1
|
Algharagholy LA, García-Suárez VM, Bardan KH. Robust nanotube-based nanosensor designed for the detection of explosive molecules. NANOSCALE ADVANCES 2024; 6:3553-3565. [PMID: 38989522 PMCID: PMC11232540 DOI: 10.1039/d4na00166d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/29/2024] [Indexed: 07/12/2024]
Abstract
The adequate determination and detection of explosive molecules is key to introducing improvements in areas related to safety, whose progress depends on an adequate and rapid determination of dangerous substances. To detect explosives down to the molecular level and accurately discriminate between different but somehow similar substances, it is necessary to design sensors that can differentiate them uniquely and efficiently. In this study, we present a new generation nanoscale sensor based on carbon nanotubes with an adapted nanopore shape that is capable of effectively discriminating between five types of explosive compounds (TATP, RDX, PENT, HMX and DNT). We show that the interaction of each compound with the walls of the nanotubes induces changes in transmission and current that allows clear differentiation of each type of molecule. Interestingly, the transport properties do not depend on the orientation of the molecules within the nanopore in most cases, making it a robust device with high reproducibility and stability. The results also show that these systems can lead to relatively high thermoelectric performances and, furthermore, the Seebeck coefficient can be used to discriminate between them.
Collapse
Affiliation(s)
- Laith A Algharagholy
- Department of Physics, College of Science, University of Sumer Al Rifaee Zip: 64005 Thi-Qar Iraq
| | | | - Kareem Hasan Bardan
- Department of Physics, College of Science, University of Sumer Al Rifaee Zip: 64005 Thi-Qar Iraq
| |
Collapse
|
2
|
Gonzalez Solveyra E, Perez Sirkin YA, Tagliazucchi M, Szleifer I. Orientational Pathways during Protein Translocation through Polymer-Modified Nanopores. ACS NANO 2024; 18:10427-10438. [PMID: 38556978 DOI: 10.1021/acsnano.3c11318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein translocation through nanopores holds significant promise for applications in biotechnology, biomolecular analysis, and medicine. However, the interpretation of signals generated by the translocation of the protein remains challenging. In this way, it is crucial to gain a comprehensive understanding on how macromolecules translocate through a nanopore and to identify what are the critical parameters that govern the process. In this study, we investigate the interplay between protein charge regulation, orientation, and nanopore surface modifications using a theoretical framework that allows us to explicitly take into account the acid-base reactions of the titrable amino acids in the proteins and in the polyelectrolytes grafted to the nanopore surface. Our goal is to thoroughly characterize the translocation process of different proteins (GFP, β-lactoglobulin, lysozyme, and RNase) through nanopores modified with weak polyacids. Our calculations show that the charge regulation mechanism exerts a profound effect on the translocation process. The pH-dependent interactions between proteins and charged polymers within the nanopore lead to diverse free energy landscapes with barriers, wells, and flat regions dictating translocation efficiency. Comparison of different proteins allows us to identify the significance of protein isoelectric point, size, and morphology in the translocation behavior. Taking advantage of these insights, we propose pH-responsive nanopores that can load proteins at one pH and release them at another, offering opportunities for controlled protein delivery, separation, and sensing applications.
Collapse
Affiliation(s)
- Estefania Gonzalez Solveyra
- Instituto de Nanosistemas, Universidad Nacional de San Martín-CONICET, San Martín, Buenos Aires B1650, Argentina
| | - Yamila A Perez Sirkin
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica Analítica y Química Física y CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE). Pabellón 2, Ciudad Universitaria, C1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - Mario Tagliazucchi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica Analítica y Química Física y CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE). Pabellón 2, Ciudad Universitaria, C1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
3
|
Özkan M, Yılmaz H, Ergenekon P, Erdoğan EM, Erbakan M. Microbial membrane transport proteins and their biotechnological applications. World J Microbiol Biotechnol 2024; 40:71. [PMID: 38225445 PMCID: PMC10789880 DOI: 10.1007/s11274-024-03891-6] [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: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024]
Abstract
Because of the hydrophobic nature of the membrane lipid bilayer, the majority of the hydrophilic solutes require special transportation mechanisms for passing through the cell membrane. Integral membrane transport proteins (MTPs), which belong to the Major Intrinsic Protein Family, facilitate the transport of these solutes across cell membranes. MTPs including aquaporins and carrier proteins are transmembrane proteins spanning across the cell membrane. The easy handling of microorganisms enabled the discovery of a remarkable number of transport proteins specific to different substances. It has been realized that these transporters have very important roles in the survival of microorganisms, their pathogenesis, and antimicrobial resistance. Astonishing features related to the solute specificity of these proteins have led to the acceleration of the research on the discovery of their properties and the development of innovative products in which these unique properties are used or imitated. Studies on microbial MTPs range from the discovery and characterization of a novel transporter protein to the mining and screening of them in a large transporter library for particular functions, from simulations and modeling of specific transporters to the preparation of biomimetic synthetic materials for different purposes such as biosensors or filtration membranes. This review presents recent discoveries on microbial membrane transport proteins and focuses especially on formate nitrite transport proteins and aquaporins, and advances in their biotechnological applications.
