1
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Wei G, Hu R, Lu W, Wang Z, Zhao Q. Bidirectional Peptide Translocation through Ultrasmall Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:20831-20839. [PMID: 39301609 DOI: 10.1021/acs.langmuir.4c03212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
It is important to obtain the configuration of polypeptides and the sequence information on amino acids for understanding various life processes and many biological applications. Nanopores, as a newly developed single-molecule detection technology, exhibit unique advantages in real-time dynamics detection. Here, we designed a special peptide chain with 10 arginine in the head and achieved successful single-molecule detection by ultrasmall solid-state nanopores (2-3 nm). Unique bidirectional translocation signals were observed and explained under the framework of charge distribution of the peptide and interaction with the nanopore wall. Two natural peptide chains, histatin-5 and angiopep-2, were also explored by nanopore experiments to confirm our conjecture. Our designed peptide chain could realize multiple detections of the same peptide chain, offering possibilities for high-resolution peptide detection and fingerprinting by solid-state nanopores in the future.
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Affiliation(s)
- Guanghao Wei
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics School of Physics, Peking University, Beijing 100871, China
| | - Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics School of Physics, Peking University, Beijing 100871, China
| | - Wenlong Lu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics School of Physics, Peking University, Beijing 100871, China
| | - Zhan Wang
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics School of Physics, Peking University, Beijing 100871, China
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics School of Physics, Peking University, Beijing 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, China
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2
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Wang R, Zhang Y, Ma QDY, Wu L. Recent advances of small molecule detection in nanopore sensing. Talanta 2024; 277:126323. [PMID: 38810384 DOI: 10.1016/j.talanta.2024.126323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/04/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
Due to its advantages of label-free and highly sensitive, the resistive pulse sensing with a nanopore has recently become even more potent for the discrimination of analytes in single molecule level. Generally, a transient interruption of ion current originated from the captured molecule passing through a nanopore will provide the rich information on the structure, charge and translocation dynamics of the analytes. Therefore, nanopore sensors have been widely used in the fields of DNA sequencing, protein recognition, and the portable detection of varied macromolecules and particles. However, the conventional nanopore devices are still lack of sufficient selectivity and sensitivity to distinguish more metabolic molecules involving ATP, glucose, amino acids and small molecular drugs because it is hard to receive a large number of identifiable signals with the fabricated pores comparable in size to small molecules for nanopore sensing. For all this, a series of innovative strategies developed in the past decades have been summarized in this review, including host-guest recognition, engineering alteration of protein channel, the introduction of nucleic acid aptamers and various delivery carriers integrating signal amplification sections based on the biological and solid nanopore platforms, to achieve the high resolution for the small molecules sensing in micro-nano environment. These works have greatly enhanced the powerful sensing capabilities and extended the potential application of nanopore sensors.
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Affiliation(s)
- Runyu Wang
- College of Science, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
| | - Yinuo Zhang
- College of Integrated Circuit Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
| | - Qianli D Y Ma
- College of Integrated Circuit Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China.
| | - Lingzhi Wu
- College of Science, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China.
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3
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Chauhan A, Chaudhury S. Multivalent Salt-Induced Self-Assembly of Amphiphilic Polyelectrolytes of Different Charge Fractions: A Coarse-Grained Molecular Dynamics Simulation Study. J Phys Chem B 2024; 128:2037-2044. [PMID: 38359799 DOI: 10.1021/acs.jpcb.3c07886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Amphiphilic polymers with both hydrophobic and hydrophilic blocks are of great interest for their potential applications in drug delivery. Their self-assembly behavior in response to environmental factors like ion charge and multivalent salt concentration has been the subject of recent investigation. Our study utilizes coarse-grained molecular dynamics simulations to investigate the aggregation behavior of amphiphilic copolymers upon introducing tetravalent salt at varying charge fractions. We identify a critical concentration, Cs*, where the aggregation number reaches its maximum for each charge fraction, followed by a subsequent decrease at the excessive salt regime. This study reveals distinct morphological transitions in response to increasing salt concentration and decreasing charged fractions, namely, (i) stable dispersed micelles, (ii) a singular micelle comprising all copolymer chains, and (iii) redispersed micelles, particularly evident at lower charged fractions. Our study highlights the significant influence of tetravalent salt and charge fractions of polyelectrolyte chains on the self-assembly behavior of polyelectrolyte copolymers.
