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Wei X, Penkauskas T, Reiner JE, Kennard C, Uline MJ, Wang Q, Li S, Aksimentiev A, Robertson JW, Liu C. Engineering Biological Nanopore Approaches toward Protein Sequencing. ACS NANO 2023; 17:16369-16395. [PMID: 37490313 PMCID: PMC10676712 DOI: 10.1021/acsnano.3c05628] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.
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Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Tadas Penkauskas
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
- School of Engineering, Brown University, Providence, RI 02912, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Celeste Kennard
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
| | - Mark J. Uline
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Sheng Li
- School of Data Science, University of Virginia, Charlottesville, VA 22903, United States
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joseph W.F. Robertson
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
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2
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Abstract
Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and out of cells, contributing to maintaining most of the fundamental processes that sustain living organisms. As in several other occasions, we have borrowed from the natural properties of these biological systems to push technology forward and have been able to hijack these nano-scale proteinaceous pores to learn about the physical and chemical features of molecules passing through them. Today, a large repertoire of biological pores is exploited as molecular sensors for characterizing biomolecules that are relevant for the advancement of life sciences and application to medicine. Although the technology has quickly matured to enable nucleic acid sensing with transformative implications for genomics, biological pores stand as some of the most promising candidates to drive the next developments in single-molecule proteomics.
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Affiliation(s)
- Simon Finn Mayer
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Chan Cao
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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3
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A H, Yang Z, Hu R, Chen YF. Roles of energy dissipation and asymmetric wettability in spontaneous imbibition dynamics in a nanochannel. J Colloid Interface Sci 2021; 607:1023-1035. [PMID: 34571292 DOI: 10.1016/j.jcis.2021.09.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/29/2021] [Accepted: 09/09/2021] [Indexed: 01/28/2023]
Abstract
HYPOTHESIS The imbibition dynamics is controlled by energy dissipation mechanisms and influenced by asymmetric wettability in a nanochannel. We hypothesize that the imbibition dynamics can be described by a combined model of the Lucas-Washburn equation and the Cox-Voinov law considering velocity-dependent contact angles. METHODS Molecular dynamics simulations are utilized to investigate the imbibition dynamics. A wide range of wetting conditions is achieved via adjusting the liquid-solid interaction parameters, and the spontaneous imbibition processes are quantified and compared. FINDINGS The critical condition for the occurrence of spontaneous imbibition is analyzed from a surface energy perspective. The analyses of energy conversion and dissipation indicate that the viscous dissipation is dominant during spontaneous imbibition. The classical Lucas-Washburn equation is modified with the Cox-Voinov law considering the effect of the dynamic contact angle and an effective equilibrium contact angle. We show that the proposed theory well captures the imbibition dynamics embodied in the growth of imbibition length as well as the transient interface shape and velocity for both the symmetric and asymmetric wetting conditions. In nanochannels with asymmetric wettability, the imbibition length difference between the sidewalls and interface oscillations increases with wetting disparity. Our findings deepen the understanding of imbibition dynamics on the nanoscale, and provide a theoretical reference for relevant applications.
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Affiliation(s)
- Hubao A
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China; Key Laboratory of Rock Mechanics in Hydraulic Structural Engineering of the Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Zhibing Yang
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China; Key Laboratory of Rock Mechanics in Hydraulic Structural Engineering of the Ministry of Education, Wuhan University, Wuhan 430072, China.
| | - Ran Hu
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China; Key Laboratory of Rock Mechanics in Hydraulic Structural Engineering of the Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Yi-Feng Chen
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China; Key Laboratory of Rock Mechanics in Hydraulic Structural Engineering of the Ministry of Education, Wuhan University, Wuhan 430072, China
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Robertson JW, Ghimire M, Reiner JE. Nanopore sensing: A physical-chemical approach. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183644. [PMID: 33989531 PMCID: PMC9793329 DOI: 10.1016/j.bbamem.2021.183644] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022]
Abstract
Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.
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Affiliation(s)
- Joseph W.F. Robertson
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg MD. 20899, correspondence to:
| | - Madhav Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, VA
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA
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5
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Mereuta L, Asandei A, Dragomir IS, Bucataru IC, Park J, Seo CH, Park Y, Luchian T. Sequence-specific detection of single-stranded DNA with a gold nanoparticle-protein nanopore approach. Sci Rep 2020; 10:11323. [PMID: 32647249 PMCID: PMC7347621 DOI: 10.1038/s41598-020-68258-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Fast, cheap and easy to use nucleic acids detection methods are crucial to mitigate adverse impacts caused by various pathogens, and are essential in forensic investigations, food safety monitoring or evolution of infectious diseases. We report here a method based on the α-hemolysin (α-HL) nanopore, working in conjunction to unmodified citrate anion-coated gold nanoparticles (AuNPs), to detect nanomolar concentrations of short single-stranded DNA sequences (ssDNA). The core idea was to use charge neutral peptide nucleic acids (PNA) as hybridization probe for complementary target ssDNAs, and monitor at the single-particle level the PNA-induced aggregation propensity AuNPs during PNA–DNA duplexes formation, by recording ionic current blockades signature of AuNP–α-HL interactions. This approach offers advantages including: (1) a simple to operate platform, producing clear-cut readout signals based on distinct size differences of PNA-induced AuNPs aggregates, in relation to the presence in solution of complementary ssDNAs to the PNA fragments (2) sensitive and selective detection of target ssDNAs (3) specific ssDNA detection in the presence of interference DNA, without sample labeling or signal amplification. The powerful synergy of protein nanopore-based nanoparticle detection and specific PNA–DNA hybridization introduces a new strategy for nucleic acids biosensing with short detection time and label-free operation.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, 'Alexandru I. Cuza' University, 700506, Iasi, Romania.
