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Singh H, Khatoon N, Bhardwaj SK, Kampani P, Nayak TK, Haridas V. Bispidine as a Versatile Scaffold: From Topological Hosts to Transmembrane Transporters. Chembiochem 2023; 24:e202300502. [PMID: 37708237 DOI: 10.1002/cbic.202300502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/24/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
The development of designer topological structures is a synthetically challenging endeavor. We present herein bispidine as a platform for the design of molecules with various topologies and functions. The bispidine-based acyclic molecule, which shows intriguing S-shape topology, is discussed. Single-crystal X-ray diffraction studies revealed that this molecule exists in the solid state as two conformational enantiomers. In addition, bispidine-based designer macrocycles were synthesized and investigated for ionophoric properties. Patch clamp experiments revealed that these macrocycles transport both anions and cations non-specifically with at least tenfold higher chloride conductance over the cations under the given experimental conditions. Ultramicroscopy and single-crystal X-ray crystallographic studies indicated that the self-assembling macrocycle forms a tubular assembly. Our design highlights the use of unconventional dihydrogen interactions in nanotube fabrication.
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Affiliation(s)
- Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Nadira Khatoon
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Surya Kant Bhardwaj
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Pradeepti Kampani
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Tapan K Nayak
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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2
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Xu W, Mei J, Wang C, Yang H, Ma X, Gao W, Ahmad S, Ai H. Origin of stronger binding of ionic pair (IP) inhibitor to Aβ42 than the equimolar neutral counterparts: synergy mechanism of IP in disrupting Aβ42 protofibril and inhibiting Aβ42 aggregation under two pH conditions. Phys Chem Chem Phys 2023; 25:21612-21630. [PMID: 37551434 DOI: 10.1039/d3cp01683h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Fibrous aggregates of beta-amyloid (Aβ) is a hallmark of Alzheimer's disease (AD). Several major strategies of drugs or inhibitors, including neutral molecules, positive or negative ions, and dual-inhibitor, are used to inhibit the misfolding or aggregation of Aβ42, among which a kind of dual-inhibitor composed of a pair of positive and negative ions is emerging as the most powerful candidate. This knowledge lacks the origin of the strong inhibitory effect and synergy mechanisms blocking the development and application of such inhibitors. To this end, we employed 1 : 1 ionic pairs (IP) of oppositely charged benzothiazole molecules (+)BAM1-EG6 (Pos) and (-)BAM1-EG6 (Neg) as well as equimolar neutral BAM1-EG6 (Neu) counterpart at two pH conditions (5.5 and 7.0) to bind Aβ42 targets, Aβ42 monomer (AβM), soluble pentamer (AβP), and pentameric protofibril (AβF) models, respectively, corresponding to the products of three toxic Aβ42 development pathways, lag, exponential and fibrillation phases. Simulated results illustrated the details of the inhibitory mechanisms of IP and Neu for the AβY (Y = M, P, or F) in the three different phases, characterizing the roles of Pos and Neg of IP as well as their charged, hydrophobic groups and linker playing in the synergistic interaction, and elucidated a previously unknown molecular mechanism governing the IP-Aβ42 interaction. Most importantly, we first revealed the origin of the stronger binding of IP inhibitors to Aβ42 than that of the equimolar neutral counterparts, observing a perplexing phenomenon that the physiological condition (pH = 7.0) than the acidic one (pH = 5.5) is more favorable to the enhancement of IP binding, and finally disclosed that solvation is responsible to the enhancement because at pH 7.0, AβP and AβF act as anionic membranes, where solvation plays a critical role in the chemoelectromechanics. The result not only provides a new dimension in dual-inhibitor/drug design and development but also a new perspective for uncovering charged protein disaggregation under IP-like inhibitors.
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Affiliation(s)
- Wen Xu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Jinfei Mei
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Chuanbo Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Huijuan Yang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Xiaohong Ma
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Wenqi Gao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Sajjad Ahmad
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
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3
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Agarwal S, Kalal P, Sethiya A, Soni J. Taurine: A Water Friendly Organocatalyst in Organic Reactions. MINI-REV ORG CHEM 2021. [DOI: 10.2174/1570193x18666211122112327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
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Organocatalysis has become a powerful tool in organic synthesis for the formation of C-C and C-X (N, S, O, etc.) bonds, leading to the formation of complex molecules from easily available starting materials. It provides an alternative platform to the conventional synthesis and fulfills the principles of green chemistry. During the last decades, taurine has emerged as a promising organocatalyst in an array of organic transformations in addition to its plentiful biological properties. It is highly stable, easy to store and separate, water-soluble, of low cost, easily available, and recyclable. The present article highlights the recent and up-to-date applications of taurine in organic transformations.
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Affiliation(s)
- Shikha Agarwal
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, MLSU, Udaipur, 313001, India
| | - Priyanka Kalal
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, MLSU, Udaipur, 313001, India
| | - Ayushi Sethiya
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, MLSU, Udaipur, 313001, India
| | - Jay Soni
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, MLSU, Udaipur, 313001, India
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5
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Xin P, Zhao L, Mao L, Xu L, Hou S, Kong H, Fang H, Zhu H, Jiang T, Chen CP. Effect of charge status on the ion transport and antimicrobial activity of synthetic channels. Chem Commun (Camb) 2020; 56:13796-13799. [DOI: 10.1039/d0cc05730d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The charge status of channels formed by pillararene–gramicidin hybrid molecules has a significant impact on their trans-membrane transport properties, membrane-association abilities and antimicrobial activities.
