1
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Wei C, Pohorille A. Multi-oligomeric states of alamethicin ion channel: Assemblies and conductance. Biophys J 2023; 122:2531-2543. [PMID: 37161094 PMCID: PMC10323028 DOI: 10.1016/j.bpj.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/03/2023] [Accepted: 05/04/2023] [Indexed: 05/11/2023] Open
Abstract
Transmembrane assemblies of the peptaibol alamethicin (ALM) are among the most extensively studied ion channels not only because of their antimicrobial activity but also as models for channel structure and aggregation. In this study, several oligomeric states of ALM are investigated with molecular dynamics simulations to establish properties of the channel and obtain free energy profiles for ion transport and the corresponding values of conductance. The hexamer, heptamer, and octamer of ALM in phospholipid membrane are found to be stable but highly dynamic in barrel-stave structures, with calculated conductance equal to 18, 195, and 1270 pS, respectively, in 1 M KCl ion solution. The corresponding free energy profiles, reported for the first time, are reconstructed from simulations at applied voltage of 200 mV with the aid of the electrodiffusion model both with and without the knowledge of diffusivity. The calculated free energy barriers are equal to 2.5, 1.5, and 0.5 kcal/mol for K+ and 4.0, 2.2, and 1.5 kcal/mol for Cl-, for hexamer, heptamer, and octamer, respectively. The calculated conductance and the ratio between conductance in consecutive states are in good agreement with those measured experimentally. This suggests that the hexamer is the lowest conducting state, with measured conductance equal to 19 pS. The selectivity of K+ over Cl- is calculated as 1.5 and 2.3 for the octameric and heptameric channels, close to the selectivity measured for high-conductance states. Selectivity increases to 13 in the hexameric channel in which the narrowest Gln7 site has a pore radius of only ∼1.6 Å, again in accord with experiment. A good agreement found between calculated and measured conductance through a hexamer templated on cyclodextrin lands additional support for the results of our simulations, and the comparison with ALM reveals the dependence of conductance on the nature of phospholipid membrane.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Moffett Field, California; SETI Institute, Mountain View, California.
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2
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Krishnan R S, Jana K, Shaji AH, Nair KS, Das AD, Vikraman D, Bajaj H, Kleinekathöfer U, Mahendran KR. Assembly of transmembrane pores from mirror-image peptides. Nat Commun 2022; 13:5377. [PMID: 36104348 PMCID: PMC9474448 DOI: 10.1038/s41467-022-33155-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Tailored transmembrane alpha-helical pores with desired structural and functional versatility have promising applications in nanobiotechnology. Herein, we present a transmembrane pore DpPorA, based on the natural pore PorACj, built from D-amino acid α-helical peptides. Using single-channel current recordings, we show that DpPorA peptides self-assemble into uniform cation-selective pores in lipid membranes and exhibit properties distinct from their L-amino acid counterparts. DpPorA shows resistance to protease and acts as a functional nanopore sensor to detect cyclic sugars, polypeptides, and polymers. Fluorescence imaging reveals that DpPorA forms well-defined pores in giant unilamellar vesicles facilitating the transport of hydrophilic molecules. A second D-amino acid peptide based on the polysaccharide transporter Wza forms transient pores confirming sequence specificity in stable, functional pore formation. Finally, molecular dynamics simulations reveal the specific alpha-helical packing and surface charge conformation of the D-pores consistent with experimental observations. Our findings will aid the design of sophisticated pores for single-molecule sensing related technologies. Alpha-helix nanopores have a range of potential applications and the inclusion of non-natural amino acids allows for modification. Here, the authors report on the creation of alpha-helix pores using D-amino acids and show the pores formed, have different properties to the L-counterparts and were resistant to proteases.
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3
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R SK, Puthumadathil N, Shaji AH, Santhosh Kumar K, Mohan G, Mahendran KR. Designed alpha-helical barrels for charge-selective peptide translocation. Chem Sci 2020; 12:639-649. [PMID: 34163795 PMCID: PMC8178987 DOI: 10.1039/d0sc04856a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/04/2020] [Indexed: 11/21/2022] Open
Abstract
Synthetic alpha-helix based pores for selective sensing of peptides have not been characterized previously. Here, we report large transmembrane pores, pPorA formed from short synthetic alpha-helical peptides of tunable conductance and selectivity for single-molecule sensing of peptides. We quantified the selective translocation kinetics of differently charged cationic and anionic peptides through these synthetic pores at single-molecule resolution. The charged peptides are electrophoretically pulled into the pores resulting in an increase in the dissociation rate with the voltage indicating successful translocation of peptides. More specifically, we elucidated the charge pattern lining the pore lumen and the orientation of the pores in the membrane based on the asymmetry in the peptide-binding kinetics. The salt and pH-dependent measurements confirm the electrostatic dominance and charge selectivity in controlling target peptide interaction with the pores. Remarkably, we tuned the selectivity of the pores to charged peptides by modifying the charge composition of the pores, thus establishing the molecular and electrostatic basis of peptide translocation. We suggest that these synthetic pores that selectively conduct specific ions and biomolecules are advantageous for nanopore proteomics analysis and synthetic nanobiotechnology applications.
