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Sampath G. Whole protein sequencing and quantification without proteolysis, terminal residue cleavage, or purification: A computational model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584825. [PMID: 38558980 PMCID: PMC10980043 DOI: 10.1101/2024.03.13.584825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Sequencing and quantification of whole proteins in a sample without separation, terminal residue cleavage, or proteolysis are modeled computationally. Similar to recent work on DNA sequencing (PNAS 113, 5233-5238, 2016), a high-volume conjugate is attached to every instance of amino acid (AA) type AAi, 1 ≤ i ≤ 20, in an unfolded whole protein, which is then translocated through a nanopore. From the volume excluded by 2L residues in a pore of length L nm (a proxy for the blockade current), a partial sequence containing AAi is obtained. Translocation is assumed to be unidirectional, with residues exiting the pore at a roughly constant rate of ~1/μs (Nature Biotechnology 41, 1130-1139, 2023). The blockade signal is sampled at intervals of 1 μs and digitized with a step precision of 70 nm3; the positions of the AAis are obtained from the positions of well-defined quantum jumps in the signal. This procedure is applied to all 20 standard AA types, the resulting 20 partial sequences are merged to obtain the whole protein sequence. The complexity of subsequence computation is O(N) for a protein with N residues. The method is illustrated with a sample protein from the human proteome (Uniprot id UP000005640_9606). A mixture of M' protein molecules (including multiple copies) can be sequenced by constructing an M' × 20 array of partial sequences from which proteins occurring multiple times are first isolated and their sequences obtained separately. The remaining M singly-occurring molecules are detected from M disjoint paths through the 20 columns of the reduced M × 20 array. Detection complexity is O(M20), which is nominally in polynomial time but practical only for small M; to use this method a sample may be subdivided into subsamples down to this level. Quantification of proteins can be done by sorting their computed sequences on the sequence strings and counting the number of duplicates. The possibility of translating this procedure into practice and related implementation issues are discussed.
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Peng Z, Iwabuchi S, Izumi K, Takiguchi S, Yamaji M, Fujita S, Suzuki H, Kambara F, Fukasawa G, Cooney A, Di Michele L, Elani Y, Matsuura T, Kawano R. Lipid vesicle-based molecular robots. LAB ON A CHIP 2024; 24:996-1029. [PMID: 38239102 PMCID: PMC10898420 DOI: 10.1039/d3lc00860f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.
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Affiliation(s)
- Zugui Peng
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoji Iwabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Misa Yamaji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoko Fujita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Harune Suzuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Fumika Kambara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Genki Fukasawa
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Aileen Cooney
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
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Motone K, Kontogiorgos-Heintz D, Wee J, Kurihara K, Yang S, Roote G, Fang Y, Cardozo N, Nivala J. Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563182. [PMID: 37905023 PMCID: PMC10614977 DOI: 10.1101/2023.10.19.563182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The ability to sequence single protein molecules in their native, full-length form would enable a more comprehensive understanding of proteomic diversity. Current technologies, however, are limited in achieving this goal. Here, we establish a method for long-range, single-molecule reading of intact protein strands on a commercial nanopore sensor array. By using the ClpX unfoldase to ratchet proteins through a CsgG nanopore, we achieve single-amino acid level sensitivity, enabling sequencing of combinations of amino acid substitutions across long protein strands. For greater sequencing accuracy, we demonstrate the ability to reread individual protein molecules, spanning hundreds of amino acids in length, multiple times, and explore the potential for high accuracy protein barcode sequencing. Further, we develop a biophysical model that can simulate raw nanopore signals a priori, based on amino acid volume and charge, enhancing the interpretation of raw signal data. Finally, we apply these methods to examine intact, folded protein domains for complete end-to-end analysis. These results provide proof-of-concept for a platform that has the potential to identify and characterize full-length proteoforms at single-molecule resolution.
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Affiliation(s)
- Keisuke Motone
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- These authors contributed equally: Keisuke Motone, Daphne Kontogiorgos-Heintz
| | - Daphne Kontogiorgos-Heintz
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- These authors contributed equally: Keisuke Motone, Daphne Kontogiorgos-Heintz
| | - Jasmine Wee
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Kyoko Kurihara
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Sangbeom Yang
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Gwendolin Roote
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Yishu Fang
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Nicolas Cardozo
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, USA
| | - Jeff Nivala
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, USA
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Wei X, Penkauskas T, Reiner JE, Kennard C, Uline MJ, Wang Q, Li S, Aksimentiev A, Robertson JW, Liu C. Engineering Biological Nanopore Approaches toward Protein Sequencing. ACS NANO 2023; 17:16369-16395. [PMID: 37490313 PMCID: PMC10676712 DOI: 10.1021/acsnano.3c05628] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.
