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Yao G, Ke W, Xia B, Gao Z. Nanopore-based glycan sequencing: state of the art and future prospects. Chem Sci 2024; 15:6229-6243. [PMID: 38699252 PMCID: PMC11062086 DOI: 10.1039/d4sc01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Sequencing of biomacromolecules is a crucial cornerstone in life sciences. Glycans, one of the fundamental biomolecules, derive their physiological and pathological functions from their structures. Glycan sequencing faces challenges due to its structural complexity and current detection technology limitations. As a highly sensitive sensor, nanopores can directly convert nucleic acid sequence information into electrical signals, spearheading the revolution of third-generation nucleic acid sequencing technologies. However, their potential for deciphering complex glycans remains untapped. Initial attempts demonstrated the significant sensitivity of nanopores in glycan sensing, which provided the theoretical basis and insights for the realization of nanopore-based glycan sequencing. Here, we present three potential technical routes to employ nanopore technology in glycan sequencing for the first time. The three novel technical routes include: strand sequencing, capturing glycan chains as they translocate through nanopores; sequential hydrolysis sequencing, capturing released monosaccharides one by one; splicing sequencing, mapping signals from hydrolyzed glycan fragments to an oligosaccharide database/library. Designing suitable nanopores, enzymes, and motors, and extracting characteristic signals pose major challenges, potentially aided by artificial intelligence. It would be highly desirable to design an all-in-one high-throughput glycan sequencer instrument by integrating a sample processing unit, nanopore array, and signal acquisition system into a microfluidic device. The nanopore sequencer invention calls for intensive multidisciplinary cooperation including electrochemistry, glycochemistry, engineering, materials, enzymology, etc. Advancing glycan sequencing will promote the development of basic research and facilitate the discovery of glycan-based drugs and disease markers, fostering progress in glycoscience and even life sciences.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- School of Life Science and Technology, Shanghai Tech University 201210 Shanghai China
- Lingang Laboratory 200031 Shanghai China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 528400 Zhongshan China
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2
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Tchabo W, Kaptso GK, Bao G, Wang K, Afoakwah NA, Mbofung CM, Wang X. Impact of encapsulation techniques (drying methods and carrier materials) on the nutraceuticals release and absorption mechanism of mulberry leaf. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- William Tchabo
- School of Food Science and Biotechnology Zhejiang Gongshang University Hangzhou P.R. China
- Department of Food Science and Nutrition National Advanced School of Agro‐Industrial Sciences (ENSAI) University of Ngaoundere Ngaoundere Cameroon
| | - Giscard Kuate Kaptso
- Department of Social Economy and Family Management, Higher Technical Teacher’s Training College (HTTTC) University of Buea Buea Road Kumba Cameroon
- Department of Chemical Engineering School of Chemical Engineering and Mineral industries (EGCIM) University of Ngaoundere Ngaoundere Cameroon
| | - Guifeng Bao
- School of Food Science and Biotechnology Zhejiang Gongshang University Hangzhou P.R. China
| | - Kenuo Wang
- School of Food Science and Biotechnology Zhejiang Gongshang University Hangzhou P.R. China
| | - Newlove A. Afoakwah
- Department of Food Science and Technology, Faculty of Agriculture, Food and Consumer Sciences University for Development Studies Tamale NR Ghana
| | - Carl Moses Mbofung
- Department of Food Science and Nutrition National Advanced School of Agro‐Industrial Sciences (ENSAI) University of Ngaoundere Ngaoundere Cameroon
| | - Xiangyang Wang
- School of Food Science and Biotechnology Zhejiang Gongshang University Hangzhou P.R. China
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3
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Novikova OD, Naberezhnykh GA, Sergeev AA. Nanostructured Biosensors Based on Components of Bacterial Membranes. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921040187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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4
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Soysa HSM, Suginta W, Moonsap W, Smith MF. Chitosugar translocation by an unexpressed monomeric protein channel. Phys Rev E 2018; 97:052417. [PMID: 29906877 DOI: 10.1103/physreve.97.052417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Indexed: 12/14/2022]
Abstract
The outer membrane protein channel EcChiP, associated with a silent gene in E. coli, is a monomeric chitoporin. In a glucose-deficient environment, E. coli can express the ChiP gene to exploit chitin degradation products. Single-channel small ion current measurements, which reveal the dynamics of single sugar molecules trapped in channel, are used here to study the exotic transport of chitosugars by E. coli. Molecules escape from the channel on multiple timescales. Voltage-dependent trapping rates observed for charged chitosan molecules, as well as model calculations, indicate that the rapid escape processes are those in which the molecule escapes back to the side of the membrane from which it originated. The probability that a sugar molecule is translocated through the membrane is thus estimated from the current data and the dependence of this translocation probability on the length of the chitosugar molecule and the applied voltage analyzed. The described method for obtaining the translocation probability and related molecular translocation current is applicable to other transport channels.