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Affiliation(s)
- Smrithi Krishnan R
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
- Manipal Academy of Higher Education Manipal Karnataka India-576104
| | - Neethu Puthumadathil
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
- Manipal Academy of Higher Education Manipal Karnataka India-576104
| | - Amina H Shaji
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
| | - K Santhosh Kumar
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
| | - Gayathri Mohan
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
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4
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Mayer SF, Ducrey J, Dupasquier J, Haeni L, Rothen-Rutishauser B, Yang J, Fennouri A, Mayer M. Targeting specific membranes with an azide derivative of the pore-forming peptide ceratotoxin A. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183023. [DOI: 10.1016/j.bbamem.2019.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/01/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
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5
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Kim YH, Hang L, Cifelli JL, Sept D, Mayer M, Yang J. Frequency-Based Analysis of Gramicidin A Nanopores Enabling Detection of Small Molecules with Picomolar Sensitivity. Anal Chem 2018; 90:1635-1642. [DOI: 10.1021/acs.analchem.7b02961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | | | | | - David Sept
- Department
of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2110, United States
| | - Michael Mayer
- Adolphe
Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
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6
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Fennouri A, Mayer SF, Schroeder TBH, Mayer M. Single channel planar lipid bilayer recordings of the melittin variant MelP5. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2017; 1859:2051-2057. [PMID: 28720433 DOI: 10.1016/j.bbamem.2017.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/27/2017] [Accepted: 07/07/2017] [Indexed: 12/26/2022]
Abstract
MelP5 is a 26 amino acid peptide derived from melittin, the main active constituent of bee venom, with five amino acid replacements. The pore-forming activity of MelP5 in lipid membranes is attracting attention because MelP5 forms larger pores and induces dye leakage through liposome membranes at a lower concentration than melittin. Studies of MelP5 have so far focused on ensemble measurements of membrane leakage and impedance; here we extend this characterization with an electrophysiological comparison between MelP5 and melittin using planar lipid bilayer recordings. These experiments reveal that MelP5 pores in lipid membranes composed of 3:1 phosphatidylcholine:cholesterol consist of an average of 10 to 12 monomers compared to an average of 3 to 9 monomers for melittin. Both peptides form transient pores with dynamically varying conductance values similar to previous findings for melittin, but MelP5 occasionally also forms stable, well-defined pores with single channel conductance values that vary greatly and range from 50 to 3000pS in an electrolyte solution containing 100mM KCl.
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Affiliation(s)
- Aziz Fennouri
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Simon Finn Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland; Biberach University of Applied Sciences, Karlstraße 11, 88400 Biberach, Germany
| | - Thomas B H Schroeder
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland.
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7
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Howorka S. Building membrane nanopores. NATURE NANOTECHNOLOGY 2017; 12:619-630. [PMID: 28681859 DOI: 10.1038/nnano.2017.99] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 04/19/2017] [Indexed: 05/28/2023]
Abstract
Membrane nanopores-hollow nanoscale barrels that puncture biological or synthetic membranes-have become powerful tools in chemical- and biosensing, and have achieved notable success in portable DNA sequencing. The pores can be self-assembled from a variety of materials, including proteins, peptides, synthetic organic compounds and, more recently, DNA. But which building material is best for which application, and what is the relationship between pore structure and function? In this Review, I critically compare the characteristics of the different building materials, and explore the influence of the building material on pore structure, dynamics and function. I also discuss the future challenges of developing nanopore technology, and consider what the next-generation of nanopore structures could be and where further practical applications might emerge.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
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8
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Agasid MT, Comi TJ, Saavedra SS, Aspinwall CA. Enhanced Temporal Resolution with Ion Channel-Functionalized Sensors Using a Conductance-Based Measurement Protocol. Anal Chem 2017; 89:1315-1322. [PMID: 27981836 PMCID: PMC5862562 DOI: 10.1021/acs.analchem.6b04226] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding of a target analyte to an ion channel (IC), which is readily detected electrochemically in a label-free manner with single-molecule selectivity and specificity, has generated widespread interest in using natural and engineered ICs as transducers in biosensing platforms. To date, the majority of developments in IC-functionalized sensing have focused on IC selectivity or sensitivity or development of suitable membrane environments and aperture geometries. Comparatively little work has addressed analytical performance criteria, particularly criteria required for temporal measurements of dynamic processes. We report a measurement protocol suitable for rapid, time-resolved monitoring (≤30 ms) of IC-modulated membrane conductance. Key features of this protocol include the reduction of membrane area and the use of small voltage steps (10 mV) and short duration voltage pulses (10 ms), which have the net effect of reducing the capacitive charging and decreasing the time required to achieve steady state currents. Application of a conductance protocol employing three sequential, 10 ms voltage steps (-10 mV, -20 mV, -30 mV) in an alternating, pyramid-like arrangement enabled sampling of membrane conductance every 30 ms. Using this protocol, dynamic IC measurements on black lipid membranes (BLMs) functionalized with gramicidin A were conducted using a fast perfusion system. BLM conductance decreased by 76 ± 7.5% within 30 ms of switching from solutions containing 0 to 1 M Ca2+, which demonstrates the feasibility of using this approach to monitor rapid, dynamic chemical processes. Rapid conductance measurements will be broadly applicable to IC-based sensors that undergo analyte-specific gating.