| | - Alina Asandei
- Sciences Department, Interdisciplinary Research Institute, 'Alexandru I. Cuza' University, 700506, Iasi, Romania
| | - Isabela S Dragomir
- Sciences Department, Interdisciplinary Research Institute, 'Alexandru I. Cuza' University, 700506, Iasi, Romania
| | - Ioana C Bucataru
- Department of Physics, 'Alexandru I. Cuza' University, 700506, Iasi, Romania
| | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, Kongju, 32588, Republic of Korea
| | - Chang Ho Seo
- Department of Bioinformatics, Kongju National University, Kongju, 32588, Republic of Korea
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, 61452, Republic of Korea.
| | - Tudor Luchian
- Department of Physics, 'Alexandru I. Cuza' University, 700506, Iasi, Romania.
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Chen L, Lv D, Wang S, Wang D, Chen X, Liu Y, Hong Z, Zhu Z, Cao Y, Chai Y. Surface Plasmon Resonance-Based Membrane Protein-Targeted Active Ingredients Recognition Strategy: Construction and Implementation in Ligand Screening from Herbal Medicines. Anal Chem 2020; 92:3972-3980. [DOI: 10.1021/acs.analchem.9b05479] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Langdong Chen
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Diya Lv
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Shaozhan Wang
- Department of Pharmacy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, PR China
| | - Dongyao Wang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Xiaofei Chen
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Yue Liu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Zhanying Hong
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Zhenyu Zhu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Yan Cao
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
| | - Yifeng Chai
- School of Pharmacy, Second Military Medical University, Shanghai 200433, PR China
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7
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Ming Z, Pang Y, Liu J. Mechanical Deformation Mediated Transmembrane Transport. Macromol Rapid Commun 2019; 41:e1900518. [PMID: 31885137 DOI: 10.1002/marc.201900518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/06/2019] [Indexed: 12/15/2022]
Abstract
Transmembrane transport is essential and plays critical roles for molecule exchange for cell survival. Methods capable of mimicking and regulating transmembrane transport have transformed the ability to create biosensors, separation membranes, and drug carriers. However, artificial channels have been largely restricted by their complicated chemical fabrication and inefficiency to dynamically manipulate the transport process. Here, a novel approach to regulate transmembrane transport is described by simply adjusting the mechanical deformation of liposomal bilayers which are covalently embedded in a crosslinked hydrogel network. This new approach is able to dynamically control transmembrane transport by stretching and loosening. The transmembrane diffusion of molecules can be switched on and off, and precisely tuned by varying strain. A potential of this method to programmably regulate cell growth is demonstrated by tuning external mechanical force. Given its unique characteristics, this method allows the development of innovative systems for controlled transmembrane transport of molecules.
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Affiliation(s)
- Zunzhen Ming
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Institute of Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yan Pang
- Department of Ophthalmology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200011, China
| | - Jinyao Liu
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Institute of Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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8
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Ferreira RJ, Kasson PM. Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics. ACS Infect Dis 2019; 5:2096-2104. [PMID: 31593635 DOI: 10.1021/acsinfecdis.9b00201] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Crossing the Gram-negative bacterial membrane poses a major barrier to antibiotic development, as many small molecules that can biochemically inhibit key bacterial processes are rendered microbiologically ineffective by their poor cellular uptake. The outer membrane is the major permeability barrier for many drug-like molecules, and the chemical properties that enable efficient uptake into mammalian cells fail to predict bacterial uptake. We have developed a computational method for accurate prospective prediction of outer membrane uptake of drug-like molecules, which we combine with a new medium-throughput experimental assay of outer membrane vesicle swelling. Parallel molecular dynamics simulations of compound uptake through Escherichia coli (E. coli) OmpF are used to successfully and quantitatively predict experimental permeabilities measured via either outer membrane swelling or prior liposome-swelling measurements. These simulations are analyzed using an inhomogeneous solubility-diffusion model to yield predictions of permeability. For most polar molecules we test, outer membrane permeability also correlates well with whole-cell uptake. The ability to accurately predict and measure outer membrane uptake of a wide variety of small molecules will enable simpler determination of which molecular scaffolds and which derivatives are most promising prior to extensive chemical synthesis. It will also assist in formulating a more systematic understanding of the chemical determinants of outer membrane permeability.
