1
|
Bidooki SH, Navarro MA, Fernandes SCM, Osada J. Thioredoxin Domain Containing 5 (TXNDC5): Friend or Foe? Curr Issues Mol Biol 2024; 46:3134-3163. [PMID: 38666927 PMCID: PMC11049379 DOI: 10.3390/cimb46040197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/25/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024] Open
Abstract
This review focuses on the thioredoxin domain containing 5 (TXNDC5), also known as endoplasmic reticulum protein 46 (ERp46), a member of the protein disulfide isomerase (PDI) family with a dual role in multiple diseases. TXNDC5 is highly expressed in endothelial cells, fibroblasts, pancreatic β-cells, liver cells, and hypoxic tissues, such as cancer endothelial cells and atherosclerotic plaques. TXNDC5 plays a crucial role in regulating cell proliferation, apoptosis, migration, and antioxidative stress. Its potential significance in cancer warrants further investigation, given the altered and highly adaptable metabolism of tumor cells. It has been reported that both high and low levels of TXNDC5 expression are associated with multiple diseases, such as arthritis, cancer, diabetes, brain diseases, and infections, as well as worse prognoses. TXNDC5 has been attributed to both oncogenic and tumor-suppressive features. It has been concluded that in cancer, TXNDC5 acts as a foe and responds to metabolic and cellular stress signals to promote the survival of tumor cells against apoptosis. Conversely, in normal cells, TXNDC5 acts as a friend to safeguard cells against oxidative and endoplasmic reticulum stress. Therefore, TXNDC5 could serve as a viable biomarker or even a potential pharmacological target.
Collapse
Affiliation(s)
- Seyed Hesamoddin Bidooki
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, E-50013 Zaragoza, Spain; (S.H.B.); (M.A.N.)
- Centre National de la Recherche Scientifique (CNRS), Institute of Analytical Sciences and Physico-Chemistry for Environment and Materials (IPREM), Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 000 Pau, France;
- MANTA—Marine Materials Research Group, Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 600 Anglet, France
| | - María A. Navarro
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, E-50013 Zaragoza, Spain; (S.H.B.); (M.A.N.)
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, E-50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, E-28029 Madrid, Spain
| | - Susana C. M. Fernandes
- Centre National de la Recherche Scientifique (CNRS), Institute of Analytical Sciences and Physico-Chemistry for Environment and Materials (IPREM), Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 000 Pau, France;
- MANTA—Marine Materials Research Group, Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 600 Anglet, France
| | - Jesus Osada
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, E-50013 Zaragoza, Spain; (S.H.B.); (M.A.N.)
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, E-50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, E-28029 Madrid, Spain
| |
Collapse
|
2
|
Winkler R, Ciria M, Ahmad M, Plank H, Marcuello C. A Review of the Current State of Magnetic Force Microscopy to Unravel the Magnetic Properties of Nanomaterials Applied in Biological Systems and Future Directions for Quantum Technologies. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2585. [PMID: 37764614 PMCID: PMC10536909 DOI: 10.3390/nano13182585] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
Magnetism plays a pivotal role in many biological systems. However, the intensity of the magnetic forces exerted between magnetic bodies is usually low, which demands the development of ultra-sensitivity tools for proper sensing. In this framework, magnetic force microscopy (MFM) offers excellent lateral resolution and the possibility of conducting single-molecule studies like other single-probe microscopy (SPM) techniques. This comprehensive review attempts to describe the paramount importance of magnetic forces for biological applications by highlighting MFM's main advantages but also intrinsic limitations. While the working principles are described in depth, the article also focuses on novel micro- and nanofabrication procedures for MFM tips, which enhance the magnetic response signal of tested biomaterials compared to commercial nanoprobes. This work also depicts some relevant examples where MFM can quantitatively assess the magnetic performance of nanomaterials involved in biological systems, including magnetotactic bacteria, cryptochrome flavoproteins, and magnetic nanoparticles that can interact with animal tissues. Additionally, the most promising perspectives in this field are highlighted to make the reader aware of upcoming challenges when aiming toward quantum technologies.