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Affiliation(s)
- Mark T. Agasid
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Troy J. Comi
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - S. Scott Saavedra
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
- BIO5 Institute, University of Arizona, Tucson, AZ 85721
| | - Craig A. Aspinwall
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
- BIO5 Institute, University of Arizona, Tucson, AZ 85721
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ 85721
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9
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Bright LK, Baker CA, Bränström R, Saavedra SS, Aspinwall CA. Methacrylate Polymer Scaffolding Enhances the Stability of Suspended Lipid Bilayers for Ion Channel Recordings and Biosensor Development. ACS Biomater Sci Eng 2016; 1:955-963. [PMID: 26925461 PMCID: PMC4764998 DOI: 10.1021/acsbiomaterials.5b00205] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Black lipid membranes (BLMs) provide a synthetic environment that facilitates measurement of ion channel activity in diverse analytical platforms. The limited electrical, mechanical and temporal stabilities of BLMs pose a significant challenge to development of highly stable measurement platforms. Here, ethylene glycol dimethacrylate (EGDMA) and butyl methacrylate (BMA) were partitioned into BLMs and photopolymerized to create a cross-linked polymer scaffold in the bilayer lamella that dramatically improved BLM stability. The commercially available methacrylate monomers provide a simple, low cost, and broadly accessible approach for preparing highly stabilized BLMs useful for ion channel analytical platforms. When prepared on silane-modified glass microapertures, the resulting polymer scaffold-stabilized (PSS)-BLMs exhibited significantly improved lifetimes of 23 ± 9 to 40 ± 14 h and > 10-fold increase in mechanical stability, with breakdown potentials > 2000 mV attainable, depending on surface modification and polymer cross-link density. Additionally, the polymer scaffold exerted minimal perturbations to membrane electrical integrity as indicated by mean conductance measurements. When gramicidin A and α-hemolysin were reconstituted into PSS-BLMs, the ion channels retained function comparable to conventional BLMs. This approach is a key advance in the formation of stabilized BLMs and should be amenable to a wide range of receptor and ion channel functionalized platforms.
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Affiliation(s)
- Leonard K. Bright
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Christopher A. Baker
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Robert Bränström
- Endocrine and Sarcoma Surgery Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - S. Scott Saavedra
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
- BIO5 Institute, University of Arizona, Tucson, AZ 85721
| | - Craig A. Aspinwall
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
- BIO5 Institute, University of Arizona, Tucson, AZ 85721
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ 85721
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10
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Yu HR, Hu JQ, Lu XH, Ju XJ, Liu Z, Xie R, Wang W, Chu LY. Insights into the Effects of 2:1 “Sandwich-Type” Crown-Ether/Metal-Ion Complexes in Responsive Host–Guest Systems. J Phys Chem B 2015; 119:1696-705. [DOI: 10.1021/jp5079423] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hai-Rong Yu
- School
of Chemical Engineering, Sichuan University, Southern 1 Section, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Jia-Qi Hu
- School
of Chemical Engineering, Sichuan University, Southern 1 Section, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Xiao-Hua Lu
- School
of Chemical Engineering, Nanjing Tech University, No. 5 Xin Mofan Road, Nanjing, Jiangsu 211816, China
| | - Xiao-Jie Ju
- School
of Chemical Engineering, Sichuan University, Southern 1 Section, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Zhuang Liu
- School
of Chemical Engineering, Sichuan University, Southern 1 Section, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Rui Xie
- School
of Chemical Engineering, Sichuan University, Southern 1 Section, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Wei Wang
- School
of Chemical Engineering, Sichuan University, Southern 1 Section, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Liang-Yin Chu
- School
of Chemical Engineering, Sichuan University, Southern 1 Section, Yihuan Road, Chengdu, Sichuan 610065, China
- State
Key Laboratory of Polymer Materials Engineering, Sichuan University, Southern 1 Section, Yihuan Road, Chengdu, Sichuan 610065, China
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11
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Macazo FC, White RJ. Monitoring charge flux to quantify unusual ligand-induced ion channel activity for use in biological nanopore-based sensors. Anal Chem 2014; 86:5519-25. [PMID: 24794413 PMCID: PMC4051251 DOI: 10.1021/ac500832a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
The
utility of biological nanopores for the development of sensors
has become a growing area of interest in analytical chemistry. Their
emerging use in chemical analysis is a result of several ideal characteristics.