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Affiliation(s)
- Ricardo J. Ferreira
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Peter M. Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
- Departments of Biomedical Engineering and Molecular Physiology and Biological Physics, University of Virginia, Box 800886, Charlottesville, Virginia 22908, United States
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9
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Hoogerheide DP, Noskov SY, Kuszak AJ, Buchanan SK, Rostovtseva TK, Nanda H. Structure of voltage-dependent anion channel-tethered bilayer lipid membranes determined using neutron reflectivity. Acta Crystallogr D Struct Biol 2018; 74:1219-1232. [PMID: 30605136 PMCID: PMC6317592 DOI: 10.1107/s2059798318011749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/20/2018] [Indexed: 01/05/2023] Open
Abstract
Neutron reflectivity (NR) has emerged as a powerful technique to study the structure and behavior of membrane proteins at planar lipid interfaces. Integral membrane proteins (IMPs) remain a significant challenge for NR owing to the difficulty of forming complete bilayers with sufficient protein density for scattering techniques. One strategy to achieve high protein density on a solid substrate is the capture of detergent-stabilized, affinity-tagged IMPs on a nitrilotriacetic acid (NTA)-functionalized self-assembled monolayer (SAM), followed by reconstitution into the lipids of interest. Such protein-tethered bilayer lipid membranes (ptBLMs) have the notable advantage of a uniform IMP orientation on the substrate. Here, NR is used to provide a structural characterization of the ptBLM process from formation of the SAM to capture of the detergent-stabilized IMP and lipid reconstitution. The mitochondrial outer-membrane voltage-dependent anion channel (VDAC), which controls the exchange of bioenergetic metabolites between mitochondria and the cytosol, was used as a model β-barrel IMP. Molecular dynamics simulations were used for comparison with the experimental results and to inform the parameters of the physical models describing the NR data. The detailed structure of the SAM is shown to depend on the density of the NTA chelating groups. The relative content of detergent and protein in surface-immobilized, detergent-stabilized VDAC is measured, while the reconstituted lipid bilayer is shown to be complete to within a few percent, using the known atomic structure of VDAC. Finally, excess lipid above the reconstituted bilayer, which is of consequence for more indirect structural and functional studies, is shown to be present.
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Affiliation(s)
- David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20878, USA
| | - Sergei Yu. Noskov
- Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Adam J. Kuszak
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan K. Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tatiana K. Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hirsh Nanda
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20878, USA
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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10
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Wang H, Ettedgui J, Forstater J, Robertson JWF, Reiner JE, Zhang H, Chen S, Kasianowicz JJ. Determining the Physical Properties of Molecules with Nanometer-Scale Pores. ACS Sens 2018; 3:251-263. [PMID: 29381331 DOI: 10.1021/acssensors.7b00680] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nanometer-scale pores have been developed for the detection, characterization, and quantification of a wide range of analytes (e.g., ions, polymers, proteins, anthrax toxins, neurotransmitters, and synthetic nanoparticles) and for DNA sequencing. We describe the key requirements that made this method possible and how the technique evolved. Finally, we show that, despite sound theoretical work, which advanced both the conceptual framework and quantitative capability of the method, there are still unresolved questions that need to be addressed to further improve the technique.
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Affiliation(s)
- Haiyan Wang
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - Jessica Ettedgui
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Chemical Engineering, Columbia University New York, New York 10027, United States
| | - Jacob Forstater
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Chemical Engineering, Columbia University New York, New York 10027, United States
| | - Joseph W. F. Robertson
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
| | - Joseph E. Reiner
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Huisheng Zhang
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - Siping Chen
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - John J. Kasianowicz
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Applied Physics Applied Mathematics, Columbia University New York, New York 10027, United States
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11
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Cao C, Long YT. Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis. Acc Chem Res 2018; 51:331-341. [PMID: 29364650 DOI: 10.1021/acs.accounts.7b00143] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis, we develop an integrated current measurement system and an accurate data processing method for nanopore sensing. The unique geometric structure of a biological nanopore offers a distinct advantage as a nanosensor for single-molecule sensing. The construction of the pore entrance is responsible for capturing the target molecule, while the lumen region determines the translocation process of the single molecule. Since the capture of the target molecule is predominantly diffusion-limited, it is expected that the capture ability of the nanopore toward the target analyte could be effectively enhanced by site-directed mutations of key amino acids with desirable groups. Additionally, changing the side chains inside the wall of the biological nanopore could optimize the geometry of the pore and realize an optimal interaction between the single-molecule interface and the analyte. These improvements would allow for high spatial and current resolution of nanopore sensors, which would ensure the possibility of dynamic study of single biomolecules, including their metastable conformations, charge distributions, and interactions. In the future, data analysis with powerful algorithms will make it possible to automatically and statistically extract detailed information while an analyte translocates through the pore. We conclude that these improvements could have tremendous potential applications for nanopore sensing in the near future.
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Affiliation(s)
- Chan Cao
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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12
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De S, C. H. R, Thamleena A. H, Joseph A, Ben A, V. U. K. Roles of different amino-acid residues towards binding and selective transport of K+ through KcsA K+-ion channel. Phys Chem Chem Phys 2018; 20:17517-17529. [DOI: 10.1039/c8cp01282b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Each amino acid in the selectivity filter plays a distinct role towards binding and transport of K+ ion through KcsA.
