1
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Luo L, Manda S, Park Y, Demir B, Sanchez J, Anantram MP, Oren EE, Gopinath A, Rolandi M. DNA nanopores as artificial membrane channels for bioprotonics. Nat Commun 2023; 14:5364. [PMID: 37666808 PMCID: PMC10477224 DOI: 10.1038/s41467-023-40870-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023] Open
Abstract
Biological membrane channels mediate information exchange between cells and facilitate molecular recognition. While tuning the shape and function of membrane channels for precision molecular sensing via de-novo routes is complex, an even more significant challenge is interfacing membrane channels with electronic devices for signal readout, which results in low efficiency of information transfer - one of the major barriers to the continued development of high-performance bioelectronic devices. To this end, we integrate membrane spanning DNA nanopores with bioprotonic contacts to create programmable, modular, and efficient artificial ion-channel interfaces. Here we show that cholesterol modified DNA nanopores spontaneously and with remarkable affinity span the lipid bilayer formed over the planar bio-protonic electrode surface and mediate proton transport across the bilayer. Using the ability to easily modify DNA nanostructures, we illustrate that this bioprotonic device can be programmed for electronic recognition of biomolecular signals such as presence of Streptavidin and the cardiac biomarker B-type natriuretic peptide, without modifying the biomolecules. We anticipate this robust interface will allow facile electronic measurement and quantification of biomolecules in a multiplexed manner.
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Affiliation(s)
- Le Luo
- Department of Electrical and Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Swathi Manda
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yunjeong Park
- Department of Electrical and Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, 06560, Turkey
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Jesse Sanchez
- Department of Electrical and Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR, 97331, USA
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, 06560, Turkey
| | - Ashwin Gopinath
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
- Institute for the Biology of Stem Cells, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
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2
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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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3
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Liu S, Wang Z, Chen K, Yu L, Shi Q, Dong X, Sun Y. Cascade chiral amine synthesis catalyzed by site-specifically co-immobilized alcohol and amine dehydrogenases. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00514j] [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
Sustainable and efficient production of chiral amines was realized with an oriented co-immobilized dual-enzyme system via SiBP-tag.
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Affiliation(s)
- Si Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Zhenfu Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Kun Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Linling Yu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Qinghong Shi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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4
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Yucesoy D, Akkineni S, Tamerler C, Hinds BJ, Sarikaya M. Solid-Binding Peptide-Guided Spatially Directed Immobilization of Kinetically Matched Enzyme Cascades in Membrane Nanoreactors. ACS OMEGA 2021; 6:27129-27139. [PMID: 34693133 PMCID: PMC8529655 DOI: 10.1021/acsomega.1c03774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/20/2021] [Indexed: 05/08/2023]
Abstract
Biocatalysis is a useful strategy for sustainable green synthesis of fine chemicals due to its high catalytic rate, reaction specificity, and operation under ambient conditions. Addressable immobilization of enzymes onto solid supports for one-pot multistep biocatalysis, however, remains a major challenge. In natural pathways, enzymes are spatially coupled to prevent side reactions, eradicate inhibitory products, and channel metabolites sequentially from one enzyme to another. Construction of a modular immobilization platform enabling spatially directed assembly of multiple biocatalysts would, therefore, not only allow the development of high-efficiency bioreactors but also provide novel synthetic routes for chemical synthesis. In this study, we developed a modular cascade flow reactor using a generalizable solid-binding peptide-directed immobilization strategy that allows selective immobilization of fusion enzymes on anodic aluminum oxide (AAO) monoliths with high positional precision. Here, the lactate dehydrogenase and formate dehydrogenase enzymes were fused with substrate-specific peptides to facilitate their self-immobilization through the membrane channels in cascade geometry. Using this cascade model, two-step biocatalytic production of l-lactate is demonstrated with concomitant regeneration of soluble nicotinamide adenine dinucleotide (NADH). Both fusion enzymes retained their catalytic activity upon immobilization, suggesting their optimal display on the support surface. The 85% cascading reaction efficiency was achieved at a flow rate that kinetically matches the residence time of the slowest enzyme. In addition, 84% of initial catalytic activity was preserved after 10 days of continuous operation at room temperature. The peptide-directed modular approach described herein is a highly effective strategy to control surface orientation, spatial localization, and loading of multiple enzymes on solid supports. The implications of this work provide insight for the single-step construction of high-power cascadic devices by enabling co-expression, purification, and immobilization of a variety of engineered fusion enzymes on patterned surfaces.