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6
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Lenhart B, Wei X, Zhang Z, Wang X, Wang Q, Liu C. Nanopore Fabrication and Application as Biosensors in Neurodegenerative Diseases. Crit Rev Biomed Eng 2020; 48:29-62. [PMID: 32749118 PMCID: PMC8020784 DOI: 10.1615/critrevbiomedeng.2020033151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Since its conception as an applied biomedical technology nearly 30 years ago, nanopore is emerging as a promising, high-throughput, biomarker-targeted diagnostic tool for clinicians. The attraction of a nanopore-based detection system is its simple, inexpensive, robust, user-friendly, high-throughput blueprint with minimal sample preparation needed prior to analysis. The goal of clinical-based nanopore biosensing is to go from sample acquisition to a meaningful readout quickly. The most extensive work in nanopore applications has been targeted at DNA, RNA, and peptide identification. Although, biosensing of pathological biomarkers, which is covered in this review, is on the rise. This review is broken into two major sections: (i) the current state of existing biological, solid state, and hybrid nanopore systems and (ii) the applications of nanopore biosensors toward detecting neurodegenerative biomarkers.
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Affiliation(s)
- Brian Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
| | - Xiaojun Wei
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC
| | - Chang Liu
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
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7
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Chate AV, Rudrawar PP, Bondle GM, Sangeshetti JN. 2-Aminoethanesulfonic acid: An efficient organocatalyst for green synthesis of spirooxindole dihydroquinazolinones and novel 1,2-(dihydroquinazolin-3(4H)isonicotinamides in water. SYNTHETIC COMMUN 2019. [DOI: 10.1080/00397911.2019.1692868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Asha V. Chate
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Priyanka P. Rudrawar
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Giribala M. Bondle
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Jaiprakash N. Sangeshetti
- Department of Quality Assurance, Y. B. Chavan College of Pharmacy, Rafiq Zakaria Campus, Aurangabad, India
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8
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Misawa N, Osaki T, Takeuchi S. Membrane protein-based biosensors. J R Soc Interface 2019; 15:rsif.2017.0952. [PMID: 29669891 DOI: 10.1098/rsif.2017.0952] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/19/2018] [Indexed: 01/09/2023] Open
Abstract
This review highlights recent development of biosensors that use the functions of membrane proteins. Membrane proteins are essential components of biological membranes and have a central role in detection of various environmental stimuli such as olfaction and gustation. A number of studies have attempted for development of biosensors using the sensing property of these membrane proteins. Their specificity to target molecules is particularly attractive as it is significantly superior to that of traditional human-made sensors. In this review, we classified the membrane protein-based biosensors into two platforms: the lipid bilayer-based platform and the cell-based platform. On lipid bilayer platforms, the membrane proteins are embedded in a lipid bilayer that bridges between the protein and a sensor device. On cell-based platforms, the membrane proteins are expressed in a cultured cell, which is then integrated in a sensor device. For both platforms we introduce the fundamental information and the recent progress in the development of the biosensors, and remark on the outlook for practical biosensing applications.
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Affiliation(s)
- Nobuo Misawa
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan.,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Shoji Takeuchi
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan .,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
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9
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Cifelli JL, Capule CC, Yang J. Noncovalent, Electrostatic Interactions Induce Positively Cooperative Binding of Small Molecules to Alzheimer's and Parkinson's Disease-Related Amyloids. ACS Chem Neurosci 2019; 10:991-995. [PMID: 30044911 DOI: 10.1021/acschemneuro.8b00280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Amyloids are self-assembled protein aggregates that represent a major hallmark of many neurologic and systemic diseases. Among the common features of amyloids is the presence of a high density of multiple binding sites for small molecule ligands, making them an attractive target for design of multimeric binding agents. Here, we demonstrate that noncovalent, intermolecular interactions between a 1:1 mixture of oppositely charged benzothiazole molecules enhances their binding to two different amyloid aggregates: Alzheimer's-related amyloid-β (Aβ) peptides or Parkinson's-related α-synuclein (αS) proteins. We show that this mixture leads to positively cooperative binding to amyloid targets, with up to 10-fold enhancement of binding compared to the uncharged parent compound. The observed enhancement of amyloid binding using noncovalent interactions was similar in magnitude to a benzothiazole dimer to aggregated Aβ. These results represent a novel strategy for designing amyloid-targeting molecules with enhanced affinity, which could aid in the development of new diagnostic or treatment strategies for amyloid-associated diseases.
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Affiliation(s)
- Jessica L. Cifelli
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Christina C. Capule
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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10
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Chen X, Wang L, Roozbahani GM, Zhang Y, Xiang J, Guan X. Nanopore label-free detection of single-nucleotide deletion in Baxα/BaxΔ2. Electrophoresis 2018; 39:2410-2416. [PMID: 29998460 PMCID: PMC6168411 DOI: 10.1002/elps.201800193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/14/2018] [Accepted: 07/01/2018] [Indexed: 12/13/2022]
Abstract
Baxα, a key tumor suppressor gene, will not be expressed correctly as a result of single nucleotide mutation in its microsatellite region; Instead, BaxΔ2, an isoform of Baxα, is often produced. In addition, lack of the exon 2 due to an alternative splicing, BaxΔ2 has the same sequence as Baxα except single base deletion from eight continuous guanines (G8) to G7. Most of the currently available methods for Bax∆2 detection are inefficient and time-consuming, and/or require the use of labels or dyes. In this work, we reported a label-free nanopore sensing strategy to differentiate between Baxα and BaxΔ2 with a DNA polymer as a molecular probe based on alternative spliced sequences. Two DNA molecules were designed to selectively detect Baxα and BaxΔ2, respectively. The method was rapid, accurate, and highly sensitive: picomolar concentrations of target nucleic acids could be detected in minutes. Our developed simple and fast nanopore-based detection strategy is not only useful for distinguishing between Baxα and Bax∆2, but also provides a useful tool for detection of other single-base mutations in genetic diagnosis.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Golbarg M Roozbahani
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jialing Xiang
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
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11
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Lee TH, Hirst DJ, Kulkarni K, Del Borgo MP, Aguilar MI. Exploring Molecular-Biomembrane Interactions with Surface Plasmon Resonance and Dual Polarization Interferometry Technology: Expanding the Spotlight onto Biomembrane Structure. Chem Rev 2018; 118:5392-5487. [PMID: 29793341 DOI: 10.1021/acs.chemrev.7b00729] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The molecular analysis of biomolecular-membrane interactions is central to understanding most cellular systems but has emerged as a complex technical challenge given the complexities of membrane structure and composition across all living cells. We present a review of the application of surface plasmon resonance and dual polarization interferometry-based biosensors to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. We first describe the optical principals and instrumentation of surface plasmon resonance, including both linear and extraordinary transmission modes and dual polarization interferometry. We then describe the wide range of model membrane systems that have been developed for deposition on the chips surfaces that include planar, polymer cushioned, tethered bilayers, and liposomes. This is followed by a description of the different chemical immobilization or physisorption techniques. The application of this broad range of engineered membrane surfaces to biomolecular-membrane interactions is then overviewed and how the information obtained using these techniques enhance our molecular understanding of membrane-mediated peptide and protein function. We first discuss experiments where SPR alone has been used to characterize membrane binding and describe how these studies yielded novel insight into the molecular events associated with membrane interactions and how they provided a significant impetus to more recent studies that focus on coincident membrane structure changes during binding of peptides and proteins. We then discuss the emerging limitations of not monitoring the effects on membrane structure and how SPR data can be combined with DPI to provide significant new information on how a membrane responds to the binding of peptides and proteins.