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Affiliation(s)
- H Sasimali M Soysa
- Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Watcharaporn Moonsap
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - M F Smith
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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5
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Chavis AE, Brady KT, Hatmaker GA, Angevine CE, Kothalawala N, Dass A, Robertson JWF, Reiner JE. Single Molecule Nanopore Spectrometry for Peptide Detection. ACS Sens 2017; 2:1319-1328. [PMID: 28812356 PMCID: PMC11274829 DOI: 10.1021/acssensors.7b00362] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Sensing and characterization of water-soluble peptides is of critical importance in a wide variety of bioapplications. Single molecule nanopore spectrometry (SMNS) is based on the idea that one can use biological protein nanopores to resolve different sized molecules down to limits set by the blockade duration and noise. Previous work has shown that this enables discrimination between polyethylene glycol (PEG) molecules that differ by a single monomer unit. This paper describes efforts to extend SMNS to a variety of biologically relevant, water-soluble peptides. We describe the use of Au25(SG)18 clusters, previously shown to improve PEG detection, to increase the on- and off-rate of peptides to the pore. In addition, we study the role that fluctuations play in the single molecule nanopore spectrometry (SMNS) methodology and show that modifying solution conditions to increase peptide flexibility (via pH or chaotropic salt) leads to a nearly 2-fold reduction in the current blockade fluctuations and a corresponding narrowing of the peaks in the blockade distributions. Finally, a model is presented that connects the current blockade depths to the mass of the peptides, which shows that our enhanced SMNS detection improves the mass resolution of the nanopore sensor more than 2-fold for the largest cationic peptides studied.
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Affiliation(s)
- Amy E. Chavis
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kyle T. Brady
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Grace A. Hatmaker
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Christopher E. Angevine
- 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 W. F. Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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6
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Soundararajan G, Bhamidimarri SP, Winterhalter M. Understanding Carbapenem Translocation through OccD3 (OpdP) of Pseudomonas aeruginosa. ACS Chem Biol 2017; 12:1656-1664. [PMID: 28440622 DOI: 10.1021/acschembio.6b01150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudomonas aeruginosa utilizes a plethora of substrate specific channels for the uptake of small nutrients. OccD3 (OpdP or PA4501) is an OprD-like arginine uptake channel of P. aeruginosa whose role has been implicated in carbapenem uptake. To understand the mechanism of selective permeation, we reconstituted single OccD3 channels in a planar lipid bilayer and characterized the interaction with Imipenem and Meropenem, analyzing the ion current fluctuation in the presence of substrates. We performed point mutations in the constriction region of OccD3 to understand the binding and translocation of antibiotic in OccD3. By mutating two key residues in the substrate binding sites of OccD3 (located in the internal loop L7 and basic ladder), we emphasize the importance of these residues. We show that carbapenem antibiotics follow a similar path as arginine through the constriction zone and the basic ladder to translocate across OccD3.