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Affiliation(s)
- Akshay Chauhan
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India
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4
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Wang L, Wang H, Chen X, Zhou S, Wang Y, Guan X. Chemistry solutions to facilitate nanopore detection and analysis. Biosens Bioelectron 2022; 213:114448. [PMID: 35716643 DOI: 10.1016/j.bios.2022.114448] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Characteristic ionic current modulations will be produced in a single molecule manner during the communication of individual molecules with a nanopore. Hence, the information regarding the length, composition, and structure of a molecule can be extracted from deciphering the electrical message. However, until now, achieving a satisfactory resolution for observation and quantification of a target analyte in a complex system remains a nontrivial task. In this review, we summarize the progress and especially the recent advance in utilizing chemistry solutions to facilitate nanopore detection and analysis. The discussed chemistry solutions are classified into several major categories, including covalent/non-covalent chemistry, redox chemistry, displacement chemistry, back titration chemistry, chelation chemistry, hydrolysis-chemistry, and click chemistry. Considering the significant success of using chemical reaction-assisted nanopore sensing strategies to improve sensor sensitivity & selectivity and to study various topics, other non-chemistry based methodologies can undoubtedly be employed by nanopore sensors to explore new applications in the interdisciplinary area of chemistry, biology, materials, and nanotechnology.
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Affiliation(s)
- Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Han Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xiaohan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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5
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Wang X, Stevens KC, Ting JM, Marras AE, Rezvan G, Wei X, Taheri-Qazvini N, Tirrell MV, Liu C. Translocation Behaviors of Synthetic Polyelectrolytes through Alpha-Hemolysin (α-HL) and Mycobacterium smegmatis Porin A (MspA) Nanopores. JOURNAL OF THE ELECTROCHEMICAL SOCIETY 2022; 169:057510. [PMID: 35599744 PMCID: PMC9121822 DOI: 10.1149/1945-7111/ac6c55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
DNAs have been used as probes for nanopore sensing of noncharged biomacromolecules due to its negative phosphate backbone. Inspired by this, we explored the potential of diblock synthetic polyelectrolytes as more flexible and inexpensive nanopore sensing probes by investigating translocation behaviors of PEO-b-PSS and PEO-b-PVBTMA through commonly used alpha-hemolysin (α-HL) and Mycobacterium smegmatis porin A (MspA) nanopores. Translocation recordings in different configurations of pore orientation and testing voltage indicated efficient PEO-b-PSS translocations through α-HL and PEO-b-PVBTMA translocations through MspA. This work provides insight into synthetic polyelectrolyte-based probes to expand probe selection and flexibility for nanopore sensing.
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Affiliation(s)
- Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Kaden C. Stevens
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Jeffrey M. Ting
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander E. Marras
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Gelareh Rezvan
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Xiaojun Wei
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Nader Taheri-Qazvini
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Matthew V. Tirrell
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Chang Liu
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
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6
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Brady MM, Meyer AS. Cataloguing the proteome: Current developments in single-molecule protein sequencing. BIOPHYSICS REVIEWS 2022; 3:011304. [PMID: 38505228 PMCID: PMC10903494 DOI: 10.1063/5.0065509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/13/2022] [Indexed: 03/21/2024]
Abstract
The cellular proteome is complex and dynamic, with proteins playing a critical role in cell-level biological processes that contribute to homeostasis, stimuli response, and disease pathology, among others. As such, protein analysis and characterization are of extreme importance in both research and clinical settings. In the last few decades, most proteomics analysis has relied on mass spectrometry, affinity reagents, or some combination thereof. However, these techniques are limited by their requirements for large sample amounts, low resolution, and insufficient dynamic range, making them largely insufficient for the characterization of proteins in low-abundance or single-cell proteomic analysis. Despite unique technical challenges, several single-molecule protein sequencing (SMPS) technologies have been proposed in recent years to address these issues. In this review, we outline several approaches to SMPS technologies and discuss their advantages, limitations, and potential contributions toward an accurate, sensitive, and high-throughput platform.