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Affiliation(s)
- Susmita De
- Department of Applied Chemistry
- Cochin University of Science and Technology
- Trikakkara
- Kochi
- India – 682 022
| | - Rinsha C. H.
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Hanna Thamleena A.
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Annu Joseph
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Anju Ben
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Krishnapriya V. U.
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
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13
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Bao B, Hao J, Bian X, Zhu X, Xiao K, Liao J, Zhou J, Zhou Y, Jiang L. 3D Porous Hydrogel/Conducting Polymer Heterogeneous Membranes with Electro-/pH-Modulated Ionic Rectification. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1702926. [PMID: 29024293 DOI: 10.1002/adma.201702926] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/07/2017] [Indexed: 05/26/2023]
Abstract
Heterogeneous membranes composed of asymmetric structures or compositions have enormous potential in sensors, molecular sieves, and energy devices due to their unique ion transport properties such as ionic current rectification and ion selectivity. So far, heterogeneous membranes with 1D nanopores have been extensively studied. However, asymmetric structures with 3D micro-/nanoscale pore networks have never been investigated. Here, a simple and versatile approach to low-costly fabricate hydrogel/conducting polymer asymmetric heterogeneous membranes with electro-/pH-responsive 3D micro-/nanoscale ion channels is introduced. Due to the asymmetric heterojunctions between positively charged nanoporous polypyrrole (PPy) and negatively charged microscale porous hydrogel poly (acrylamide-co-acrylic acid) (P(AAm-co-AA)), the membrane can rectify ion transmembrane transport in response to both electro- and pH-stimuli. Numerical simulations based on coupled Poisson and Nernst-Plank equations are carried out to explain the ionic rectification mechanisms for the membranes. The membranes are not dependent on elaborately fabricated 1D ion channel substrates and hence can be facilely prepared in a low-cost and large-area way. The hybridization of hydrogel and conducting polymer offers a novel strategy for constructing low-cost, large-area and multifunctional membranes, expanding the tunable ionic rectification properties into macroscopic membranes with micro-/nanoscale pores, which would stimulate practical applications of the membranes.
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Affiliation(s)
- Bin Bao
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Junran Hao
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Xiujie Bian
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Xuanbo Zhu
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Kai Xiao
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Jingwen Liao
- Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, 511458, P. R. China
| | - Jiajia Zhou
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Yahong Zhou
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lei Jiang
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
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14
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Egorova KS, Gordeev EG, Ananikov VP. Biological Activity of Ionic Liquids and Their Application in Pharmaceutics and Medicine. Chem Rev 2017; 117:7132-7189. [PMID: 28125212 DOI: 10.1021/acs.chemrev.6b00562] [Citation(s) in RCA: 906] [Impact Index Per Article: 129.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ionic liquids are remarkable chemical compounds, which find applications in many areas of modern science. Because of their highly tunable nature and exceptional properties, ionic liquids have become essential players in the fields of synthesis and catalysis, extraction, electrochemistry, analytics, biotechnology, etc. Apart from physical and chemical features of ionic liquids, their high biological activity has been attracting significant attention from biochemists, ecologists, and medical scientists. This Review is dedicated to biological activities of ionic liquids, with a special emphasis on their potential employment in pharmaceutics and medicine. The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems. Dedicated attention is given to a novel active pharmaceutical ingredient-ionic liquid (API-IL) concept, which suggests using traditional drugs in the form of ionic liquid species. The main aim of this Review is to attract a broad audience of chemical, biological, and medical scientists to study advantages of ionic liquid pharmaceutics. Overall, the discussed data highlight the importance of the research direction defined as "Ioliomics", studies of ions in liquids in modern chemistry, biology, and medicine.
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Affiliation(s)
- Ksenia S Egorova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia
| | - Evgeniy G Gordeev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia
| | - Valentine P Ananikov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia.,Department of Chemistry, Saint Petersburg State University , Stary Petergof 198504, Russia
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15
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Vu T, Davidson SL, Borgesi J, Maksudul M, Jeon TJ, Shim J. Piecing together the puzzle: nanopore technology in detection and quantification of cancer biomarkers. RSC Adv 2017. [DOI: 10.1039/c7ra08063h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This mini-review paper is a comprehensive outline of nanopore technology applications in the detection and study of various cancer causal factors.
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Affiliation(s)
- Trang Vu
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Shanna-Leigh Davidson
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Julia Borgesi
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Mowla Maksudul
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Tae-Joon Jeon
- Department of Biological Engineering
- Inha University
- Incheon 22212
- Republic of Korea
| | - Jiwook Shim
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
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16
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Roy A, Biswas O, Talukdar P. Bis(sulfonamide) transmembrane carriers allow pH-gated inversion of ion selectivity. Chem Commun (Camb) 2017; 53:3122-3125. [DOI: 10.1039/c7cc00165g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bis(sulfonamide) based synthetic carriers are reported for inversion of ion selectivity upon deviation of pH within a narrow window. A liposomal membrane potential is also generated when potassium ions are passively transported by these carriers.