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Affiliation(s)
- Gowrishankar Soundararajan
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | | | - Mathias Winterhalter
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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7
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Suginta W, Winterhalter M, Smith MF. Correlated trapping of sugar molecules by the trimeric protein channel chitoporin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:3032-3040. [PMID: 27638174 DOI: 10.1016/j.bbamem.2016.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/02/2016] [Accepted: 09/09/2016] [Indexed: 10/21/2022]
Abstract
The protein channel chitoporin (ChiP), which is used by marine bacteria to translocate selected sugar molecules through the outer cell membrane, is studied via single channel current measurements in water and heavy water sugar solutions. The dynamic trapping and escape probabilities of sugar molecules from different monomers in the trimeric channel are characterized, including their dependence on channel orientation and sensitivity to a deuterium isotope effect. A detailed analysis of stochastic current fluctuations reveals that the trapping properties of chitoporin exhibit memory effects: the rate of trapping transitions depends on the previous sequence of transitions; and intermonomer correlations: the average trapping rate of an unblocked monomer is larger when its neighboring monomers are blocked. The latter, likely resulting from rapid re-trapping of recently escaped sugar molecules, is considered as a possible design strategy to enhance sugar transport.
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Affiliation(s)
- Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | | | - M F Smith
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
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8
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Rokitskaya TI, Antonenko YN. Fullerenol C60(OH)24 increases ion permeability of lipid membranes in a pH-dependent manner. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1165-74. [PMID: 26874205 DOI: 10.1016/j.bbamem.2016.02.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/07/2016] [Accepted: 02/09/2016] [Indexed: 02/07/2023]
Abstract
Fullerenols are water-soluble analogs of fullerene exhibiting both antioxidant and prooxidant activities in vitro and in vivo. Here we report, for the first time, that fullerenol C60(OH)24 can induce ion permeability of a planar lipid bilayer membrane via the formation of ion pores or conductive defects with a preference for cations over anions. The fullerenol-mediated electrical current displayed non-linear concentration dependence and was reversibly enhanced by alkalinization. Calcium and magnesium ions decreased the fullerenol-induced potassium ion permeability. Voltage dependence of the current was sensitive to membrane composition, with the conductance being well pronounced in fully saturated diphytanoylphosphatidylcholine. Fullerenol did not induce carboxyfluorescein leakage from liposomes, suggesting a small size of fullerenol-induced pores. In contrast to ion permeability, the binding of C60(OH)24 to liposomes increased at acidic pH, as measured by fluorescence quenching of pyrene-labeled lipid. In line with this, the photodynamic action of fullerenol on the peptide gramicidin A also increased at low pH. It is hypothesized that aggregates of fullerenol may stabilize transient conductive lipid defects or pores formed under a variety of stress conditions.
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Affiliation(s)
- Tatyana I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation.
| | - Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation.
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9
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Suginta W, Smith MF. Single-molecule trapping dynamics of sugar-uptake channels in marine bacteria. PHYSICAL REVIEW LETTERS 2013; 110:238102. [PMID: 25167532 DOI: 10.1103/physrevlett.110.238102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Indexed: 06/03/2023]
Abstract
Stochastic fluctuations of ion current through one chitoporin (ChiP) channel within a bilayer lipid membrane in sugar solution are analyzed. These reflect single-molecule dynamics, which indicate that ChiP has multiple binding sites for sugar and exploits interactions between bound molecules to direct sugar passage. Since ChiP is used by marine bacteria, this is likely an adaptive strategy to enhance sugar translocation from rough water.
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Affiliation(s)
- Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, Schools of Chemistry and Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - M F Smith
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand and Thailand Center of Excellence in Physics (ThEP), Commission of Higher Education, Ministry of Education, Bangkok 10400, Thailand
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10
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Suginta W, Chumjan W, Mahendran KR, Schulte A, Winterhalter M. Chitoporin from Vibrio harveyi, a channel with exceptional sugar specificity. J Biol Chem 2013; 288:11038-46. [PMID: 23447539 DOI: 10.1074/jbc.m113.454108] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chitoporin (VhChiP) is a sugar-specific channel responsible for the transport of chitooligosaccharides through the outer membrane of the marine bacterium Vibrio harveyi. Single channel reconstitution into black lipid membrane allowed single chitosugar binding events in the channel to be resolved. VhChiP has an exceptionally high substrate affinity, with a binding constant of K = 5.0 × 10(6) M(-1) for its best substrate (chitohexaose). The on-rates of chitosugars depend on applied voltages, as well as the side of the sugar addition, clearly indicating the inherent asymmetry of the VhChiP lumen. The binding affinity of VhChiP for chitohexaose is 1-5 orders of magnitude larger than that of other known sugar-specific porins for their preferred substrates. Thus, VhChiP is the most potent sugar-specific channel reported to date, with its high efficiency presumably reflecting the need for the bacterium to take up chitin-containing nutrients promptly under turbulent aquatic conditions to exploit them efficiently as its sole source of energy.