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Affiliation(s)
- Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Daniel J Hirst
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Mark P Del Borgo
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
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12
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Chen X, Roozbahani GM, Ye Z, Zhang Y, Ma R, Xiang J, Guan X. Label-Free Detection of DNA Mutations by Nanopore Analysis. ACS APPLIED MATERIALS & INTERFACES 2018; 10:11519-11528. [PMID: 29537824 PMCID: PMC6760912 DOI: 10.1021/acsami.7b19774] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cancers are caused by mutations to genes that regulate cell normal functions. The capability to rapid and reliable detection of specific target gene variations can facilitate early disease detection and diagnosis and also enables personalized treatment of cancer. Most of the currently available methods for DNA mutation detection are time-consuming and/or require the use of labels or sophisticated instruments. In this work, we reported a label-free enzymatic reaction-based nanopore sensing strategy to detect DNA mutations, including base substitution, deletion, and insertion. The method was rapid and highly sensitive with a detection limit of 4.8 nM in a 10 min electrical recording. Furthermore, the nanopore assay could differentiate among perfect match, one mismatch, and two mismatches. In addition, simulated serum samples were successfully analyzed. Our developed nanopore-based DNA mutation detection strategy should find useful application in genetic diagnosis.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Golbarg M Roozbahani
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Zijing Ye
- Department of Biology, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Rui Ma
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Jialing Xiang
- Department of Biology, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
- Corresponding author: Tel: 312-567-8922. Fax: 312-567-3494.
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13
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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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14
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Wang Y, Tian K, Du X, Shi RC, Gu LQ. Remote Activation of a Nanopore for High-Performance Genetic Detection Using a pH Taxis-Mimicking Mechanism. Anal Chem 2017; 89:13039-13043. [PMID: 29183111 PMCID: PMC6174115 DOI: 10.1021/acs.analchem.7b03979] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aerolysin protein pore has been widely used for sensing peptides and proteins. However, only a few groups explored this nanopore for nucleic acids detection. The challenge is the extremely low capture efficiency for nucleic acids (>10 bases), which severely lowers the sensitivity of an aerolysin-based genetic biosensor. Here we reported a simple and easy-to-operate approach to noncovalently transform aerolysin into a highly nucleic acids-sensitive nanopore. Through a remote pH-modulation mechanism, we simply lower the pH on one side of the pore, then aerolysin is immediately "activated" and enabled to capture target DNA/RNA efficiently from the opposite side of the pore. This mechanism also decelerates DNA translocation, a desired property for sequencing and gene detection, allowing temporal separation of DNAs in different lengths. This method provides insight into the nanopore engineering for biosensing, making aerolysin applicable in genetic and epigenetic detections of long nucleic acids.
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Affiliation(s)
- Yong Wang
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Kai Tian
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Xiao Du
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Rui-Cheng Shi
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
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15
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Sugawara M. Transmembrane Signaling with Lipid-Bilayer Assemblies as a Platform for Channel-Based Biosensing. CHEM REC 2017; 18:433-444. [PMID: 29135061 DOI: 10.1002/tcr.201700046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/02/2017] [Indexed: 11/08/2022]
Abstract
Artificial and natural lipid membranes that elicit transmembrane signaling is are useful as a platform for channel-based biosensing. In this account we summarize our research on the design of transmembrane signaling associated with lipid bilayer membranes containing nanopore-forming compounds. Channel-forming compounds, such as receptor ion-channels, channel-forming peptides and synthetic channels, are embedded in planar and spherical bilayer lipid membranes to develop highly sensitive and selective biosensing methods for a variety of analytes. The membrane-bound receptor approach is useful for introducing receptor sites on both planar and spherical bilayer lipid membranes. Natural receptors in biomembranes are also used for designing of biosensing methods.