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Affiliation(s)
- Arundhati Roy
- Department of Chemistry
- Indian Institute of Science Education and Research Pune
- Pune 411008
- India
| | - Oindrila Biswas
- Department of Chemistry
- Indian Institute of Science Education and Research Pune
- Pune 411008
- India
| | - Pinaki Talukdar
- Department of Chemistry
- Indian Institute of Science Education and Research Pune
- Pune 411008
- India
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17
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Roy A, Saha D, Mandal PS, Mukherjee A, Talukdar P. pH-Gated Chloride Transport by a Triazine-Based Tripodal Semicage. Chemistry 2016; 23:1241-1247. [DOI: 10.1002/chem.201605033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Arundhati Roy
- Department of Chemistry; Indian Institute of Science Education and Research Pune; Dr. Homi Bhabha Road, Pashan Pune 411008, Maharashtra India
| | - Debasis Saha
- Department of Chemistry; Indian Institute of Science Education and Research Pune; Dr. Homi Bhabha Road, Pashan Pune 411008, Maharashtra India
| | - Prashant Sahebrao Mandal
- Department of Chemistry; Institute of Chemical Technology, Matunga; Mumbai- 400019, Maharashtra India
| | - Arnab Mukherjee
- Department of Chemistry; Indian Institute of Science Education and Research Pune; Dr. Homi Bhabha Road, Pashan Pune 411008, Maharashtra India
| | - Pinaki Talukdar
- Department of Chemistry; Indian Institute of Science Education and Research Pune; Dr. Homi Bhabha Road, Pashan Pune 411008, Maharashtra India
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18
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Silin V, Kasianowicz JJ, Michelman-Ribeiro A, Panchal RG, Bavari S, Robertson JWF. Biochip for the Detection of Bacillus anthracis Lethal Factor and Therapeutic Agents against Anthrax Toxins. MEMBRANES 2016; 6:E36. [PMID: 27348008 PMCID: PMC5041027 DOI: 10.3390/membranes6030036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 01/18/2023]
Abstract
Tethered lipid bilayer membranes (tBLMs) have been used in many applications, including biosensing and membrane protein structure studies. This report describes a biosensor for anthrax toxins that was fabricated through the self-assembly of a tBLM with B. anthracis protective antigen ion channels that are both the recognition element and electrochemical transducer. We characterize the sensor and its properties with electrochemical impedance spectroscopy and surface plasmon resonance. The sensor shows a sensitivity similar to ELISA and can also be used to rapidly screen for molecules that bind to the toxins and potentially inhibit their lethal effects.
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Affiliation(s)
- Vitalii Silin
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899-8120, USA.
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8120, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20899, USA.
| | - John J Kasianowicz
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899-8120, USA.
| | - Ariel Michelman-Ribeiro
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899-8120, USA.
| | - Rekha G Panchal
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702-5011, USA.
| | - Sina Bavari
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702-5011, USA.
| | - Joseph W F Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899-8120, USA.
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19
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Cooper DR, Dolino DM, Jaurich H, Shuang B, Ramaswamy S, Nurik CE, Chen J, Jayaraman V, Landes CF. Conformational transitions in the glycine-bound GluN1 NMDA receptor LBD via single-molecule FRET. Biophys J 2016; 109:66-75. [PMID: 26153703 PMCID: PMC4572502 DOI: 10.1016/j.bpj.2015.05.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 12/30/2022] Open
Abstract
The N-methyl-D-aspartate receptor (NMDAR) is a member of the glutamate receptor family of proteins and is responsible for excitatory transmission. Activation of the receptor is thought to be controlled by conformational changes in the ligand binding domain (LBD); however, glutamate receptor LBDs can occupy multiple conformations even in the activated form. This work probes equilibrium transitions among NMDAR LBD conformations by monitoring the distance across the glycine-bound LBD cleft using single-molecule Förster resonance energy transfer (smFRET). Recent improvements in photoprotection solutions allowed us to monitor transitions among the multiple conformations. Also, we applied a recently developed model-free algorithm called "step transition and state identification" to identify the number of states, their smFRET efficiencies, and their interstate kinetics. Reversible interstate conversions, corresponding to transitions among a wide range of cleft widths, were identified in the glycine-bound LBD, on much longer timescales compared to channel opening. These transitions were confirmed to be equilibrium in nature by shifting the distribution reversibly via denaturant. We found that the NMDAR LBD proceeds primarily from one adjacent smFRET state to the next under equilibrium conditions, consistent with a cleft-opening/closing mechanism. Overall, by analyzing the state-to-state transition dynamics and distributions, we achieve insight into specifics of long-lived LBD equilibrium structural dynamics, as well as obtain a more general description of equilibrium folding/unfolding in a conformationally dynamic protein. The relationship between such long-lived LBD dynamics and channel function in the full receptor remains an open and interesting question.
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Affiliation(s)
- David R Cooper
- Department of Chemistry, Rice University, Houston, Texas
| | - Drew M Dolino
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas
| | | | - Bo Shuang
- Department of Chemistry, Rice University, Houston, Texas
| | - Swarna Ramaswamy
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas
| | - Caitlin E Nurik
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas
| | - Jixin Chen
- Department of Chemistry, Rice University, Houston, Texas
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas.
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, Texas; Department of Electrical and Computer Engineering, Rice University, Houston, Texas.