First, they provide reproducible control over nanoscale pore sizes
with an atomic level of precision. Second, they are amenable to resistive-pulse
type measurement systems when embedded into an artificial lipid bilayer.
A single binding event causes a change in the flow of millions of
ions across the membrane per second that is readily measured as a
change in current with excellent signal-to-noise ratio. To date, ion
channel-based biosensors have been limited to well-behaved proteins.
Most demonstrations of using ion channels as sensors have been limited
to proteins that remain in the open, conducting state, unless occupied
by an analyte of interest. Furthermore, these proteins are nonspecific,
requiring chemical, biochemical, or genetic manipulations to impart
chemical specificity. Here, we report on the use of the pore-forming
abilities of heat shock cognate 70 (Hsc70) to quantify a specific
analyte. Hsc70 reconstitutes into phospholipid membranes and opens
to form multiple conductance states specifically in the presence of
ATP. We introduce the measurement of “charge flux” to
characterize the ATP-regulated multiconductance nature of Hsc70, which
enables sensitive quantification of ATP (100 μM–4 mM).
We believe that monitoring protein-induced charge flux across a bilayer
membrane represents a universal method for quantitatively monitoring
ion-channel activity. This measurement has the potential to broaden
the library of usable proteins in the development of nanopore-based
biosensors.
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Affiliation(s)
- Florika C Macazo
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County , 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
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12
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Movileanu L. Watching single proteins using engineered nanopores. Protein Pept Lett 2014; 21:235-46. [PMID: 24370252 PMCID: PMC3924890 DOI: 10.2174/09298665113209990078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 11/03/2012] [Accepted: 11/10/2012] [Indexed: 12/22/2022]
Abstract
Recent studies in the area of single-molecule detection of proteins with nanopores show a great promise in fundamental science, bionanotechnology and proteomics. In this mini-review, I discuss a comprehensive array of examinations of protein detection and characterization using protein and solid-state nanopores. These investigations demonstrate the power of the single-molecule nanopore measurements to reveal a broad range of functional, structural, biochemical and biophysical features of proteins, such as their backbone flexibility, enzymatic activity, binding affinity as well as their concentration, size and folding state. Engineered nanopores in organic materials and in inorganic membranes coupled with surface modification and protein engineering might provide a new generation of sensing devices for molecular biomedical diagnostics.
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Affiliation(s)
- Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA.
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13
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Kredics L, Szekeres A, Czifra D, Vágvölgyi C, Leitgeb B. Recent results in alamethicin research. Chem Biodivers 2013; 10:744-71. [PMID: 23681724 DOI: 10.1002/cbdv.201200390] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 12/20/2022]
Affiliation(s)
- László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged.
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14
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Mayer M, Yang J. Engineered ion channels as emerging tools for chemical biology. Acc Chem Res 2013; 46:2998-3008. [PMID: 23932142 DOI: 10.1021/ar400129t] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Over the last 25 years, researchers have developed exogenously expressed, genetically engineered, semi-synthetic, and entirely synthetic ion channels. These structures have sufficient fidelity to serve as unique tools that can reveal information about living organisms. One of the most exciting success stories is optogenetics: the use of light-gated channels to trigger action potentials in specific neurons combined with studies of the response from networks of cells or entire live animals. Despite this breakthrough, the use of molecularly engineered ion channels for studies of biological systems is still in its infancy. Historically, researchers studied ion channels in the context of their own function in single cells or in multicellular signaling and regulation. Only recently have researchers considered ion channels and pore-forming peptides as responsive tools to report on the chemical and physical changes produced by other biochemical processes and reactions. This emerging class of molecular probes has a number of useful characteristics. For instance, these structures can greatly amplify the signal of chemical changes: the binding of one molecule to a ligand-gated ion channel can result in flux of millions of ions across a cell membrane. In addition, gating occurs on sub-microsecond time scales, resulting in fast response times. Moreover, the signal is complementary to existing techniques because the output is ionic current rather than fluorescence or radioactivity. And finally, ion channels are also localized at the membrane of cells where essential processes such as signaling and regulation take place. This Account highlights examples, mostly from our own work, of uses of ion channels and pore-forming peptides such as gramicidin in chemical biology. We discuss various strategies for preparing synthetically tailored ion channels that range from de novo designed synthetic molecules to genetically engineered or simply exogenously expressed or reconstituted wild-type channels. Next we consider aspects of experimental design by comparing various membrane environments or systems that make it possible to quantify the response of ion channels to biochemical processes of interest. We present applications of ion channels to answer questions in chemical biology, and propose potential future developments and applications of these single molecule probes. Finally we discuss the hurdles that impede the routine use of ion channel probes in biochemistry and cell biology laboratories and developments and strategies that could overcome these problems. Optogenetics has facilitated breakthroughs in neuroscience, and these results give a dramatic idea of what may lie ahead for designed ion channels as a functional class of molecular probes. If researchers can improve molecular engineering to increase ion channel versatility and can overcome the barriers to collaborating across disciplines, we conclude that these structures could have tremendous potential as novel tools for chemical biology studies.