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Affiliation(s)
- Masao Sugawara
- Department of chemistry, College of humanities and sciences, Nihon University, Tokyo, Japan
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16
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Lee J, Kim YH, T Arce F, Gillman AL, Jang H, Kagan BL, Nussinov R, Yang J, Lal R. Amyloid β Ion Channels in a Membrane Comprising Brain Total Lipid Extracts. ACS Chem Neurosci 2017; 8:1348-1357. [PMID: 28135799 PMCID: PMC6197823 DOI: 10.1021/acschemneuro.7b00006] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Amyloid β (Aβ) oligomers are the predominant toxic species in the pathology of Alzheimer's disease. The prevailing mechanism for toxicity by Aβ oligomers includes ionic homeostasis destabilization in neuronal cells by forming ion channels. These channel structures have been previously studied in model lipid bilayers. In order to gain further insight into the interaction of Aβ oligomers with natural membrane compositions, we have examined the structures and conductivities of Aβ oligomers in a membrane composed of brain total lipid extract (BTLE). We utilized two complementary techniques: atomic force microscopy (AFM) and black lipid membrane (BLM) electrical recording. Our results indicate that Aβ1-42 forms ion channel structures in BTLE membranes, accompanied by a heterogeneous population of ionic current fluctuations. Notably, the observed current events generated by Aβ1-42 peptides in BTLE membranes possess different characteristics compared to current events generated by the presence of Aβ1-42 in model membranes comprising a 1:1 mixture of DOPS and POPE lipids. Oligomers of the truncated Aβ fragment Aβ17-42 (p3) exhibited similar ion conductivity behavior as Aβ1-42 in BTLE membranes. However, the observed macroscopic ion flux across the BTLE membranes induced by Aβ1-42 pores was larger than for p3 pores. Our analysis of structure and conductance of oligomeric Aβ pores in a natural lipid membrane closely mimics the in vivo cellular environment suggesting that Aβ pores could potentially accelerate the loss of ionic homeostasis and cellular abnormalities. Hence, these pore structures may serve as a target for drug development and therapeutic strategies for AD treatment.
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Affiliation(s)
| | | | - Fernando T Arce
- Division of Translational and Regenerative Medicine, Department of Medicine, Department of Biomedical Engineering, University of Arizona , Tucson, Arizona 85721, United States
| | | | - Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Bruce L Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California , Los Angeles, California 90024, United States
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
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17
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Koyanagi T, Cao KJ, Leriche G, Onofrei D, Holland GP, Mayer M, Sept D, Yang J. Hybrid Lipids Inspired by Extremophiles and Eukaryotes Afford Serum‐Stable Membranes with Low Leakage. Chemistry 2017; 23:6757-6762. [DOI: 10.1002/chem.201701378] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Takaoki Koyanagi
- Department of Chemistry and Biochemistry University of California San Diego La Jolla California 92093-0358 USA
| | - Kevin J. Cao
- Department of Chemistry and Biochemistry University of California San Diego La Jolla California 92093-0358 USA
| | - Geoffray Leriche
- Department of Chemistry and Biochemistry University of California San Diego La Jolla California 92093-0358 USA
| | - David Onofrei
- Department of Chemistry and Biochemistry San Diego State University San Diego California 92182-1030 USA
| | - Gregory P. Holland
- Department of Chemistry and Biochemistry San Diego State University San Diego California 92182-1030 USA
| | - Michael Mayer
- Adolphe Merkle Institute University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
| | - David Sept
- Department of Biomedical Engineering University of Michigan Ann Arbor Michigan 48109-2110 USA
| | - Jerry Yang
- Department of Chemistry and Biochemistry University of California San Diego La Jolla California 92093-0358 USA
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18
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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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19
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Xin P, Tan S, Wang Y, Sun Y, Wang Y, Xu Y, Chen CP. Functionalized hydrazide macrocycle ion channels showing pH-sensitive ion selectivities. Chem Commun (Camb) 2017; 53:625-628. [DOI: 10.1039/c6cc08943g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The protonation and deprotonation of multiple amines and carboxyls in channels change the charge distribution, which leads to pH-sensitive ion selectivity.
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Affiliation(s)
- Pengyang Xin
- School of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang
- China
| | - Si Tan
- School of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang
- China
| | - Yaodong Wang
- School of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang
- China
| | - Yonghui Sun
- School of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang
- China
| | - Yan Wang
- School of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang
- China
| | - Yuqing Xu
- School of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang
- China
| | - Chang-Po Chen
- School of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang
- China
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20
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Affiliation(s)
- Toshihisa Osaki
- Artificial Cell
Membrane
Systems Group, Kanagawa Academy of Science and Technology, 3-2-1
Sakado, Takatsu, 213-0012 Kawasaki, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, 153-8505 Tokyo, Japan
| | - Shoji Takeuchi
- Artificial Cell
Membrane
Systems Group, Kanagawa Academy of Science and Technology, 3-2-1
Sakado, Takatsu, 213-0012 Kawasaki, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, 153-8505 Tokyo, Japan
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21
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Su G, Zhang M, Si W, Li ZT, Hou JL. Directional Potassium Transport through a Unimolecular Peptide Channel. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608428] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ge Su
- Department of Chemistry; Fudan University; 220 Handan Road Shanghai 200433 China
| | - Min Zhang
- Department of Chemistry; Fudan University; 220 Handan Road Shanghai 200433 China
| | - Wen Si
- Department of Chemistry; Fudan University; 220 Handan Road Shanghai 200433 China
| | - Zhan-Ting Li
- Department of Chemistry; Fudan University; 220 Handan Road Shanghai 200433 China
| | - Jun-Li Hou
- Department of Chemistry; Fudan University; 220 Handan Road Shanghai 200433 China
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22
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Su G, Zhang M, Si W, Li Z, Hou J. Directional Potassium Transport through a Unimolecular Peptide Channel. Angew Chem Int Ed Engl 2016; 55:14678-14682. [DOI: 10.1002/anie.201608428] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Ge Su
- Department of Chemistry Fudan University 220 Handan Road Shanghai 200433 China
| | - Min Zhang
- Department of Chemistry Fudan University 220 Handan Road Shanghai 200433 China
| | - Wen Si
- Department of Chemistry Fudan University 220 Handan Road Shanghai 200433 China
| | - Zhan‐Ting Li
- Department of Chemistry Fudan University 220 Handan Road Shanghai 200433 China
| | - Jun‐Li Hou
- Department of Chemistry Fudan University 220 Handan Road Shanghai 200433 China
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23
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Cole CM, Brea RJ, Kim YH, Hardy MD, Yang J, Devaraj NK. Spontaneous Reconstitution of Functional Transmembrane Proteins During Bioorthogonal Phospholipid Membrane Synthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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24
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Cole CM, Brea RJ, Kim YH, Hardy MD, Yang J, Devaraj NK. Spontaneous Reconstitution of Functional Transmembrane Proteins During Bioorthogonal Phospholipid Membrane Synthesis. Angew Chem Int Ed Engl 2015; 54:12738-42. [PMID: 26316292 DOI: 10.1002/anie.201504339] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/02/2015] [Indexed: 11/11/2022]
Abstract
Transmembrane proteins are critical for signaling, transport, and metabolism, yet their reconstitution in synthetic membranes is often challenging. Non-enzymatic and chemoselective methods to generate phospholipid membranes in situ would be powerful tools for the incorporation of membrane proteins. Herein, the spontaneous reconstitution of functional integral membrane proteins during the de novo synthesis of biomimetic phospholipid bilayers is described. The approach takes advantage of bioorthogonal coupling reactions to generate proteoliposomes from micelle-solubilized proteins. This method was successfully used to reconstitute three different transmembrane proteins into synthetic membranes. This is the first example of the use of non-enzymatic chemical synthesis of phospholipids to prepare proteoliposomes.