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20
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Smeazzetto S, Tadini-Buoninsegni F, Thiel G, Berti D, Montis C. Phospholamban spontaneously reconstitutes into giant unilamellar vesicles where it generates a cation selective channel. Phys Chem Chem Phys 2015; 18:1629-36. [PMID: 26673394 DOI: 10.1039/c5cp05893g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phospholamban (PLN) is a small integral membrane protein, which modulates the activity of the Sarcoplasmic Reticulum Ca(2+)-ATPase (SERCA) of cardiac myocytes. PLN, as a monomer, can directly interact and tune SERCA activity, but the physiological function of the pentameric form is not yet fully understood and still debated. In this work, we reconstituted PLN in Giant Unilamellar Vesicles (GUVs), a simple and reliable experimental model system to monitor the activity of proteins in membranes. By Laser Scanning Confocal Microscopy (LSCM) and Fluorescence Correlation Spectroscopy (FCS) we verified a spontaneous reconstitution of PLN into the phospholipid bilayer. In parallel experiments, we measured with the patch clamp technique canonical ion channel fluctuations, which highlight a preference for Cs(+) over K(+) and do not conduct Ca(2+). The results prove that PLN forms, presumably in its pentameric form, a cation selective ion channel.
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Affiliation(s)
- S Smeazzetto
- Department of Chemistry "Ugo Schiff", University of Florence, Firenze, Italy
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21
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Kasianowicz JJ, Balijepalli AK, Ettedgui J, Forstater JH, Wang H, Zhang H, Robertson JWF. Analytical applications for pore-forming proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:593-606. [PMID: 26431785 DOI: 10.1016/j.bbamem.2015.09.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/28/2015] [Accepted: 09/25/2015] [Indexed: 01/13/2023]
Abstract
Proteinaceous nanometer-scale pores are ubiquitous in biology. The canonical ionic channels (e.g., those that transport Na(+), K(+), Ca(2+), and Cl(-) across cell membranes) play key roles in many cellular processes, including nerve and muscle activity. Another class of channels includes bacterial pore-forming toxins, which disrupt cell function, and can lead to cell death. We describe here the recent development of these toxins for a wide range of biological sensing applications. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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Affiliation(s)
- John J Kasianowicz
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States.
| | | | - Jessica Ettedgui
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Jacob H Forstater
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Haiyan Wang
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Huisheng Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Dept. of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
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22
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Ding Y, Fleming AM, He L, Burrows CJ. Unfolding Kinetics of the Human Telomere i-Motif Under a 10 pN Force Imposed by the α-Hemolysin Nanopore Identify Transient Folded-State Lifetimes at Physiological pH. J Am Chem Soc 2015; 137:9053-60. [PMID: 26110559 PMCID: PMC4513840 DOI: 10.1021/jacs.5b03912] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Cytosine
(C)-rich DNA can adopt i-motif folds under acidic conditions,
with the human telomere i-motif providing a well-studied example.
The dimensions of this i-motif are appropriate for capture in the
nanocavity of the α-hemolysin (α-HL) protein pore under
an electrophoretic force. Interrogation of the current vs time (i–t) traces when the i-motif interacts
with α-HL identified characteristic signals that were pH dependent.
These features were evaluated from pH 5.0 to 7.2, a region surrounding
the transition pH of the i-motif (6.1). When the i-motif without polynucleotide
tails was studied at pH 5.0, the folded structure entered the nanocavity
of α-HL from either the top or bottom face to yield characteristic
current patterns. Addition of a 5′ 25-mer poly-2′-deoxyadensosine
tail allowed capture of the i-motif from the unfolded terminus, and
this was used to analyze the pH dependency of unfolding. At pH values
below the transition point, only folded strands were observed, and
when the pH was increased above the transition pH, the number of folded
events decreased, while the unfolded events increased. At pH 6.8 and
7.2 4% and 2% of the strands were still folded, respectively. The
lifetimes for the folded states at pH 6.8 and 7.2 were 21 and 9 ms,
respectively, at 160 mV electrophoretic force. These lifetimes are
sufficiently long to affect enzymes operating on DNA. Furthermore,
these transient lifetimes are readily obtained using the α-HL
nanopore, a feature that is not easily achievable by other methods.
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Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Lidong He
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
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23
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Nanoscale monitoring of drug actions on cell membrane using atomic force microscopy. Acta Pharmacol Sin 2015; 36:769-82. [PMID: 26027658 DOI: 10.1038/aps.2015.28] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/13/2015] [Indexed: 02/06/2023] Open
Abstract
Knowledge of the nanoscale changes that take place in individual cells in response to a drug is useful for understanding the drug action. However, due to the lack of adequate techniques, such knowledge was scarce until the advent of atomic force microscopy (AFM), which is a multifunctional tool for investigating cellular behavior with nanometer resolution under near-physiological conditions. In the past decade, researchers have applied AFM to monitor the morphological and mechanical dynamics of individual cells following drug stimulation, yielding considerable novel insight into how the drug molecules affect an individual cell at the nanoscale. In this article we summarize the representative applications of AFM in characterization of drug actions on cell membrane, including topographic imaging, elasticity measurements, molecular interaction quantification, native membrane protein imaging and manipulation, etc. The challenges that are hampering the further development of AFM for studies of cellular activities are aslo discussed.