Collapse
Affiliation(s)
- Melek Özkan
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye.
| | - Hilal Yılmaz
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Pınar Ergenekon
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Esra Meşe Erdoğan
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Mustafa Erbakan
- Biosystem Engineering Department, Bozok University, Yozgat , 66900, Türkiye
| |
Collapse
|
4
|
Wang Y, Zhou J, Zheng T, Li L, Zhu M. Adsorption Kinetics of Poly(benzyl acrylate) Chains onto Alumina Interface during the Flow-Driven Translocation through Cylindrical Nanochannels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:13303-13315. [PMID: 37669096 DOI: 10.1021/acs.langmuir.3c01913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
In this work, the adsorption kinetics of the PBAN/AAO system under flushing condition has been investigated, where PBAN and AAO represent poly(benzyl acrylate) and anodic alumina oxide (AAO, average pore radius R0 ≈ 10 nm) nanochannel, respectively. Our specially designed double-pump flushing system is proved to eliminate the overshoot phenomenon and in situ monitor transmembrane pressure (ΔP) as a function of flushing time (t) and flow rate (Q), which gives the effective pore radius (R), cross-sectional coverage factor (χ = [1 - (R/R0)2]), and characteristic ratio (rc) of the increments of χ during each adsorption/desorption cycle at a given bulk solution concentration (Cbulk). Our findings include: (1) by gradient increasing Cbulk from 10 to 200 mg/L at Q = 10 mL/h, the shortest PBA40 displays a saturation adsorption behavior when Cbulk ≥ 80 mg/L and t ≥ 2000 s, which agrees well with the prediction of blob model, whereas for the longer PBAN chains, the chain length (N) and concentration-dependent adsorption tendency get stronger as N increases from 40 to 620 at t ≥ 2000 s, in particular, R/R0 ∼ N-0.20 is observed at Cbulk = 140 mg/L; (2) by focusing on the platform χ in the saturation adsorption regime (χsat), the longer PBAN displays a stronger adsorption trend with partially reversible feature at Q = 5.0 mL/h, namely, as N increases from 40 to 620, χsat increases from 0.15 to 0.83 at Cbulk = 100 mg/L, where rc changes from 0.25 ± 0.10 to 0.80 ± 0.10 as the adsorption/desorption flushing cycle increases from 1 to 8 at Cbulk = 100 mg/L; (3) by further assuming a solvent nonpenetrating and nondraining adsorption layer, χsat determined in the case of curved surface can be comparable to the physical meaning of adsorption thickness (Δad) in the case of flat-surface adsorption, and the fitting result indicates χsat ∼ Δad ∼ N0.58, falling between Δad ∼ N1/2 and Δad ∼ N1.0 predicted by the mean-field and scaling theories for real multichain adsorption, respectively. Overall, the present work not only clarifies some controversies but also provides unambiguous evidence supporting the existence of tightly adsorbed internal and loosely adsorbed external layers.
Collapse
Affiliation(s)
- Yiren Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jianing Zhou
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Tao Zheng
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Lianwei Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Mo Zhu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| |
Collapse
|
5
|
Hua L, Wang D, Wang K, Wang Y, Gu J, Zhang Q, You Q, Wang L. Design of Tracers in Fluorescence Polarization Assay for Extensive Application in Small Molecule Drug Discovery. J Med Chem 2023; 66:10934-10958. [PMID: 37561645 DOI: 10.1021/acs.jmedchem.3c00881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Development of fluorescence polarization (FP) assays, especially in a competitive manner, is a potent and mature tool for measuring the binding affinities of small molecules. This approach is suitable for high-throughput screening (HTS) for initial ligands and is also applicable for further study of the structure-activity relationships (SARs) of candidate compounds for drug discovery. Buffer and tracer, especially rational design of the tracer, play a vital role in an FP assay system. In this perspective, we provided different kinds of approaches for tracer design based on successful cases in recent years. We classified these tracers by different types of ligands in tracers, including peptide, nucleic acid, natural product, and small molecule. To make this technology accessible for more targets, we briefly described the basic theory and workflow, followed by highlighting the design and application of typical FP tracers from a perspective of medicinal chemistry.
Collapse
Affiliation(s)
- Liwen Hua
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Danni Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Keran Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jinying Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|