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Affiliation(s)
- Christian M Cole
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Urey Hall 4120, La Jolla, CA 92093 (USA) http://devarajgroup.ucsd.edu
| | - Roberto J Brea
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Urey Hall 4120, La Jolla, CA 92093 (USA) http://devarajgroup.ucsd.edu
| | - Young Hun Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Pacific Hall 6160, La Jolla, CA 92093 (USA)
| | - Michael D Hardy
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Urey Hall 4120, La Jolla, CA 92093 (USA) http://devarajgroup.ucsd.edu
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Pacific Hall 6160, La Jolla, CA 92093 (USA)
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Urey Hall 4120, La Jolla, CA 92093 (USA) http://devarajgroup.ucsd.edu.
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25
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Majd S, Yusko EC, Yang J, Sept D, Mayer M. A model for the interfacial kinetics of phospholipase D activity on long-chain lipids. Biophys J 2014; 105:146-53. [PMID: 23823233 DOI: 10.1016/j.bpj.2013.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 05/02/2013] [Accepted: 05/06/2013] [Indexed: 11/26/2022] Open
Abstract
The membrane-active enzyme phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond in phospholipids and plays a critical role in cell signaling. This catalytic reaction proceeds on lipid-water interfaces and is an example of heterogeneous catalysis in biology. Recently we showed that planar lipid bilayers, a previously unexplored model membrane for these kinetic studies, can be used for monitoring interfacial catalytic reactions under well-defined experimental conditions with chemical and electrical access to both sides of the lipid membrane. Employing an assay that relies on the conductance of the pore-forming peptide gramicidin A to monitor PLD activity, the work presented here reveals the kinetics of hydrolysis of long-chain phosphatidylcholine lipids in situ. We have developed an extension of a basic kinetic model for interfacial catalysis that includes product activation and substrate depletion. This model describes the kinetic behavior very well and reveals two kinetic parameters, the specificity constant and the interfacial quality constant. This approach results in a simple and general model to account for product accumulation in interfacial enzyme kinetics.
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Affiliation(s)
- Sheereen Majd
- Department of Bioengineering, Pennsylvania State University, University Park, Pennsylvania, USA.
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26
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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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27
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Gurnev PA, Bezrukov SM. Inversion of membrane surface charge by trivalent cations probed with a cation-selective channel. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:15824-30. [PMID: 23088396 PMCID: PMC4307797 DOI: 10.1021/la302676t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We demonstrate that the cation-selective channel formed by gramicidin A can be used as a reliable sensor for studying the multivalent ion accumulation at the surfaces of charged lipid membranes and the "charge inversion" phenomenon. In asymmetrically charged membranes with the individual leaflets formed from pure negative and positive lipids bathed by 0.1 M CsCl solutions the channel exhibits current rectification, which is comparable to that of a typical n/p semiconductor diode. We show that even at these highly asymmetrical conditions the channel conductance can be satisfactorily described by the electrodiffusion equation in the constant field approximation but, due to predictable limitations, only when the applied voltages do not exceed 50 mV. Analysis of the changes in the voltage-dependent channel conductance upon addition of trivalent cations allows us to gauge their interactions with the membrane surface. The inversion of the sign of the effective surface charge takes place at the concentrations, which correlate with the cation size. Specifically, these concentrations are close to 0.05 mM for lanthanum, 0.25 mM for hexaamminecobalt, and 4 mM for spermidine.
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Affiliation(s)
- Philip A Gurnev
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States.
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28
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Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels. Biophys J 2012; 103:1698-705. [PMID: 23083713 DOI: 10.1016/j.bpj.2012.08.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 11/22/2022] Open
Abstract
Water permeability through single-file channels is affected by intrinsic factors such as their size and polarity and by external determinants like their lipid environment in the membrane. Previous computational studies revealed that the obstruction of the channel by lipid headgroups can be long-lived, in the range of nanoseconds, and that pore-length-matching membrane mimetics could speed up water permeability. To test the hypothesis of lipid-channel interactions modulating channel permeability, we designed different gramicidin A derivatives with attached acyl chains. By combining extensive molecular-dynamics simulations and single-channel water permeation measurements, we show that by tuning lipid-channel interactions, these modifications reduce the presence of lipid headgroups in the pore, which leads to a clear and selective increase in their water permeability.