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24
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Placement of oppositely charged aminoacids at a polypeptide termini determines the voltage-controlled braking of polymer transport through nanometer-scale pores. Sci Rep 2015; 5:10419. [PMID: 26029865 PMCID: PMC4450769 DOI: 10.1038/srep10419] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/13/2015] [Indexed: 11/09/2022] Open
Abstract
Protein and solid-state nanometer-scale pores are being developed for the detection, analysis, and manipulation of single molecules. In the simplest embodiment, the entry of a molecule into a nanopore causes a reduction in the latter's ionic conductance. The ionic current blockade depth and residence time have been shown to provide detailed information on the size, adsorbed charge, and other properties of molecules. Here we describe the use of the nanopore formed by Staphylococcus aureus α-hemolysin and polypeptides with oppositely charged segments at the N- and C-termini to increase both the polypeptide capture rate and mean residence time of them in the pore, regardless of the polarity of the applied electrostatic potential. The technique provides the means to improve the signal to noise of single molecule nanopore-based measurements.
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25
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Church AT, Hughes ZE, Walsh TR. Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ-carboxyglutamic acid: revised CHARMM22* parameters. RSC Adv 2015. [DOI: 10.1039/c5ra11268k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We show that the CHARMM22* force-field over-binds the interaction between aqueous carboxylates and Ca2+, and introduce a modification that can recover experimentally-determined binding free energies for these systems.
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Affiliation(s)
- Andrew T. Church
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Zak E. Hughes
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Tiffany R. Walsh
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
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26
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Angevine CE, Chavis AE, Kothalawala N, Dass A, Reiner JE. Enhanced Single Molecule Mass Spectrometry via Charged Metallic Clusters. Anal Chem 2014; 86:11077-85. [DOI: 10.1021/ac503425g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christopher E. Angevine
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Amy E. Chavis
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Nuwan Kothalawala
- Department
of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Amala Dass
- Department
of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Joseph E. Reiner
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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27
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Homeyer N, Gohlke H. Extension of the free energy workflow FEW towards implicit solvent/implicit membrane MM-PBSA calculations. Biochim Biophys Acta Gen Subj 2014; 1850:972-982. [PMID: 25450172 DOI: 10.1016/j.bbagen.2014.10.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 10/13/2014] [Accepted: 10/14/2014] [Indexed: 01/12/2023]
Abstract
BACKGROUND The number of high-resolution structures of pharmacologically relevant membrane proteins has been strongly increasing. This makes computing relative affinities of chemically similar compounds binding to a membrane protein possible in order to guide decision making in drug design. However, the preparation step of such calculations is time-consuming and complex. METHODS We extended the free energy workflow tool FEW, available in AMBER, towards facilitating the setup of molecular dynamics simulations with explicit membrane, and the setup and execution of effective binding energy calculations according to a 1-trajectory implicit solvent/implicit membrane MM-PBSA approach for multiple ligands binding to the same membrane protein. RESULTS We validated the implemented protocol initially on two model systems, a sodium ion in the presence of an implicit membrane slab and a proton traversing the M2 proton-channel of the influenza A virus. For the latter, we found a good agreement for several important events along the proton pathway with those obtained in a recent computational study. Finally, we performed a case study on effective binding energy calculations for a set of inhibitors binding to the M2 proton-channel. CONCLUSIONS From the case study, we estimate a considerable speed up in the setup and analysis times for implicit solvent/implicit membrane MM-PBSA calculations by the extended version of FEW compared to a manual preparation. GENERAL SIGNIFICANCE Together with the overall runtime and the analysis results, this suggests that such type of calculations can be valuable in later stages of drug design projects on membrane proteins. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Nadine Homeyer
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Germany.
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28
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Smeazzetto S, Sacconi A, Schwan AL, Margheri G, Tadini-Buoninsegni F. Binding of a monoclonal antibody to the phospholamban cytoplasmic domain interferes with the channel activity of phospholamban reconstituted in a tethered bilayer lipid membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:10384-10388. [PMID: 25121716 DOI: 10.1021/la501660u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Phospholamban (PLN), a membrane protein present in the sarcoplasmic reticulum of cardiac myocytes, is a crucial regulator of cardiac function. It is known that PLN appears as a monomer and as a pentamer. However, the role of the PLN pentamer and its ability to generate an ion channel are a matter of debate. To address this issue we employed an experimental approach that combines electrochemical impedance spectroscopy and surface plasmon resonance measurements. In particular, we investigated the channel activity of wild-type PLN reconstituted in a tethered bilayer lipid membrane (tBLM) on a gold surface. Our results indicate that reconstituted PLN can generate ion-conducting channels in a tBLM. Experiments with a PLN monoclonal antibody support an oriented incorporation of PLN in the tBLM. We show that the binding of the antibody to the PLN cytoplasmic domain interferes with PLN channel activity.