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Affiliation(s)
- Michael Mayer
- Department of Chemical Engineering and Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110, United States
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093-0358, United States
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15
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Noshiro D, Asami K, Futaki S. Control of leakage activities of alamethicin analogs by metals: Side chain-dependent adverse gating response to Zn2+. Bioorg Med Chem 2012; 20:6870-6. [DOI: 10.1016/j.bmc.2012.09.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 09/16/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
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16
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Prangkio P, Yusko EC, Sept D, Yang J, Mayer M. Multivariate analyses of amyloid-beta oligomer populations indicate a connection between pore formation and cytotoxicity. PLoS One 2012; 7:e47261. [PMID: 23077580 PMCID: PMC3471831 DOI: 10.1371/journal.pone.0047261] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/07/2012] [Indexed: 11/18/2022] Open
Abstract
Aggregates of amyloid-beta (Aβ) peptides are thought to be involved in the development of Alzheimer's disease because they can change synaptic plasticity and induce neuronal cell death by inflammation, oxidative damage, and transmembrane pore formation. Exactly which oligomeric species underlie these cytotoxic effects remains unclear. The work presented here established well-controlled aggregation conditions of Aβ₁₋₄₀ or Aβ₁₋₄₂ peptides over a 20-day period and characterized these preparations with regard to their β-sheet content, degree of fibril formation, relative abundance of various oligomer sizes, and propensity to induce membrane pore formation and cytotoxicity. Using this multivariate data set, a systematic and inherently unbiased partial least squares (PLS) approach showed that for both peptides the abundance of oligomers in the tetramer to 13-mer range contributed positively to both pore formation and cytotoxicity, while monomers, dimers, trimers, and the largest oligomers (>210 kDa) were negatively correlated to both phenomena. Multivariate PLS analysis is ideally suited to handle complex data sets and interdependent variables such as relative oligomer concentrations, making it possible to elucidate structure function relationships in complex mixtures. This approach, therefore, introduces an enabling tool to the field of amyloid research, in which it is often difficult to interpret the activity of individual species within a complex mixture of bioactive species.
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Affiliation(s)
- Panchika Prangkio
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
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17
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de la Escosura-Muñiz A, Merkoçi A. Nanochannels preparation and application in biosensing. ACS NANO 2012; 6:7556-83. [PMID: 22880686 DOI: 10.1021/nn301368z] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Selective transport in nanochannels (protein-based ion channels) is already used in living systems for electrical signaling in nerves and muscles, and this natural behavior is being approached for the application of biomimetic nanochannels in biosensors. On the basis of this principle, single nanochannels and nanochannel arrays seem to bring new advantages for biosensor development and applications. The purpose of this review is to provide a general comprehensive and critical overview on the latest trends in the development of nanochannel-based biosensing systems. A detailed description and discussion of representative and recent works covering the main nanochannel fabrication techniques, nanoporous material characterizations, and especially their application in both electrochemical and optical sensing systems is given. The state-of-the-art of the developed technology may open the way to new advances in the integration of nanochannels with (bio)molecules and synthetic receptors for the development of novel biodetection systems that can be extended to many other applications with interest for clinical analysis, safety, and security as well as environmental and other industrial studies and applications.