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29
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Itoh H, Matsuoka S, Kreir M, Inoue M. Design, Synthesis and Functional Analysis of Dansylated Polytheonamide Mimic: An Artificial Peptide Ion Channel. J Am Chem Soc 2012; 134:14011-8. [DOI: 10.1021/ja303831a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Hiroaki Itoh
- Graduate School of Pharmaceutical
Sciences, The University of Tokyo, Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigeru Matsuoka
- Graduate School of Pharmaceutical
Sciences, The University of Tokyo, Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mohamed Kreir
- Nanion Technologies GmbH, Gabrielenstrasse 9, D-80636 Munich, Germany
| | - Masayuki Inoue
- Graduate School of Pharmaceutical
Sciences, The University of Tokyo, Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
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30
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Capone R, Jang H, Kotler S, Kagan BL, Nussinov R, Lal R. Probing structural features of Alzheimer's amyloid-β pores in bilayers using site-specific amino acid substitutions. Biochemistry 2012; 51:776-85. [PMID: 22242635 PMCID: PMC3265145 DOI: 10.1021/bi2017427] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/29/2011] [Indexed: 11/28/2022]
Abstract
A current hypothesis for the pathology of Alzheimer's disease (AD) proposes that amyloid-β (Aβ) peptides induce uncontrolled, neurotoxic ion flux across cellular membranes. The mechanism of ion flux is not fully understood because no experiment-based Aβ channel structures at atomic resolution are currently available (only a few polymorphic states have been predicted by computational models). Structural models and experimental evidence lend support to the view that the Aβ channel is an assembly of loosely associated mobile β-sheet subunits. Here, using planar lipid bilayers and molecular dynamics (MD) simulations, we show that amino acid substitutions can be used to infer which residues are essential for channel structure. We created two Aβ(1-42) peptides with point mutations: F19P and F20C. The substitution of Phe19 with Pro inhibited channel conductance. MD simulation suggests a collapsed pore of F19P channels at the lower bilayer leaflet. The kinks at the Pro residues in the pore-lining β-strands induce blockage of the solvated pore by the N-termini of the chains. The cysteine mutant is capable of forming channels, and the conductance behavior of F20C channels is similar to that of the wild type. Overall, the mutational analysis of the channel activity performed in this work tests the proposition that the channels consist of a β-sheet rich organization, with the charged/polar central strand containing the mutation sites lining the pore, and the C-terminal strands facing the hydrophobic lipid tails. A detailed understanding of channel formation and its structure should aid studies of drug design aiming to control unregulated Aβ-dependent ion fluxes.
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Affiliation(s)
- Ricardo Capone
- Department of Bioengineering,
Department of Mechanical and Aerospace Engineering, and Material Science
Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, Maryland 21702, United States
| | - Samuel
A. Kotler
- Department of Bioengineering,
Department of Mechanical and Aerospace Engineering, and Material Science
Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Bruce L. Kagan
- Department of Psychiatry, David
Geffen School of Medicine, Semel Institute for Neuroscience and Human
Behavior, University of California, Los
Angeles, California 90024, United States
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, Maryland 21702, United States
- Department of Human Molecular
Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ratnesh Lal
- Department of Bioengineering,
Department of Mechanical and Aerospace Engineering, and Material Science
Program, University of California, San Diego, La Jolla, California 92093, United States
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31
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Steller L, Kreir M, Salzer R. Natural and artificial ion channels for biosensing platforms. Anal Bioanal Chem 2011; 402:209-30. [PMID: 22080413 DOI: 10.1007/s00216-011-5517-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 10/14/2011] [Accepted: 10/18/2011] [Indexed: 10/15/2022]
Abstract
The single-molecule selectivity and specificity of the binding process together with the expected intrinsic gain factor obtained when utilizing flow through a channel have attracted the attention of analytical chemists for two decades. Sensitive and selective ion channel biosensors for high-throughput screening are having an increasing impact on modern medical care, drug screening, environmental monitoring, food safety, and biowarefare control. Even virus antigens can be detected by ion channel biosensors. The study of ion channels and other transmembrane proteins is expected to lead to the development of new medications and therapies for a wide range of illnesses. From the first attempts to use membrane proteins as the receptive part of a sensor, ion channels have been engineered as chemical sensors. Several other types of peptidic or nonpeptidic channels have been investigated. Various gating mechanisms have been implemented in their pores. Three technical problems had to be solved to achieve practical biosensors based on ion channels: the fabrication of stable lipid bilayer membranes, the incorporation of a receptor into such a structure, and the marriage of the modified membrane to a transducer. The current status of these three areas of research, together with typical applications of ion-channel biosensors, are discussed in this review.
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Affiliation(s)
- L Steller
- Department of Magnetic and Acoustic Resonances, Leibniz Institute for Solid State and Materials Research, Dresden, Germany.
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32
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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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33
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Macrae MX, Schlamadinger D, Kim JE, Mayer M, Yang J. Using charge to control the functional properties of self-assembled nanopores in membranes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:2016-2020. [PMID: 21626687 DOI: 10.1002/smll.201100394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Indexed: 05/30/2023]
Affiliation(s)
- Michael X Macrae
- University of California-San Diego, Department of Chemistry and Biochemistry, La Jolla, CA 92093-0358, USA
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34
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Thapliyal T, Poulos JL, Schmidt JJ. Automated lipid bilayer and ion channel measurement platform. Biosens Bioelectron 2011; 26:2651-4. [DOI: 10.1016/j.bios.2010.01.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 01/16/2010] [Accepted: 01/19/2010] [Indexed: 10/19/2022]
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35
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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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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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39
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Capone R, Mustata M, Jang H, Arce FT, Nussinov R, Lal R. Antimicrobial protegrin-1 forms ion channels: molecular dynamic simulation, atomic force microscopy, and electrical conductance studies. Biophys J 2010; 98:2644-52. [PMID: 20513409 PMCID: PMC2877344 DOI: 10.1016/j.bpj.2010.02.024] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 01/27/2010] [Accepted: 02/03/2010] [Indexed: 10/19/2022] Open
Abstract
Antimicrobial peptides (AMPs) are an emerging class of antibiotics for controlling health effects of antibiotic-resistant microbial strains. Protegrin-1 (PG-1) is a model antibiotic among beta-sheet AMPs. Antibiotic activity of AMPs involves cell membrane damage, yet their membrane interactions, their 3D membrane-associated structures and the mechanism underlying their ability to disrupt cell membrane are poorly understood. Using complementary approaches, including molecular dynamics simulations, atomic force microscopy (AFM) imaging, and planar lipid bilayer reconstitution, we provide computational and experimental evidence that PG-1, a beta-hairpin peptide, forms ion channels. Simulations indicate that PG-1 forms channel-like structures with loosely attached subunits when reconstituted in anionic lipid bilayers. AFM images show the presence of channel-like structures when PG-1 is reconstituted in dioleoylphosphatidylserine/palmitoyloleoyl phosphatidylethanolamine bilayers or added to preformed bilayers. Planar lipid bilayer electrical recordings show multiple single channel conductances that are consistent with the heterogeneous oligomeric channel structures seen in AFM images. PG-1 channel formation seems to be lipid-dependent: PG-1 does not easily show ion channel electrical activity in phosphatidylcholine membranes, but readily shows channel activity in membranes rich in phosphatidylethanolamine or phosphatidylserine. The combined results support a model wherein the beta-hairpin PG-1 peptide acts as an antibiotic by altering cell ionic homeostasis through ion channel formation in cell membranes.