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Affiliation(s)
- Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
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11
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Prangkio P, Rao DK, Lance KD, Rubinshtein M, Yang J, Mayer M. Self-assembled, cation-selective ion channels from an oligo(ethylene glycol) derivative of benzothiazole aniline. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2877-85. [PMID: 21889925 DOI: 10.1016/j.bbamem.2011.08.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 07/22/2011] [Accepted: 08/18/2011] [Indexed: 01/01/2023]
Abstract
This paper describes the spontaneous formation of well-defined pores in planar lipid bilayers from the self-assembly of a small synthetic molecule that contains a benzothiazole aniline (BTA) group attached to a tetra-ethylene glycol (EG4) moiety. Macroscopic and single-channel current recordings suggest that these pores are formed by the assembly of four BTA-EG4 monomers with an open pore diameter that appears similar to the one of gramicidin pores (~0.4 nm). The single-channel conductance of these pores is modulated by the pH of the electrolyte and has a minimum at pH~3. Self-assembled pores from BTA-EG4 are selective for monovalent cations and have long open channel lifetimes on the order of seconds. BTA-EG4 monomers in these pores appear to be arranged symmetrically across both leaflets of the bilayer, and spectroscopy studies suggest that the fluorescent BTA group is localized inside the lipid bilayers. In terms of biological activity, BTA-EG4 molecules inhibited growth of gram-positive Bacillus subtilis bacteria (IC50~50 μM) and human neuroblastoma SH-SY5Y cells (IC50~60 μM), while they were not toxic to gram-negative Escherichia coli bacteria at a concentration up to 500 μM. Based on these properties, this drug-like, synthetic, pore-forming molecule with a molecular weight below 500 g mol(-1) might be appealing as a starting material for development of antibiotics or membrane-permeating moieties for drug delivery. From a biophysical point of view, long-lived, well-defined ion-selective pores from BTA-EG4 molecules offer an example of a self-assembled synthetic supramolecule with biological function.
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Affiliation(s)
- Panchika Prangkio
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110, USA
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12
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Lolicato M, Reina S, Messina A, Guarino F, Winterhalter M, Benz R, De Pinto V. Generation of artificial channels by multimerization of β-strands from natural porin. Biol Chem 2011; 392:617-24. [PMID: 21627534 DOI: 10.1515/bc.2011.063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
General diffusion porins are passive transmembrane channels. We have explored the possibility to create artificial nanopores starting from natural β-barrel structures. Structural elements of bacterial porins were used to build a series of artificial nanopores. The basic module was selected by multi-alignment of general diffusion porins. The sequence corresponded to a highly conserved motif containing two β-strands, which was obtained from Escherichia coli OmpF. Dimeric to octameric repeats were obtained through cDNA recombinant technology. The hexameric repeat was used to test its properties. This protein was expressed, purified and reconstituted in the planar bilayer membranes. It was able to form channels in membranes with a conductance of 300 pS in 150 mm KCl and did not show any relevant voltage-dependence.
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Affiliation(s)
- Marco Lolicato
- Department of Biology, Laboratory of Biochemistry and Molecular Biology, University of Catania, Italy
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13
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Mohammad MM, Howard KR, Movileanu L. Redesign of a plugged beta-barrel membrane protein. J Biol Chem 2011; 286:8000-8013. [PMID: 21189254 PMCID: PMC3048687 DOI: 10.1074/jbc.m110.197723] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 12/16/2010] [Indexed: 11/06/2022] Open
Abstract
The redesign of biological nanopores is focused on bacterial outer membrane proteins and pore-forming toxins, because their robust β-barrel structure makes them the best choice for developing stochastic biosensing elements. Using membrane protein engineering and single-channel electrical recordings, we explored the ferric hydroxamate uptake component A (FhuA), a monomeric 22-stranded β-barrel protein from the outer membrane of Escherichia coli. FhuA has a luminal cross-section of 3.1 × 4.4 nm and is filled by a globular N-terminal cork domain. Various redesigned FhuA proteins were investigated, including single, double, and multiple deletions of the large extracellular loops and the cork domain. We identified four large extracellular loops that partially occlude the lumen when the cork domain is removed. The newly engineered protein, FhuAΔC/Δ4L, was the result of a removal of almost one-third of the total number of amino acids of the wild-type FhuA (WT-FhuA) protein. This extensive protein engineering encompassed the entire cork domain and four extracellular loops. Remarkably, FhuAΔC/Δ4L forms a functional open pore in planar lipid bilayers, with a measured unitary conductance of ∼4.8 nanosiemens, which is much greater than the values recorded previously with other engineered FhuA protein channels. There are numerous advantages and prospects of using such an engineered outer membrane protein not only in fundamental studies of membrane protein folding and design, and the mechanisms of ion conductance and gating, but also in more applicative areas of stochastic single-molecule sensing of proteins and nucleic acids.