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Affiliation(s)
- Alfredo de la Escosura-Muñiz
- Nanobioelectronics & Biosensors Group, CIN2, ICN-CSIC, Catalan Institute of Nanotechnology, Campus UAB, Bellaterra, Barcelona, Spain
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18
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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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19
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Wilson CP, Boglio C, Ma L, Cockroft SL, Webb SJ. Palladium(II)-Mediated Assembly of Biotinylated Ion Channels. Chemistry 2011; 17:3465-73. [DOI: 10.1002/chem.201002031] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2010] [Revised: 10/12/2010] [Indexed: 11/10/2022]
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Rokitskaya TI, Macrae MX, Blake S, Egorova NS, Kotova EA, Yang J, Antonenko YN. Mechanistic insight into gramicidin-based detection of protein-ligand interactions via sensitized photoinactivation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:454118. [PMID: 21339605 DOI: 10.1088/0953-8984/22/45/454118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Among the many challenges for the development of ion channel-based sensors is the poor understanding of how to engineer modified transmembrane pores with tailored functionality that can respond to external stimuli. Here, we use the method of sensitized photoinactivation of gramicidin A (gA) channels in planar bilayer lipid membranes to help elucidate the underlying mechanistic details for changes in macroscopic transmembrane ionic current observed upon interaction of C-terminally attached gA ligands with specific proteins in solution. Three different systems were studied: (i) carbonic anhydrase (CA) and gA-sulfonamide, (ii) PSD-95 protein (belonging to the 'PDZ domain-containing protein') and a gA analog carrying the KGGHRRSARYLESSV peptide sequence at the C-terminus, and (iii) an anti-biotin antibody and gA-biotin. The results challenge a previously proposed mechanistic hypothesis suggesting that protein-induced current suppression is due to steric blockage of the ion passage through gA channels, while they reveal new insight for consideration in alternative mechanistic models. Additionally, we demonstrate that the length of a linker between the ligand and the gA channel may be less important for gramicidin-based detection of monovalent compared to multivalent protein-ligand interactions. These studies collectively shed new light on the mechanism of protein-induced current alterations in bilayer recordings of gA derivatives, which may be important in the design of new gramicidin-based sensors.
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Affiliation(s)
- Tatyana I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia
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21
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Yusko EC, Billeh YN, Mayer M. Current oscillations generated by precipitate formation in the mixing zone between two solutions inside a nanopore. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:454127. [PMID: 21339613 DOI: 10.1088/0953-8984/22/45/454127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Unlike biological protein pores in lipid membranes, nanopores fabricated in synthetic materials can withstand a wide range of environmental conditions including the presence of organic solvents. This capability expands the potential of synthetic nanopores to monitor chemical reactions occurring at the interface between solutions of organic and aqueous character. In this work, nanopores fabricated in borosilicate glass or silicon nitride connected a predominantly organic solvent to an aqueous solvent, thereby generating a mixing zone between these solutions inside the pore. This configuration was exploited to precipitate small organic molecules with low aqueous solubility inside the nanopores, and concomitantly, to monitor this precipitation by the decrease of the ionic conductance through the nanopores over time. Hence, this method provides a means to induce and investigate the formation of nanoprecipitates or nanoparticles. Interestingly, precipitates with a slight electric charge were cleared from the pore, causing the conductance of the pore to return to its original value. This process repeated, resulting in stable oscillations of the ionic current. Although such oscillations might be useful in fluidic logic circuits, few conditions capable of generating oscillations in ionic currents have been reported. The frequency and amplitude of oscillations could be tuned by changing the concentration of the precipitating molecule, the pH of the electrolyte, and the applied potential bias. In addition to generating oscillations, nanopores that separate two different solutions may be useful for monitoring and mediating chemical reactions in the mixing zone between two solutions.
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Affiliation(s)
- Erik C Yusko
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Lurie Biomedical Engineering Building, Room 2174, Ann Arbor, MI 48109-2110, USA
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Majd S, Yusko EC, Billeh YN, Macrae MX, Yang J, Mayer M. Applications of biological pores in nanomedicine, sensing, and nanoelectronics. Curr Opin Biotechnol 2010; 21:439-76. [PMID: 20561776 PMCID: PMC3121537 DOI: 10.1016/j.copbio.2010.05.002] [Citation(s) in RCA: 264] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 05/03/2010] [Accepted: 05/06/2010] [Indexed: 12/29/2022]
Abstract
Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated - often regulated - functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics.
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Affiliation(s)
- Sheereen Majd
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110, USA
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Noshiro D, Asami K, Futaki S. Metal-assisted channel stabilization: disposition of a single histidine on the N-terminus of alamethicin yields channels with extraordinarily long lifetimes. Biophys J 2010; 98:1801-8. [PMID: 20441743 DOI: 10.1016/j.bpj.2010.01.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 11/08/2009] [Accepted: 01/04/2010] [Indexed: 10/19/2022] Open
Abstract
Alamethicin, a member of the peptaibol family of antibiotics, is a typical channel-forming peptide with a helical structure. The self-assembly of the peptide in the membranes yields voltage-dependent channels. In this study, three alamethicin analogs possessing a charged residue (His, Lys, or Glu) on their N-termini were designed with the expectation of stabilizing the transmembrane structure. A slight elongation of channel lifetime was observed for the Lys and Glu analogs. On the other hand, extensive stabilization of certain channel open states was observed for the His analog. This stabilization was predominantly observed in the presence of metal ions such as Zn(2+), suggesting that metal coordination with His facilitates the formation of a supramolecular assembly in the membranes. Channel stability was greatly diminished by acetylation of the N-terminal amino group, indicating that the N-terminal amino group also plays an important role in metal coordination.