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Affiliation(s)
- Deniz
T. Yucesoy
- Department
of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Susrut Akkineni
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
| | - Candan Tamerler
- Department
of Mechanical Engineering, Institute for Bioengineering Research, University of Kansas, Lawrence, Kansas 66045, United States
| | - Bruce J. Hinds
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
| | - Mehmet Sarikaya
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
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5
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Pushpavanam K, Ma J, Cai Y, Naser NY, Baneyx F. Solid-Binding Proteins: Bridging Synthesis, Assembly, and Function in Hybrid and Hierarchical Materials Fabrication. Annu Rev Chem Biomol Eng 2021; 12:333-357. [PMID: 33852353 DOI: 10.1146/annurev-chembioeng-102020-015923] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is considerable interest in the development of hybrid organic-inorganic materials because of the potential for harvesting the unique capabilities that each system has to offer. Proteins are an especially attractive organic component owing to the high amount of chemical information encoded in their amino acid sequence, their amenability to molecular and computational (re)design, and the many structures and functions they specify. Genetic installation of solid-binding peptides (SBPs) within protein frameworks affords control over the position and orientation of adhesive and morphogenetic segments, and a path toward predictive synthesis and assembly of functional materials and devices, all while harnessing the built-in properties of the host scaffold. Here, we review the current understanding of the mechanisms through which SBPs bind to technologically relevant interfaces, with an emphasis on the variables that influence the process, and highlight the last decade of progress in the use of solid-binding proteins for hybrid and hierarchical materials synthesis.
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Affiliation(s)
- Karthik Pushpavanam
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - Jinrong Ma
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98115, USA
| | - Yifeng Cai
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - Nada Y Naser
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA; .,Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98115, USA
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6
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Zhong H, Wu G, Fu Z, Lv H, Xu G, Wang R. Flexible Porous Organic Polymer Membranes for Protonic Field-Effect Transistors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2000730. [PMID: 32301209 DOI: 10.1002/adma.202000730] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/06/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Artificial transistors represent an ideal means for meeting the requirements in interfacing with biological systems. It is pivotal to develop new proton-conductive materials for the transduction between biochemical events and electronic signals. Herein, the first demonstration of a porous organic polymer membrane (POPM) as a proton-conductive material for protonic field-effect transistors is presented. The POPM is readily prepared through a thiourea-formation condensation reaction. Under hydrated conditions and at room temperature, the POPM delivers a proton mobility of 5.7 × 10-3 cm2 V-1 s-1 ; the charge carrier densities are successfully modulated from 4.3 × 1017 to 14.1 × 1017 cm-3 by the gate voltage. This study provides a type of promising modular proton-conductive materials for bioelectronics application.
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Affiliation(s)
- Hong Zhong
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guodong Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, China
| | - Zhihua Fu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, China
| | - Haowei Lv
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, China
| | - Gang Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruihu Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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7
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Nag OK, Muroski ME, Hastman DA, Almeida B, Medintz IL, Huston AL, Delehanty JB. Nanoparticle-Mediated Visualization and Control of Cellular Membrane Potential: Strategies, Progress, and Remaining Issues. ACS NANO 2020; 14:2659-2677. [PMID: 32078291 DOI: 10.1021/acsnano.9b10163] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The interfacing of nanoparticle (NP) materials with cells, tissues, and organisms for a range of applications including imaging, sensing, and drug delivery continues at a rampant pace. An emerging theme in this area is the use of NPs and nanostructured surfaces for the imaging and/or control of cellular membrane potential (MP). Given the important role that MP plays in cellular biology, both in normal physiology and in disease, new materials and methods are continually being developed to probe the activity of electrically excitable cells such as neurons and muscle cells. In this Review, we highlight the current state of the art for both the visualization and control of MP using traditional materials and techniques, discuss the advantageous features of NPs for performing these functions, and present recent examples from the literature of how NP materials have been implemented for the visualization and control of the activity of electrically excitable cells. We conclude with a forward-looking perspective of how we expect to see this field progress in the near term and further into the future.
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Affiliation(s)
- Okhil K Nag
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
| | - Megan E Muroski
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
- American Society for Engineering Education, Washington, D.C. 20036, United States
| | - David A Hastman
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Bethany Almeida
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
- American Society for Engineering Education, Washington, D.C. 20036, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
| | - Alan L Huston
- Division of Optical Sciences, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - James B Delehanty
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
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8
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Levin M, Selberg J, Rolandi M. Endogenous Bioelectrics in Development, Cancer, and Regeneration: Drugs and Bioelectronic Devices as Electroceuticals for Regenerative Medicine. iScience 2019; 22:519-533. [PMID: 31837520 PMCID: PMC6920204 DOI: 10.1016/j.isci.2019.11.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/15/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022] Open
Abstract
A major frontier in the post-genomic era is the investigation of the control of coordinated growth and three-dimensional form. Dynamic remodeling of complex organs in regulative embryogenesis, regeneration, and cancer reveals that cells and tissues make decisions that implement complex anatomical outcomes. It is now essential to understand not only the genetics that specifies cellular hardware but also the physiological software that implements tissue-level plasticity and robust morphogenesis. Here, we review recent discoveries about the endogenous mechanisms of bioelectrical communication among non-neural cells that enables them to cooperate in vivo. We discuss important advances in bioelectronics, as well as computational and pharmacological tools that are enabling the taming of biophysical controls toward applications in regenerative medicine and synthetic bioengineering.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA.