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Affiliation(s)
- Mohammad M Mohammad
- From the Department of Physics, Syracuse University, Syracuse, New York 13244-1130
| | - Khalil R Howard
- the Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, Syracuse, New York 13244-4100, and
| | - Liviu Movileanu
- From the Department of Physics, Syracuse University, Syracuse, New York 13244-1130,; the Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, Syracuse, New York 13244-4100, and; the Syracuse Biomaterials Institute, Syracuse University, Syracuse, New York 13244.
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14
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Mechanisms involved in governing adherence of Vibrio cholerae to granular starch. Appl Environ Microbiol 2009; 76:1034-43. [PMID: 20023099 DOI: 10.1128/aem.01533-09] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae has been shown to adhere to cornstarch granules. The present work explored the mechanisms involved in this adhesion and the possibility of its occurrence in vivo. The findings suggest that both specific and nonspecific interactions are involved in the adhesion. Nonspecific hydrophobic interactions may play a role, since both V. cholerae and cornstarch granules exhibited hydrophobic properties when they were tested using a xylene-water system. In addition, the presence of bile acids reduced the adhesion. The adhesion also involves some specific carbohydrate-binding moieties on the cell surface, as reflected by reduced adhesion following pretreatment of the bacteria with proteinase K and sodium m-periodate. Further investigations supported these observations and showed that media containing low-molecular-weight carbohydrates had a significant inhibitory effect. Binding cell lysate to starch granules and removing the adhered proteins using either glucose or bile acids led to identification (by liquid chromatography-tandem mass spectrometry analysis) of several candidate V. cholerae outer membrane-associated starch-binding proteins. Different sets of proteins were isolated by removal in a glucose solution or bile acids. When the upper gastrointestinal tract conditions were simulated in vitro, both bile salts and the amylolytic activity of the pancreatic juices were found to have an inhibitory effect on the adherence of V. cholerae to starch. However, during acute diarrhea, this inhibitory effect may be significantly reduced due to dilution, suggesting that adhesion does occur in vivo. Such adhesion may contribute to the beneficial effects observed following administration of granular starch-based oral rehydration solutions to cholera patients.
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15
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Uram JD, Ke K, Mayer M. Noise and bandwidth of current recordings from submicrometer pores and nanopores. ACS NANO 2008; 2:857-72. [PMID: 19206482 DOI: 10.1021/nn700322m] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nanopores and submicrometer pores have recently been explored for applications ranging from detection of single molecules, assemblies of nanoparticles, nucleic acids, occurrence of chemical reactions, and unfolding of proteins. Most of these applications rely on monitoring electrical current through these pores, hence the noise and signal bandwidth of these current recordings are critical for achieving accurate and sensitive measurements. In this report, we present a detailed theoretical and experimental study on the noise and signal bandwidth of current recordings from glass and polyethylene terephthalate (PET) membranes that contain a single submicrometer pore or nanopore. We examined the theoretical signal bandwidth of two different pore geometries, and we measured the signal bandwidth of the electronics used to record the ionic current. We also investigated the theoretical noise generated by the substrate material, the pore, and the electronics used to record the current. Employing a combination of theory and experimental results, we were able to predict the noise in current traces recorded from glass and PET pores with no applied voltage with an error of less than 12% in a range of signal bandwidths from 1 to 40 kHz. In approximately half of all experiments, application of a voltage did not significantly increase the noise. In the other half of experiments, however, application of a voltage resulted in an additional source of noise. For these pores, predictions of the noise were usually still accurate within 35% error at signal bandwidths of at least 10 kHz. The power spectra of this extra noise suggested a 1/f(alpha) origin with best fits to the power spectrum for alpha = 0.4-0.8. This work provides the theoretical background and experimental data for understanding the bandwidth requirements and the main sources of noise in current recordings; it will be useful for minimizing noise and achieving accurate recordings.