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Affiliation(s)
- Daisuke Noshiro
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
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24
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Majd S, Yusko EC, MacBriar AD, Yang J, Mayer M. Gramicidin pores report the activity of membrane-active enzymes. J Am Chem Soc 2010; 131:16119-26. [PMID: 19886696 DOI: 10.1021/ja904072s] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phospholipases constitute a ubiquitous class of membrane-active enzymes that play a key role in cellular signaling, proliferation, and membrane trafficking. Aberrant phospholipase activity is implicated in a range of diseases including cancer, inflammation, and myocardial disease. Characterization of these enzymes is therefore important, both for improving the understanding of phospholipase catalysis and for accelerating pharmaceutical and biotechnological applications. This paper describes a novel approach to monitor, in situ and in real-time, the activity of phospholipase D (PLD) and phospholipase C (PLC) on planar lipid bilayers. This method is based on lipase-induced changes in the electrical charge of lipid bilayers and on the concomitant change in ion concentration near lipid membranes. The approach reports these changes in local ion concentration by a measurable change in the single channel ion conductance through pores of the ion channel-forming peptide gramicidin A. This enzyme assay takes advantage of the amplification characteristics of gramicidin pores to sense the activity of picomolar to nanomolar concentrations of membrane-active enzymes without requiring labeled substrates or products. The resulting method proceeds on lipid bilayers without the need for detergents, quantifies enzyme activity on native lipid substrates within minutes, and provides unique access to both leaflets of well-defined lipid bilayers; this method also makes it possible to generate planar lipid bilayers with transverse lipid asymmetry.
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Affiliation(s)
- Sheereen Majd
- Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110, USA
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Macrae MX, Blake S, Jiang X, Capone R, Estes DJ, Mayer M, Yang J. A semi-synthetic ion channel platform for detection of phosphatase and protease activity. ACS NANO 2009; 3:3567-80. [PMID: 19860382 PMCID: PMC2805247 DOI: 10.1021/nn901231h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Sensitive methods to probe the activity of enzymes are important for clinical assays and for elucidating the role of these proteins in complex biochemical networks. This paper describes a semi-synthetic ion channel platform for detecting the activity of two different classes of enzymes with high sensitivity. In the first case, this method uses single ion channel conductance measurements to follow the enzyme-catalyzed hydrolysis of a phosphate group attached to the C-terminus of gramicidin A (gA, an ion channel-forming peptide) in the presence of alkaline phosphatase (AP). Enzymatic hydrolysis of this phosphate group removes negative charges from the entrance of the gA pore, resulting in a product with measurably reduced single ion channel conductance compared to the original gA-phosphate substrate. This technique employs a standard, commercial bilayer setup and takes advantage of the catalytic turnover of enzymes and the amplification characteristics of ion flux through individual gA pores to detect picomolar concentrations of active AP in solution. Furthermore, this technique makes it possible to study the kinetics of an enzyme and provides an estimate for the observed rate constant (k(cat)) and the Michaelis constant (K(M)) by following the conversion of the gA-phosphate substrate to product over time in the presence of different concentrations of AP. In the second case, modification of gA with a substrate for proteolytic cleavage by anthrax lethal factor (LF) afforded a sensitive method for detection of LF activity, illustrating the utility of ion channel-based sensing for detection of a potential biowarfare agent. This ion channel-based platform represents a powerful, novel approach to monitor the activity of femtomoles to picomoles of two different classes of enzymes in solution. Furthermore, this platform has the potential for realizing miniaturized, cost-effective bioanalytical assays that complement currently established assays.
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Affiliation(s)
- Michael X. Macrae
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, CA 92093-0358
| | - Steven Blake
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, CA 92093-0358
| | - Xiayun Jiang
- Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109-2110
| | - Ricardo Capone
- Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109-2110
| | - Daniel J. Estes
- Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109-2110
| | - Michael Mayer
- Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109-2110
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, CA 92093-0358
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27
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A synthetic membrane protein in tethered lipid bilayers for immunosensing in whole blood. J Struct Biol 2009; 168:177-82. [DOI: 10.1016/j.jsb.2009.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 03/20/2009] [Accepted: 03/22/2009] [Indexed: 01/09/2023]
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Capone R, Quiroz FG, Prangkio P, Saluja I, Sauer AM, Bautista MR, Turner RS, Yang J, Mayer M. Amyloid-beta-induced ion flux in artificial lipid bilayers and neuronal cells: resolving a controversy. Neurotox Res 2009; 16:1-13. [PMID: 19526294 PMCID: PMC2864106 DOI: 10.1007/s12640-009-9033-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 12/15/2008] [Accepted: 12/15/2008] [Indexed: 10/20/2022]
Abstract
Understanding the pathogenicity of amyloid-beta (Abeta) peptides constitutes a major goal in research on Alzheimer's disease (AD). One hypothesis entails that Abeta peptides induce uncontrolled, neurotoxic ion flux through cellular membranes. The exact biophysical mechanism of this ion flux is, however, a subject of an ongoing controversy which has attenuated progress toward understanding the importance of Abeta-induced ion flux in AD. The work presented here addresses two prevalent controversies regarding the nature of transmembrane ion flux induced by Alphabeta peptides. First, the results clarify that Alphabeta can induce stepwise ion flux across planar lipid bilayers as opposed to a gradual increase in transmembrane current; they show that the previously reported gradual thinning of membranes with concomitant increase in transmembrane current arises from residues of the solvent hexafluoroisopropanol, which is commonly used for the preparation of amyloid samples. Second, the results provide additional evidence suggesting that Abeta peptides can induce ion channel-like ion flux in cellular membranes that is independent from the postulated ability of Alphabeta to modulate intrinsic cellular ion channels or transporter proteins.