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Affiliation(s)
- Ricardo Capone
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
| | - Mirela Mustata
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology Program, NCI-Frederick, SAIC-Frederick, Inc., Frederick, Maryland
| | - Fernando Teran Arce
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, NCI-Frederick, SAIC-Frederick, Inc., Frederick, Maryland
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ratnesh Lal
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
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40
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Black lipid membranes stabilized through substrate conjugation to a hydrogel. Biointerphases 2010; 3:FA96. [PMID: 20408676 DOI: 10.1116/1.2948314] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Recent research in stabilizing lipid bilayer membranes has been directed toward tethering the membrane to a solid surface or contacting the membrane with a solid support such as a gel. It is also known that the solvent annulus plays an important role in lipid bilayer stability. In this work, the authors set out to stabilize the solvent annulus. Glass substrates with approximately 500 mum apertures were functionalized with 3-methacryloxypropyltrimethoxysilane to allow cross-linking with a surrounding polyethyleneglycol dimethacrylate hydrogel. The hydrogel makes a conformal mold around both the lipid bilayer and the solvent reservoir. Since the hydrogel is covalently conjugated with the glass substrate via vinyl groups, the solvent annulus is prevented from leaving the aperture boundary. Measurements of a membrane created with this approach showed that it remained a stable bilayer with a resistance greater than 1 GOmega for 12 days. Measurements of the ion channel gramicidin A, alpha-hemolysin, and alamethicin incorporated into these membranes showed the same conductance behavior as conventional membranes.
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Jang H, Arce FT, Ramachandran S, Capone R, Azimova R, Kagan BL, Nussinov R, Lal R. Truncated beta-amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome. Proc Natl Acad Sci U S A 2010; 107:6538-43. [PMID: 20308552 PMCID: PMC2851998 DOI: 10.1073/pnas.0914251107] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Full-length amyloid beta peptides (Abeta(1-40/42)) form neuritic amyloid plaques in Alzheimer's disease (AD) patients and are implicated in AD pathology. However, recent transgenic animal models cast doubt on their direct role in AD pathology. Nonamyloidogenic truncated amyloid-beta fragments (Abeta(11-42) and Abeta(17-42)) are also found in amyloid plaques of AD and in the preamyloid lesions of Down syndrome, a model system for early-onset AD study. Very little is known about the structure and activity of these smaller peptides, although they could be the primary AD and Down syndrome pathological agents. Using complementary techniques of molecular dynamics simulations, atomic force microscopy, channel conductance measurements, calcium imaging, neuritic degeneration, and cell death assays, we show that nonamyloidogenic Abeta(9-42) and Abeta(17-42) peptides form ion channels with loosely attached subunits and elicit single-channel conductances. The subunits appear mobile, suggesting insertion of small oligomers, followed by dynamic channel assembly and dissociation. These channels allow calcium uptake in amyloid precursor protein-deficient cells. The channel mediated calcium uptake induces neurite degeneration in human cortical neurons. Channel conductance, calcium uptake, and neurite degeneration are selectively inhibited by zinc, a blocker of amyloid ion channel activity. Thus, truncated Abeta fragments could account for undefined roles played by full length Abetas and provide a unique mechanism of AD and Down syndrome pathologies. The toxicity of nonamyloidogenic peptides via an ion channel mechanism necessitates a reevaluation of the current therapeutic approaches targeting the nonamyloidogenic pathway as avenue for AD treatment.
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Affiliation(s)
- Hyunbum Jang
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., National Cancer Institute, Frederick, MD 21702
| | - Fernando Teran Arce
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Srinivasan Ramachandran
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Ricardo Capone
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Rushana Azimova
- Semel Neuropsychiatric Institute, The David Geffen School of Medicine, University of California at Los Angeles and Greater Los Angeles Veterans Administration Health System, Los Angeles, CA 90024; and
| | - Bruce L. Kagan
- Semel Neuropsychiatric Institute, The David Geffen School of Medicine, University of California at Los Angeles and Greater Los Angeles Veterans Administration Health System, Los Angeles, CA 90024; and
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., National Cancer Institute, Frederick, MD 21702
- Department of Human Molecular Genetics and Biochemistry, The Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ratnesh Lal
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, IL 60637
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Macrae MX, Blake S, Mayer M, Yang J. Nanoscale Ionic Diodes with Tunable and Switchable Rectifying Behavior. J Am Chem Soc 2010; 132:1766-7. [DOI: 10.1021/ja909876h] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael X. Macrae
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093-0358, and Departments of Chemical Engineering and Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110
| | - Steven Blake
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093-0358, and Departments of Chemical Engineering and Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110
| | - Michael Mayer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093-0358, and Departments of Chemical Engineering and Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093-0358, and Departments of Chemical Engineering and Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110
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43
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Mustata M, Capone R, Jang H, Arce FT, Ramachandran S, Lal R, Nussinov R. K3 fragment of amyloidogenic beta(2)-microglobulin forms ion channels: implication for dialysis related amyloidosis. J Am Chem Soc 2010; 131:14938-45. [PMID: 19824733 DOI: 10.1021/ja9049299] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Beta(2)-microglobulin (beta(2)m) amyloid deposits are linked to dialysis-related amyloidosis (DRA) in hemodialysis patients. The mechanism by which beta(2)m causes DRA is not understood. It is also unclear whether only the full-length beta(2)m induces pathophysiology or if proteolytic fragments are sufficient for inducing this effect. Ser20-Lys41 (K3) is a digestion fragment of full-length beta(2)m. Solid state NMR (ssNMR) combined with X-ray diffraction and atomic force microscopy (AFM) revealed the characteristic oligomeric amyloid conformation of the U-turn beta-strand-turn-beta-strand motif stacked in parallel and stabilized by intermolecular interactions also shown by Abeta(9-40)/Abeta(17-42) and the CA150 WW domain. Here we use the K3 U-turn atomic coordinates and molecular dynamic (MD) simulations to model K3 channels in the membrane. Consistent with previous AFM imaging of other amyloids that show channel-like structures in the membrane, in the simulations K3 also forms ion channels with 3-6 loosely attached mobile subunits. We carry out AFM, single channel electrical recording, and fluorescence imaging experiments. AFM images display 3D ion channel topography with shapes, morphologies, and dimensions consistent with the theoretical model. Electrical conductance measurements indicate multiple single channel conductances, suggesting that various K3 oligomer sizes can constitute the channel structure. Fluorescence measurements in kidney cells show channel-mediated cell calcium uptake. These results suggest that the beta(2)m-induced DRA can be mediated by ion channels formed by its K3 fragment. Because the beta-strand-turn-beta-strand motif appears to be a universal amyloid feature, its ability to form ion channels further suggests that the motif may play a generic role in toxicity.