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Affiliation(s)
- Morgan M. Brady
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Anne S. Meyer
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
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7
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Motone K, Cardozo N, Nivala J. Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis. iScience 2021; 24:103032. [PMID: 34527891 PMCID: PMC8433247 DOI: 10.1016/j.isci.2021.103032] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Proteins carry out life's essential functions. Comprehensive proteome analysis technologies are thus required for a full understanding of the operating principles of biological systems. While current proteomics techniques suffer from limitations in sensitivity and/or throughput, nanopore technology has the potential to enable de novo protein identification through single-molecule sequencing. However, a significant barrier to achieving this goal is controlling protein/peptide translocation through the nanopore sensor for processive strand analysis. Here, we review recent approaches that use a range of techniques, from oligonucleotide conjugation to molecular motors, aimed at driving protein strands and peptides through protein nanopores. We further discuss site-specific protein conjugation chemistry that could be combined with these translocation approaches as future directions to achieve single-molecule protein detection and sequencing of native proteins.
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Affiliation(s)
- Keisuke Motone
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Nicolas Cardozo
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
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8
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Yan S, Zhang J, Wang Y, Guo W, Zhang S, Liu Y, Cao J, Wang Y, Wang L, Ma F, Zhang P, Chen HY, Huang S. Single Molecule Ratcheting Motion of Peptides in a Mycobacterium smegmatis Porin A (MspA) Nanopore. NANO LETTERS 2021; 21:6703-6710. [PMID: 34319744 DOI: 10.1021/acs.nanolett.1c02371] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Diverse functions of proteins, including synthesis, catalysis, and signaling, result from their highly variable amino acid sequences. The technology allowing for direct analysis of protein sequences, however, is still unsatisfactory. Recent developments of nanopore sequencing of DNA or RNA have motivated attempts to realize nanopore sequencing of peptides in a similar manner. The core challenge has been to achieve a controlled ratcheting motion of the target peptide, which is currently restricted to a limited choice of compatible enzymes. By constructing peptide-oligonucleotide conjugates (POCs) and measurements with nanopore-induced phase-shift sequencing (NIPSS), direct observation of the ratcheting motion of peptides has been successfully achieved. The generated events show a clear sequence dependence on the peptide that is being tested. The method is compatible with peptides with either a conjugated N- or C-terminus. The demonstrated results suggest a proof of concept of nanopore sequencing of peptide and can be useful for peptide fingerprinting.
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Affiliation(s)
- Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jinyue Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yu Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Weiming Guo
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jiao Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Fubo Ma
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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9
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Nivala J, Mulroney L, Luan Q, Abu-Shumays R, Akeson M. Unfolding and Translocation of Proteins Through an Alpha-Hemolysin Nanopore by ClpXP. Methods Mol Biol 2021; 2186:145-155. [PMID: 32918735 DOI: 10.1007/978-1-0716-0806-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Proteins present a significant challenge for nanopore-based sequence analysis. This is partly due to their stable tertiary structures that must be unfolded for linear translocation, and the absence of regular charge density. To address these challenges, here we describe how ClpXP, an ATP-dependent protein unfoldase, can be harnessed to unfold and processively translocate multi-domain protein substrates through an alpha-hemolysin nanopore sensor. This process results in ionic current patterns that are diagnostic of protein sequence and structure at the single-molecule level.