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Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Tadas Penkauskas
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
- School of Engineering, Brown University, Providence, RI 02912, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Celeste Kennard
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
| | - Mark J. Uline
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Sheng Li
- School of Data Science, University of Virginia, Charlottesville, VA 22903, United States
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joseph W.F. Robertson
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
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Liang L, Qin F, Wang S, Wu J, Li R, Wang Z, Ren M, Liu D, Wang D, Astruc D. Overview of the materials design and sensing strategies of nanopore devices. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Fujita S, Kawamura I, Kawano R. Cell-Free Expression of De Novo Designed Peptides That Form β-Barrel Nanopores. ACS NANO 2023; 17:3358-3367. [PMID: 36731872 PMCID: PMC9979648 DOI: 10.1021/acsnano.2c07970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/03/2023] [Indexed: 06/18/2023]
Abstract
Nanopore sensing has attracted much attention as a rapid, simple, and label-free single-molecule detection technology. To apply nanopore sensing to extensive targets including polypeptides, nanopores are required to have a size and structure suitable for the target. We recently designed a de novo β-barrel peptide nanopore (SVG28) that constructs a stable and monodispersely sized nanopore. To develop the sizes and functionality of peptide nanopores, systematic exploration is required. Here we attempt to use a cell-free synthesis system that can readily express peptides using transcription and translation. Hydrophilic variants of SVG28 were designed and expressed by the PURE system. The peptides form a monodispersely sized nanopore, with a diameter 1.1 or 1.5 nm smaller than that of SVG28. Such cell-free synthesizable peptide nanopores have the potential to enable the systematic custom design of nanopores and comprehensive sequence screening of nanopore-forming peptides.
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Affiliation(s)
- Shoko Fujita
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, Tokyo184-8588, Japan
| | - Izuru Kawamura
- Graduate
School of Engineering Science, Yokohama
National University, Yokohama240-8501, Japan
| | - Ryuji Kawano
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, Tokyo184-8588, Japan
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Guo H, Zhao Y, Chang JS, Lee DJ. Inhibitor formation and detoxification during lignocellulose biorefinery: A review. BIORESOURCE TECHNOLOGY 2022; 361:127666. [PMID: 35878776 DOI: 10.1016/j.biortech.2022.127666] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
For lignocellulose biorefinery, pretreatment is needed to maximize the cellulose accessibility, frequently generating excess inhibitory substances to decline the efficiency of the subsequent fermentation processes. This mini-review updates the current research efforts to detoxify the adverse impacts of generated inhibitors on the performance of biomass biorefinery. The lignocellulose pretreatment processes are first reviewed. The generation of inhibitors, furans, furfural, phenols, formic acid, and acetic acid, from the lignocellulose, with their action mechanisms, are listed. Then the detoxification processes are reviewed, from which the biological detoxification processes are noted as promising and worth further study. The challenges and prospects for applying biological detoxification in lignocellulose biorefinery are outlined. Integrated studies considering the entire biorefinery should be performed on a case-by-case basis.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Ying Zhao
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jo-Shu Chang
- Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-li 32003, Taiwan.
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Probing the Hepatitis B Virus E-Antigen with a Nanopore Sensor Based on Collisional Events Analysis. BIOSENSORS 2022; 12:bios12080596. [PMID: 36004992 PMCID: PMC9405897 DOI: 10.3390/bios12080596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/24/2022]
Abstract
Real-time monitoring, simple operation, and cheaper methods for detecting immunological proteins hold the potential for a solid influence on proteomics and human biology, as they can promote the onset of timely diagnoses and adequate treatment protocols. In this work we present an exploratory study suggesting the applicability of resistive-pulse sensing technology in conjunction with the α-hemolysin (α-HL) protein nanopore, for the detection of the chronic hepatitis B virus (HBV) e-antigen (HBeAg). In this approach, the recognition between HBeAg and a purified monoclonal hepatitis B e antibody (Ab(HBeAg)) was detected via transient ionic current spikes generated by partial occlusions of the α-HL nanopore by protein aggregates electrophoretically driven toward the nanopore’s vestibule entrance. Despite the steric hindrance precluding antigen, antibody, or antigen–antibody complex capture inside the nanopore, their stochastic bumping with the nanopore generated clear transient blockade events. The subsequent analysis suggested the detection of protein subpopulations in solution, rendering the approach a potentially valuable label-free platform for the sensitive, submicromolar-scale screening of HBeAg targets.
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Mereuta L, Asandei A, Dragomir I, Park J, Park Y, Luchian T. A Nanopore Sensor for Multiplexed Detection of Short Polynucleotides Based on Length-Variable, Poly-Arginine-Conjugated Peptide Nucleic Acids. Anal Chem 2022; 94:8774-8782. [PMID: 35666169 DOI: 10.1021/acs.analchem.2c01587] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Real-time and easy-to-use detection of nucleic acids is crucial for many applications, including medical diagnostics, genetic screening, forensic science, or monitoring the onset and progression of various diseases. Herein, an exploratory single-molecule approach for multiplexed discrimination among similar-sized single-stranded DNAs (ssDNA) is presented. The underlying strategy combined (i) a method based on length-variable, short arginine (poly-Arg) tags appended to peptide nucleic acid (PNA) probes, designed to hybridize with selected regions from complementary ssDNA targets (cDNA) in solution and (ii) formation and subsequent detection with the α-hemolysin nanopore of (poly-Arg)-PNA-cDNA duplexes containing two overhangs associated with the poly-Arg tail and the non-hybridized segment from ssDNA. We discovered that the length-variable poly-Arg tail marked distinctly the molecular processes associated with the nanopore-mediated duplexes capture, trapping and unzipping. This enabled the detection of ssDNA targets via the signatures of (poly-Arg)-PNA-cDNA blockade events, rendered most efficient from the β-barrel entrance of the nanopore, and scaled proportional in efficacy with a larger poly-Arg moiety. We illustrate the approach by sensing synthetic ssDNAs designed to emulate fragments from two regions of SARS-CoV-2 nucleocapsid phosphoprotein N-gene.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Isabela Dragomir
- Interdisciplinary Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, 38065 Kongju, Republic of Korea
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, 61452 Gwangju, Republic of Korea
| | - Tudor Luchian
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
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