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Affiliation(s)
- Ricardo Capone
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Ave, Ann Arbor, MI 48109-2110, USA
| | - Felipe Garcia Quiroz
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Ave, Ann Arbor, MI 48109-2110, USA
| | - Panchika Prangkio
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Ave, Ann Arbor, MI 48109-2110, USA
| | | | - Anna M. Sauer
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Ave, Ann Arbor, MI 48109-2110, USA
| | - Mahealani R. Bautista
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, CA 92093-0358, USA
| | | | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, CA 92093-0358, USA
| | - Michael Mayer
- Departments of Biomedical Engineering and Chemical Engineering, University of Michigan, 1101 Beal Ave, Ann Arbor, MI 48109-2110, USA
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Movileanu L. Interrogating single proteins through nanopores: challenges and opportunities. Trends Biotechnol 2009; 27:333-41. [PMID: 19394097 DOI: 10.1016/j.tibtech.2009.02.008] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2009] [Revised: 02/18/2009] [Accepted: 02/20/2009] [Indexed: 11/18/2022]
Abstract
A single nanopore represents an amazingly versatile single-molecule probe that can be employed to reveal several important features of polypeptides, such as their folding state, backbone flexibility, mechanical stability, binding affinity to other interacting ligands and enzymatic activity. Moreover, groundwork in this area using engineered protein nanopores has demonstrated new opportunities for discovering the biophysical rules that govern the transport of proteins through transmembrane protein pores. In this review, I summarize the current knowledge in the field and discuss how nanopore probe techniques will provide a new generation of research tools in nanomedicine for quantitatively examining the details of complex recognition and, furthermore, will represent a crucial step in designing other pore-based nanostructures and high-throughput devices for molecular biomedical diagnosis.
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Affiliation(s)
- Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA.
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31
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Poulos JL, Jeon TJ, Damoiseaux R, Gillespie EJ, Bradley KA, Schmidt JJ. Ion channel and toxin measurement using a high throughput lipid membrane platform. Biosens Bioelectron 2008; 24:1806-10. [PMID: 18849158 DOI: 10.1016/j.bios.2008.08.041] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Revised: 07/30/2008] [Accepted: 08/14/2008] [Indexed: 11/19/2022]
Abstract
Measurements of ion channels are important for scientific, sensing and pharmaceutical applications. Reconstitution of ion channels into lipid vesicles and planar lipid bilayers for measurement at the single molecule level is a laborious and slow process incompatible with the high throughput methods and equipment used for sensing and drug discovery. A recently published method of lipid bilayer formation mechanically combines lipid monolayers self-assembled at the interfaces of aqueous and apolar phases. We have expanded on this method by vertically orienting these phases and using gravity as the driving force to combine the monolayers. As this method only requires fluid dispensation, it is trivially integrated with high throughput automated liquid-handling robotics. In a proof-of-concept demonstration, we created over 2200 lipid bilayers in 3h. We show single molecule measurements of technologically and physiologically relevant ion channels incorporated into lipid bilayers formed with this method.
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Affiliation(s)
- Jason L Poulos
- Department of Bioengineering, University of California, Los Angeles, USA
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Blake S, Capone R, Mayer M, Yang J. Chemically Reactive Derivatives of Gramicidin A for Developing Ion Channel-Based Nanoprobes. Bioconjug Chem 2008; 19:1614-24. [DOI: 10.1021/bc800180z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steven Blake
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093-0358, and Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109
| | - Ricardo Capone
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093-0358, and Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109
| | - Michael Mayer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093-0358, and Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093-0358, and Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109
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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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Krishnamurthy VM, Kaufman GK, Urbach AR, Gitlin I, Gudiksen KL, Weibel DB, Whitesides GM. Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chem Rev 2008; 108:946-1051. [PMID: 18335973 PMCID: PMC2740730 DOI: 10.1021/cr050262p] [Citation(s) in RCA: 561] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Vijay M. Krishnamurthy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George K. Kaufman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Adam R. Urbach
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Irina Gitlin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Katherine L. Gudiksen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Douglas B. Weibel
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
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