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Affiliation(s)
- Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
| | - Logan Mulroney
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Qing Luan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Robin Abu-Shumays
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Mark Akeson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
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10
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Samanta M, Chaudhury S. Coarse-grained molecular dynamics simulations study of the conformational properties of single polyelectrolyte diblock copolymers. Biophys Chem 2020; 266:106437. [PMID: 32771806 DOI: 10.1016/j.bpc.2020.106437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023]
Abstract
We use coarse-grained molecular dynamics simulations to study a single di block polyelectrolyte chain in solution. We analyze the conformational properties of the chain and localization of counterions as a function of the charge fraction, backbone stiffness, Bjerrum length, and counterion valence. The interplay between the excluded-volume effects and the electrostatic interactions among charged residues leads to variation in block-polyelectrolyte architecture. Our computational findings indicate that varying such system properties lead to nontrivial effects and can be a powerful mechanism to tune the conformational properties of block polyelectrolytes.
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Affiliation(s)
- Mrityunjay Samanta
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India.
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11
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Callahan N, Tullman J, Kelman Z, Marino J. Strategies for Development of a Next-Generation Protein Sequencing Platform. Trends Biochem Sci 2019; 45:76-89. [PMID: 31676211 DOI: 10.1016/j.tibs.2019.09.005] [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: 04/17/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 02/08/2023]
Abstract
Proteomic analysis can be a critical bottleneck in cellular characterization. The current paradigm relies primarily on mass spectrometry of peptides and affinity reagents (i.e., antibodies), both of which require a priori knowledge of the sample. An unbiased protein sequencing method, with a dynamic range that covers the full range of protein concentrations in proteomes, would revolutionize the field of proteomics, allowing a more facile characterization of novel gene products and subcellular complexes. To this end, several new platforms based on single-molecule protein-sequencing approaches have been proposed. This review summarizes four of these approaches, highlighting advantages, limitations, and challenges for each method towards advancing as a core technology for next-generation protein sequencing.
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Affiliation(s)
- Nicholas Callahan
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA.
| | - Jennifer Tullman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA; Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
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12
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Jin J, Baker EG, Wood CW, Bath J, Woolfson DN, Turberfield AJ. Peptide Assembly Directed and Quantified Using Megadalton DNA Nanostructures. ACS NANO 2019; 13:9927-9935. [PMID: 31381314 PMCID: PMC6764022 DOI: 10.1021/acsnano.9b04251] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/05/2019] [Indexed: 05/02/2023]
Abstract
In nature, co-assembly of polypeptides, nucleic acids, and polysaccharides is used to create functional supramolecular structures. Here, we show that DNA nanostructures can be used to template interactions between peptides and to enable the quantification of multivalent interactions that would otherwise not be observable. Our functional building blocks are peptide-oligonucleotide conjugates comprising de novo designed dimeric coiled-coil peptides covalently linked to oligonucleotide tags. These conjugates are incorporated in megadalton DNA origami nanostructures and direct nanostructure association through peptide-peptide interactions. Free and bound nanostructures can be counted directly from electron micrographs, allowing estimation of the dissociation constants of the peptides linking them. Results for a single peptide-peptide interaction are consistent with the measured solution-phase free energy; DNA nanostructures displaying multiple peptides allow the effects of polyvalency to be probed. This use of DNA nanostructures as identifiers allows the binding strengths of homo- and heterodimeric peptide combinations to be measured in a single experiment and gives access to dissociation constants that are too low to be quantified by conventional techniques. The work also demonstrates that hybrid biomolecules can be programmed to achieve spatial organization of complex synthetic biomolecular assemblies.