| | - John Selberg
- Electrical and Computer Engineering Department, University of California, Santa Cruz, CA 95064, USA
| | - Marco Rolandi
- Electrical and Computer Engineering Department, University of California, Santa Cruz, CA 95064, USA
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9
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Strakosas X, Selberg J, Pansodtee P, Yonas N, Manapongpun P, Teodorescu M, Rolandi M. A non-enzymatic glucose sensor enabled by bioelectronic pH control. Sci Rep 2019; 9:10844. [PMID: 31350439 PMCID: PMC6659689 DOI: 10.1038/s41598-019-46302-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/10/2019] [Indexed: 12/17/2022] Open
Abstract
Continuous glucose monitoring from sweat and tears can improve the quality of life of diabetic patients and provide data for more accurate diagnosis and treatment. Current continuous glucose sensors use enzymes with a one-to-two week lifespan, which forces periodic replacement. Metal oxide sensors are an alternative to enzymatic sensors with a longer lifetime. However, metal oxide sensors do not operate in sweat and tears because they function at high pH (pH > 10), and sweat and tears are neutral (pH = 7). Here, we introduce a non-enzymatic metal oxide glucose sensor that functions in neutral fluids by electronically inducing a reversible and localized pH change. We demonstrate glucose monitoring at physiologically relevant levels in neutral fluids mimicking sweat, and wireless communication with a personal computer via an integrated circuit board.
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Affiliation(s)
- Xenofon Strakosas
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - John Selberg
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Pattawong Pansodtee
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Nebyu Yonas
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Pattawut Manapongpun
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mircea Teodorescu
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
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10
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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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11
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Hemmatian Z, Tunuguntla RH, Noy A, Rolandi M. Electronic control of H+ current in a bioprotonic device with carbon nanotube porins. PLoS One 2019; 14:e0212197. [PMID: 30794578 PMCID: PMC6386364 DOI: 10.1371/journal.pone.0212197] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 01/29/2019] [Indexed: 01/04/2023] Open
Abstract
Hybrid biotic abiotic devices can be used to interface electronics with biological systems for novel therapies or to increase device functionality beyond silicon. Many strategies exist to merge the electronic and biological worlds, one dominated by electrons and holes as charge carriers, the other by ions. In the biological world, lipid bilayers and ion channels are essential to compartmentalize the cell machinery and regulate ionic fluxes across the cell membrane. Here, we demonstrate a bioelectronic device in which a lipid bilayer supported on H+-conducting Pd/PdHx contacts contains carbon nanotubes porin (CNTP) channels. This bioelectronic device uses CNTPs to control of H+ flow across the lipid bilayer with a voltage applied to the Pd/PdHx contacts. Potential applications of these devices include local pH sensing and control.
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Affiliation(s)
- Zahra Hemmatian
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
| | - Ramya H. Tunuguntla
- Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Aleksandr Noy
- Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
- School of Natural Sciences, University of California Merced, Merced, CA, United States of America
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
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12
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Soto-Rodríguez J, Hemmatian Z, Black J, Rolandi M, Baneyx F. Two-Channel Bioprotonic Photodetector. ACS APPLIED BIO MATERIALS 2019; 2:930-935. [DOI: 10.1021/acsabm.8b00789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jessica Soto-Rodríguez
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington 98195, United States
| | - Zahra Hemmatian
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, California 95064, United States
| | - Jennifer Black
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, California 95064, United States
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, California 95064, United States
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington 98195, United States
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13
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Soto-Rodríguez J, Baneyx F. Role of the signal sequence in proteorhodopsin biogenesis in E. coli. Biotechnol Bioeng 2018; 116:912-918. [PMID: 30475397 DOI: 10.1002/bit.26878] [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: 09/06/2018] [Revised: 10/16/2018] [Accepted: 11/21/2018] [Indexed: 12/16/2022]
Abstract
Blue-absorbing proteorhodopsin (BPR) from marine bacteria is a retinal-bound, light-activated, outwards proton transporter containing seven α-helical transmembrane segments (TMS). It is synthesized as a precursor species (pre-BPR) with a predicted N-terminal signal sequence that is cleaved to yield the mature protein. While optimizing the production of BPR in Escherichia coli to facilitate the construction of bioprotonic devices, we observed significant pre-BPR accumulation in the inner membrane and explored signal sequence requirements and export pathway. We report here that BPR does not rely on the Sec pathway for inner membrane integration, and that although it greatly enhances yields, its signal sequence is not necessary to obtain a functional product. We further show that an unprocessable version of pre-BPR obtained by mutagenesis of the signal peptidase I site exhibits all functional attributes of the wild-type protein and has the advantage of being produced at higher levels. Our results are consistent with the BPR signal sequence being recognized by the signal recognition particle (SRP; a protein that orchestrates the cotranslational biogenesis of inner membrane proteins) and serving as a beneficial "pro" domain rather than a traditional secretory peptide.