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Affiliation(s)
- Mirela Mustata
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
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44
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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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45
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Abstract
Molecular-scale pore structures, called nanopores, can be assembled by protein ion channels through genetic engineering or be artificially fabricated on solid substrates using fashion nanotechnology. When target molecules interact with the functionalized lumen of a nanopore, they characteristically block the ion pathway. The resulting conductance changes allow for identification of single molecules and quantification of target species in the mixture. In this review, we first overview nanopore-based sensory techniques that have been created for the detection of myriad biomedical targets, from metal ions, drug compounds, and cellular second messengers to proteins and DNA. Then we introduce our recent discoveries in nanopore single molecule detection: (1) using the protein nanopore to study folding/unfolding of the G-quadruplex aptamer; (2) creating a portable and durable biochip that is integrated with a single-protein pore sensor (this chip is compared with recently developed protein pore sensors based on stabilized bilayers on glass nanopore membranes and droplet interface bilayer); and (3) creating a glass nanopore-terminated probe for single-molecule DNA detection, chiral enantiomer discrimination, and identification of the bioterrorist agent ricin with an aptamer-encoded nanopore.
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Affiliation(s)
- Li-Qun Gu
- Biological Engineering and Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park, Columbia, Missouri 65211, USA.
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46
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Perry M, Vissing T, Boesen TP, Hansen JS, Emnéus J, Nielsen CH. Automated sampling and data processing derived from biomimetic membranes. BIOINSPIRATION & BIOMIMETICS 2009; 4:044001. [PMID: 19901449 DOI: 10.1088/1748-3182/4/4/044001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Recent advances in biomimetic membrane systems have resulted in an increase in membrane lifetimes from hours to days and months. Long-lived membrane systems demand the development of both new automated monitoring equipment capable of measuring electrophysiological membrane characteristics and new data processing software to analyze and organize the large amounts of data generated. In this work, we developed an automated instrumental voltage clamp solution based on a custom-designed software controller application (the WaveManager), which enables automated on-line voltage clamp data acquisition applicable to long-time series experiments. We designed another software program for off-line data processing. The automation of the on-line voltage clamp data acquisition and off-line processing was furthermore integrated with a searchable database (DiscoverySheet) for efficient data management. The combined solution provides a cost efficient and fast way to acquire, process and administrate large amounts of voltage clamp data that may be too laborious and time consuming to handle manually.
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Affiliation(s)
- M Perry
- Aquaporin A/S, Diplomvej 377, DK-2800 Kgs. Lyngby, Denmark
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47
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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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48
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Hansen JS, Perry M, Vogel J, Groth JS, Vissing T, Larsen MS, Geschke O, Emneús J, Bohr H, Nielsen CH. Large scale biomimetic membrane arrays. Anal Bioanal Chem 2009; 395:719-27. [DOI: 10.1007/s00216-009-3010-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 07/22/2009] [Accepted: 07/23/2009] [Indexed: 10/20/2022]
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49
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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: 84] [Impact Index Per Article: 5.6] [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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Mustafa M, Henderson DJ, Busath DD. Computational studies of gramicidin permeation: an entry way sulfonate enhances cation occupancy at entry sites. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1404-12. [PMID: 19361485 DOI: 10.1016/j.bbamem.2009.03.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/15/2009] [Accepted: 03/29/2009] [Indexed: 11/15/2022]
Abstract
The impact on the cation-transport free-energy profile of replacing the C-terminal ethanolamine in the gramicidin A channel with a taurine residue is studied using molecular dynamics simulations of gramicidin A (1JNO) embedded in a lipid bilayer (DMPC) with 1 mol/kg NaCl saline solution. The potential of mean force for ion transport is obtained by umbrella sampling. The presence of a negatively charged sulfonate group at the entrance of the gramicidin channel affects the depth and the location of the binding sites, producing a strong attraction for the cations in the bulk. The potential of mean force by the sulfonate acting directly through electrostatics and van der Waals interactions on the test ion is highly modulated by indirect effects (i.e., sulfonate effects on other components of the system that, in turn, affect the ion free-energy profile in the channel). Because the "entry" sites are located symmetrically at both entry and exit of the channel, the deeper free-energy wells should inhibit exit. Given that the channel has increased conductance experimentally, the simulation results suggest that the channel conductance is normally entry limited.
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Affiliation(s)
- Morad Mustafa
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
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