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Affiliation(s)
- Jeffrey D Uram
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
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16
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Mayer M, Semetey V, Gitlin I, Yang J, Whitesides GM. Using ion channel-forming peptides to quantify protein-ligand interactions. J Am Chem Soc 2008; 130:1453-65. [PMID: 18179217 DOI: 10.1021/ja077555f] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper proposes a method for sensing affinity interactions by triggering disruption of self-assembly of ion channel-forming peptides in planar lipid bilayers. It shows that the binding of a derivative of alamethicin carrying a covalently attached sulfonamide ligand to carbonic anhydrase II (CA II) resulted in the inhibition of ion channel conductance through the bilayer. We propose that the binding of the bulky CA II protein (MW approximately 30 kD) to the ion channel-forming peptides (MW approximately 2.5 kD) either reduced the tendency of these peptides to self-assemble into a pore or extracted them from the bilayer altogether. In both outcomes, the interactions between the protein and the ligand lead to a disruption of self-assembled pores. Addition of a competitive inhibitor, 4-carboxybenzenesulfonamide, to the solution released CA II from the alamethicin-sulfonamide conjugate and restored the current flow across the bilayer by allowing reassembly of the ion channels in the bilayer. Time-averaged recordings of the current over discrete time intervals made it possible to quantify this monovalent ligand binding interaction. This method gave a dissociation constant of approximately 2 microM for the binding of CA II to alamethicin-sulfonamide in the bilayer recording chamber: this value is consistent with a value obtained independently with CA II and a related sulfonamide derivative by isothermal titration calorimetry.
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Affiliation(s)
- Michael Mayer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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Mach T, Chimerel C, Fritz J, Fertig N, Winterhalter M, Fütterer C. Miniaturized planar lipid bilayer: increased stability, low electric noise and fast fluid perfusion. Anal Bioanal Chem 2007; 390:841-6. [DOI: 10.1007/s00216-007-1647-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 09/20/2007] [Accepted: 09/20/2007] [Indexed: 10/22/2022]
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Uram JD, Mayer M. Estimation of solid phase affinity constants using resistive-pulses from functionalized nanoparticles. Biosens Bioelectron 2006; 22:1556-60. [PMID: 16889953 DOI: 10.1016/j.bios.2006.06.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 06/15/2006] [Accepted: 06/23/2006] [Indexed: 11/21/2022]
Abstract
This paper describes a method for estimating the solid phase affinity constant of antibodies by using resistive-pulse (Coulter counting) data from spherical nanoparticles that expose antigens. We developed this technique by analyzing data published recently by Saleh, O.A., Sohn, L.L., 2003a. Proc. Natl. Acad. Sci. U.S.A. 100, 820-824. These authors used resistive-pulse sensing to detect an increase in the diameter of streptavidin-functionalized colloids due to the binding of monoclonal anti-streptavidin antibodies. Based on further analysis of their data, we were able to determine the number of antibodies bound to the colloids at various antibody concentrations. This information made it possible to estimate the solid phase affinity constant of the interaction by fitting the data with binding isotherms that describe the binding equilibrium between antibody and antigen. We calculated a value of 2.6x10(8)+/-0.8x10(8) M-1 which is in agreement with the specifications of the supplier of the antibody.
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Affiliation(s)
- Jeffrey D Uram
- Department of Biomedical Engineering University of Michigan, Ann Arbor, MI 48109, USA
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Uram JD, Ke K, Hunt AJ, Mayer M. Submicrometer pore-based characterization and quantification of antibody-virus interactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2006; 2:967-72. [PMID: 17193151 DOI: 10.1002/smll.200600006] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
- Jeffrey D Uram
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109-2099, USA
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