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Affiliation(s)
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, Washington
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14
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The Potential for Convergence between Synthetic Biology and Bioelectronics. Cell Syst 2018; 7:231-244. [DOI: 10.1016/j.cels.2018.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/30/2018] [Accepted: 08/13/2018] [Indexed: 01/20/2023]
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15
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A protonic biotransducer controlling mitochondrial ATP synthesis. Sci Rep 2018; 8:10423. [PMID: 30002478 PMCID: PMC6043558 DOI: 10.1038/s41598-018-28435-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/20/2018] [Indexed: 12/14/2022] Open
Abstract
In nature, protons (H+) play an important role in biological activities such as in mitochondrial ATP synthesis, which is driven by a H+ gradient across the inner membrane, or in the activation of acid sensing ion channels in neuron cells. Bioprotonic devices directly interface with the H+ concentration (pH) to facilitate engineered interactions with these biochemical processes. Here we develop a H+ biotransducer that changes the pH in a mitochondrial matrix by controlling the flow of H+ between a conductive polymer of sulfonated polyaniline and solution. We have successfully modulated the rate of ATP synthesis in mitochondria by altering the solution pH. Our H+ biotransducer provides a new way to monitor and modulate pH dependent biological functions at the interface between the electronic devices and biological materials.
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Strakosas X, Selberg J, Hemmatian Z, Rolandi M. Taking Electrons out of Bioelectronics: From Bioprotonic Transistors to Ion Channels. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2017; 4:1600527. [PMID: 28725527 PMCID: PMC5515233 DOI: 10.1002/advs.201600527] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/14/2017] [Indexed: 05/08/2023]
Abstract
From cell-to-cell communication to metabolic reactions, ions and protons (H+) play a central role in many biological processes. Examples of H+ in action include oxidative phosphorylation, acid sensitive ion channels, and pH dependent enzymatic reactions. To monitor and control biological reactions in biology and medicine, it is desirable to have electronic devices with ionic and protonic currents. Here, we summarize our latest efforts on bioprotonic devices that monitor and control a current of H+ in physiological conditions, and discuss future potential applications. Specifically, we describe the integration of these devices with enzymatic logic gates, bioluminescent reactions, and ion channels.
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Affiliation(s)
- Xenofon Strakosas
- Department of Electrical EngineeringUniversity of California Santa CruzSanta CruzCalifornia95064USA
| | - John Selberg
- Department of Electrical EngineeringUniversity of California Santa CruzSanta CruzCalifornia95064USA
| | - Zahra Hemmatian
- Department of Electrical EngineeringUniversity of California Santa CruzSanta CruzCalifornia95064USA
| | - Marco Rolandi
- Department of Electrical EngineeringUniversity of California Santa CruzSanta CruzCalifornia95064USA
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17
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Hemmatian Z, Keene S, Josberger E, Miyake T, Arboleda C, Soto-Rodríguez J, Baneyx F, Rolandi M. Electronic control of H + current in a bioprotonic device with Gramicidin A and Alamethicin. Nat Commun 2016; 7:12981. [PMID: 27713411 PMCID: PMC5059763 DOI: 10.1038/ncomms12981] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 08/19/2016] [Indexed: 12/04/2022] Open
Abstract
In biological systems, intercellular communication is mediated by membrane proteins and ion channels that regulate traffic of ions and small molecules across cell membranes. A bioelectronic device with ion channels that control ionic flow across a supported lipid bilayer (SLB) should therefore be ideal for interfacing with biological systems. Here, we demonstrate a biotic-abiotic bioprotonic device with Pd contacts that regulates proton (H+) flow across an SLB incorporating the ion channels Gramicidin A (gA) and Alamethicin (ALM). We model the device characteristics using the Goldman-Hodgkin-Katz (GHK) solution to the Nernst-Planck equation for transport across the membrane. We derive the permeability for an SLB integrating gA and ALM and demonstrate pH control as a function of applied voltage and membrane permeability. This work opens the door to integrating more complex H+ channels at the Pd contact interface to produce responsive biotic-abiotic devices with increased functionality.
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Affiliation(s)
- Zahra Hemmatian
- Department of Electrical Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Scott Keene
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Erik Josberger
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, USA
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Takeo Miyake
- Department of Electrical Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Carina Arboleda
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Jessica Soto-Rodríguez
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Marco Rolandi
- Department of Electrical Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, USA
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