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Affiliation(s)
- Serena Smeazzetto
- Department of Chemistry "Ugo Schiff", University of Florence , 50019 Sesto Fiorentino, Italy
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29
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Progress in measuring biophysical properties of membrane proteins with AFM single-molecule force spectroscopy. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0290-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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30
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Balijepalli A, Ettedgui J, Cornio AT, Robertson JWF, Cheung KP, Kasianowicz JJ, Vaz C. Quantifying short-lived events in multistate ionic current measurements. ACS NANO 2014; 8:1547-53. [PMID: 24397836 PMCID: PMC3943493 DOI: 10.1021/nn405761y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 01/07/2014] [Indexed: 05/22/2023]
Abstract
We developed a generalized technique to characterize polymer-nanopore interactions via single channel ionic current measurements. Physical interactions between analytes, such as DNA, proteins, or synthetic polymers, and a nanopore cause multiple discrete states in the current. We modeled the transitions of the current to individual states with an equivalent electrical circuit, which allowed us to describe the system response. This enabled the estimation of short-lived states that are presently not characterized by existing analysis techniques. Our approach considerably improves the range and resolution of single-molecule characterization with nanopores. For example, we characterized the residence times of synthetic polymers that are three times shorter than those estimated with existing algorithms. Because the molecule's residence time follows an exponential distribution, we recover nearly 20-fold more events per unit time that can be used for analysis. Furthermore, the measurement range was extended from 11 monomers to as few as 8. Finally, we applied this technique to recover a known sequence of single-stranded DNA from previously published ion channel recordings, identifying discrete current states with subpicoampere resolution.
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31
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Zhang J, Yang Y, Zhang Z, Wang P, Wang X. Biomimetic multifunctional nanochannels based on the asymmetric wettability of heterogeneous nanowire membranes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:1071-1075. [PMID: 24282127 DOI: 10.1002/adma.201304270] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 09/13/2013] [Indexed: 06/02/2023]
Abstract
A charged heterogeneous nanowire membrane with asymmetric wettability serves as a biomimetic passive channel when the bilayer is hydrophilic; It also functions as pH valve based on the hydrophobic CaWO4 layer (contact angle of 145.3˚±0.3˚) and hydrophilic MnO2 layer. Moreover, a reversible ionic rectification is realized in the above-mentioned semi-hydrophobic and hydrophilic state with strong acid environment or in the complete hydrophobic stage with a moderate discrepancy (CA of CaWO4 and MnO2 layer are 141.3˚±0.3˚ and 157.6˚±2.0˚, respectively) in near neuter condition.
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Affiliation(s)
- Jingchao Zhang
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
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32
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Li M, Liu L, Xi N, Wang Y, Dong Z, Xiao X, Zhang W. Progress of AFM single-cell and single-molecule morphology imaging. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-5906-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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33
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Wolna AH, Fleming AM, An N, He L, White HS, Burrows CJ. Electrical Current Signatures of DNA Base Modifications in Single Molecules Immobilized in the α-Hemolysin Ion Channel. Isr J Chem 2013; 53:417-430. [PMID: 24052667 PMCID: PMC3773884 DOI: 10.1002/ijch.201300022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nanopore technology holds high potential for next-generation DNA sequencing. This method operates by drawing an individual single-stranded DNA molecule through a nanoscale pore while monitoring the current deflections that occur as the DNA passes through. Individual current levels for the four DNA nucleotides have been established by immobilization of an end biotinylated strand in the pore in which the nucleotide of interest is suspended at the most sensitive region of the ion channel. Due to the inherent reactivity of the DNA bases, many modified nucleotides in the genome exist resulting from oxidative and UV insults, among others. Herein, the current levels for the common DNA damages 8-oxo-7,8-dihydroguanine (OG), spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), uridine (U), abasic sites (AP), thymine dimers (T=T), thymine glycol (Tg) and 5-iodocytosine (5-I-C) were assessed via immobilization experiments. In some cases, the current difference between the damaged and canonical nucleotides was not well resolved; therefore, we took advantage of the chemical reactivity of the new functional groups present to make amine adducts that shifted the current levels outside the range of the native nucleotides. Among adducts studied, only the 2-aminomethyl-18-crown-6 adduct was able to give a large current shift in the immobilization experiment, as well as to be observed in a translocation experiment. The results show potential in providing current level modulators for identification of some types of DNA damage. In principle, any DNA base modification that can be converted chemically or enzymatically to an abasic site could be identified in this way.
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Affiliation(s)
- Anna H. Wolna
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Aaron M. Fleming
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Na An
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Lidong He
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Henry S. White
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Cynthia J. Burrows
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
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34
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Reiner JE, Balijepalli A, Robertson JWF, Campbell J, Suehle J, Kasianowicz JJ. Disease Detection and Management via Single Nanopore-Based Sensors. Chem Rev 2012; 112:6431-51. [DOI: 10.1021/cr300381m] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Joseph E. Reiner
- Department of Physics, Virginia
Commonwealth University, 701 W. Grace Street, Richmond, Virginia 23284,
United States
| | - Arvind Balijepalli
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
- Laboratory of Computational Biology,
National Heart Lung and Blood Institute, Rockville, Maryland 20852,
United States
| | - Joseph W. F. Robertson
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - Jason Campbell
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - John Suehle
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - John J. Kasianowicz
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
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