliation(s)
- Lukmaan A Bawazer
- Department of Molecular, Cellular and Developmental Biology, Institute for Collaborative Biotechnologies, and Biomolecular Science and Engineering Program, University of California , Santa Barbara, California 93106 , United States
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22
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Tong Z, Jiang Y, Yang D, Shi J, Zhang S, Liu C, Jiang Z. Biomimetic and bioinspired synthesis of titania and titania-based materials. RSC Adv 2014. [DOI: 10.1039/c3ra47336h] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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Park JH, Kim JY, Cho WK, Choi IS. Bioinspired, Cysteamine-Catalyzed Co-Silicification of (1 H, 1 H, 2 H, 2 H-Perfluorooctyl)triethoxysilane and Tetraethyl Orthosilicate: Formation of Superhydrophobic Surfaces. Chem Asian J 2013; 9:764-8. [DOI: 10.1002/asia.201301213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Leconte AM, Dickinson BC, Yang DD, Chen IA, Allen B, Liu DR. A population-based experimental model for protein evolution: effects of mutation rate and selection stringency on evolutionary outcomes. Biochemistry 2013; 52:1490-9. [PMID: 23360105 DOI: 10.1021/bi3016185] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein evolution is a critical component of organismal evolution and a valuable method for the generation of useful molecules in the laboratory. Few studies, however, have experimentally characterized how fundamental parameters influence protein evolution outcomes over long evolutionary trajectories or multiple replicates. In this work, we applied phage-assisted continuous evolution (PACE) as an experimental platform to study evolving protein populations over hundreds of rounds of evolution. We varied evolutionary conditions as T7 RNA polymerase evolved to recognize the T3 promoter DNA sequence and characterized how specific combinations of both mutation rate and selection stringency reproducibly result in different evolutionary outcomes. We observed significant and dramatic increases in the activity of the evolved RNA polymerase variants on the desired target promoter after selection for 96 h, confirming positive selection occurred under all conditions. We used high-throughput sequencing to quantitatively define convergent genetic solutions, including mutational "signatures" and nonsignature mutations that map to specific regions of protein sequence. These findings illuminate key determinants of evolutionary outcomes, inform the design of future protein evolution experiments, and demonstrate the value of PACE as a method for studying protein evolution.
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Affiliation(s)
- Aaron M Leconte
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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26
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Otzen D. The role of proteins in biosilicification. SCIENTIFICA 2012; 2012:867562. [PMID: 24278750 PMCID: PMC3820600 DOI: 10.6064/2012/867562] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 09/24/2012] [Indexed: 05/19/2023]
Abstract
Although the use of silicon dioxide (silica) as a constituent of living organisms is mainly restricted to diatoms and sponges, the ways in which this process is controlled by nature continue to inspire and fascinate. Both diatoms and sponges carry out biosilificiation using an organic matrix but they adopt very different strategies. Diatoms use small and heavily modified peptides called silaffins, where the most characteristic feature is a modulation of charge by attaching long chain polyamines (LCPAs) to lysine groups. Free LCPAs can also cooperate with silaffins. Sponges use the enzyme silicatein which is homologous to the cysteine protease cathepsin. Both classes of proteins form higher-order structures which act both as structural templates and mechanistic catalysts for the polycondensation reaction. In both cases, additional proteins are continuously being discovered which modulate the process further. This paper concentrates on the role of these proteins in the biosilification process as well as in various applications, highlighting areas where focus on specific protein properties may provide further insight. The field of biosilification is a crossroads of different disciplines, where insight into the energetics and mechanisms of molecular self-assembly combine with fundamental biology, complex multicomponent colloidal systems, and an impressive array of potential technological applications.
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Affiliation(s)
- Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Center for Insoluble Protein Structures (inSPIN), and Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
- *Daniel Otzen:
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