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Affiliation(s)
- Juan Jin
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Emily G. Baker
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Christopher W. Wood
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Jonathan Bath
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
- Bristol
BioDesign Institute, BrisSynBio, University
of Bristol Research Centre in Synthetic Biology, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - Andrew J. Turberfield
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
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13
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Restrepo-Pérez L, Joo C, Dekker C. Paving the way to single-molecule protein sequencing. NATURE NANOTECHNOLOGY 2018; 13:786-796. [PMID: 30190617 DOI: 10.1038/s41565-018-0236-6] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/16/2018] [Indexed: 05/22/2023]
Abstract
Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example, requiring a sizable amount of sample. Single-molecule techniques would revolutionize proteomics research, providing ultimate sensitivity for the detection of low-abundance proteins and the realization of single-cell proteomics. In recent years, novel single-molecule protein sequencing schemes that use fluorescence, tunnelling currents and nanopores have been proposed. Here, we present a review of these approaches, together with the first experimental efforts towards their realization. We discuss their advantages and drawbacks, and present our perspective on the development of single-molecule protein sequencing techniques.
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Affiliation(s)
- Laura Restrepo-Pérez
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Chirlmin Joo
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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14
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Chinappi M, Cecconi F. Protein sequencing via nanopore based devices: a nanofluidics perspective. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:204002. [PMID: 29595524 DOI: 10.1088/1361-648x/aababe] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Proteins perform a huge number of central functions in living organisms, thus all the new techniques allowing their precise, fast and accurate characterization at single-molecule level certainly represent a burst in proteomics with important biomedical impact. In this review, we describe the recent progresses in the developing of nanopore based devices for protein sequencing. We start with a critical analysis of the main technical requirements for nanopore protein sequencing, summarizing some ideas and methodologies that have recently appeared in the literature. In the last sections, we focus on the physical modelling of the transport phenomena occurring in nanopore based devices. The multiscale nature of the problem is discussed and, in this respect, some of the main possible computational approaches are illustrated.
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Affiliation(s)
- Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, via del Politecnico 1, 00133 Roma, Italy
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15
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Gooding M, Malhotra M, Evans JC, Darcy R, O'Driscoll CM. Oligonucleotide conjugates - Candidates for gene silencing therapeutics. Eur J Pharm Biopharm 2016; 107:321-40. [PMID: 27521696 DOI: 10.1016/j.ejpb.2016.07.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/24/2016] [Accepted: 07/25/2016] [Indexed: 11/18/2022]
Abstract
The potential therapeutic and diagnostic applications of oligonucleotides (ONs) have attracted great attention in recent years. The capability of ONs to selectively inhibit target genes through antisense and RNA interference mechanisms, without causing un-intended sideeffects has led them to be investigated for various biomedical applications, especially for the treatment of viral diseases and cancer. In recent years, many researchers have focused on enhancing the stability and target specificity of ONs by encapsulating/complexing them with polymers or lipid chains to formulate nanoparticles/nanocomplexes/micelles. Also, chemical modification of nucleic acids has emerged as an alternative to impart stability to ONs against nucleases and other degrading enzymes and proteins found in blood. In addition to chemically modifying the nucleic acids directly, another strategy that has emerged, involves conjugating polymers/peptide/aptamers/antibodies/proteins, preferably to the sense strand (3'end) of siRNAs. Conjugation to the siRNA not only enhances the stability and targeting specificity of the siRNA, but also allows for the development of self-administering siRNA formulations, with a much smaller size than what is usually observed for nanoparticle (∼200nm). This review concentrates mainly on approaches and studies involving ON-conjugates for biomedical applications.
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Affiliation(s)
- Matt Gooding
- Pharmacodelivery Group, School of Pharmacy, University College Cork, Cork, Ireland
| | - Meenakshi Malhotra
- Pharmacodelivery Group, School of Pharmacy, University College Cork, Cork, Ireland
| | - James C Evans
- Pharmacodelivery Group, School of Pharmacy, University College Cork, Cork, Ireland
| | - Raphael Darcy
- Pharmacodelivery Group, School of Pharmacy, University College Cork, Cork, Ireland
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