Collapse
Affiliation(s)
- Robert Winkler
- Christian Doppler Laboratory—DEFINE, Graz University of Technology, 8010 Graz, Austria; (R.W.); (H.P.)
| | - Miguel Ciria
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain;
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Margaret Ahmad
- Photobiology Research Group, IBPS, UMR8256 CNRS, Sorbonne Université, 75005 Paris, France;
| | - Harald Plank
- Christian Doppler Laboratory—DEFINE, Graz University of Technology, 8010 Graz, Austria; (R.W.); (H.P.)
- Graz Centre for Electron Microscopy, 8010 Graz, Austria
- Institute of Electron Microscopy, Graz University of Technology, 8010 Graz, Austria
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain;
- Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
| |
Collapse
|
3
|
Pele KG, Amaveda H, Mora M, Marcuello C, Lostao A, Alamán-Díez P, Pérez-Huertas S, Ángeles Pérez M, García-Aznar JM, García-Gareta E. Hydrocolloids of Egg White and Gelatin as a Platform for Hydrogel-Based Tissue Engineering. Gels 2023; 9:505. [PMID: 37367175 DOI: 10.3390/gels9060505] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Innovative materials are needed to produce scaffolds for various tissue engineering and regenerative medicine (TERM) applications, including tissue models. Materials derived from natural sources that offer low production costs, easy availability, and high bioactivity are highly preferred. Chicken egg white (EW) is an overlooked protein-based material. Whilst its combination with the biopolymer gelatin has been investigated in the food technology industry, mixed hydrocolloids of EW and gelatin have not been reported in TERM. This paper investigates these hydrocolloids as a suitable platform for hydrogel-based tissue engineering, including 2D coating films, miniaturized 3D hydrogels in microfluidic devices, and 3D hydrogel scaffolds. Rheological assessment of the hydrocolloid solutions suggested that temperature and EW concentration can be used to fine-tune the viscosity of the ensuing gels. Fabricated thin 2D hydrocolloid films presented globular nano-topography and in vitro cell work showed that the mixed hydrocolloids had increased cell growth compared with EW films. Results showed that hydrocolloids of EW and gelatin can be used for creating a 3D hydrogel environment for cell studies inside microfluidic devices. Finally, 3D hydrogel scaffolds were fabricated by sequential temperature-dependent gelation followed by chemical cross-linking of the polymeric network of the hydrogel for added mechanical strength and stability. These 3D hydrogel scaffolds displayed pores, lamellae, globular nano-topography, tunable mechanical properties, high affinity for water, and cell proliferation and penetration properties. In conclusion, the large range of properties and characteristics of these materials provide a strong potential for a large variety of TERM applications, including cancer models, organoid growth, compatibility with bioprinting, or implantable devices.
Collapse
Affiliation(s)
- Karinna Georgiana Pele
- Multiscale in Mechanical & Biological Engineering Research Group, Aragon Institute of Engineering Research (I3A), School of Engineering & Architecture, University of Zaragoza, 50018 Zaragoza, Aragon, Spain
| | - Hippolyte Amaveda
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC and University of Zaragoza, 50018 Zaragoza, Aragon, Spain
| | - Mario Mora
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC and University of Zaragoza, 50018 Zaragoza, Aragon, Spain
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC and University of Zaragoza, 50018 Zaragoza, Aragon, Spain
- Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018 Zaragoza, Aragon, Spain
| | - Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC and University of Zaragoza, 50018 Zaragoza, Aragon, Spain
- Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018 Zaragoza, Aragon, Spain
- Fundación ARAID, 50018 Zaragoza, Aragon, Spain
| | - Pilar Alamán-Díez
- Multiscale in Mechanical & Biological Engineering Research Group, Aragon Institute of Engineering Research (I3A), School of Engineering & Architecture, University of Zaragoza, 50018 Zaragoza, Aragon, Spain
| | - Salvador Pérez-Huertas
- Department of Chemical Engineering, Faculty of Sciences, University of Granada, 18071 Granada, Andalusia, Spain
| | - María Ángeles Pérez
- Multiscale in Mechanical & Biological Engineering Research Group, Aragon Institute of Engineering Research (I3A), School of Engineering & Architecture, University of Zaragoza, 50018 Zaragoza, Aragon, Spain
- Aragon Institute for Health Research (IIS Aragon), Miguel Servet University Hospital, 50009 Zaragoza, Aragon, Spain
| | - José Manuel García-Aznar
- Multiscale in Mechanical & Biological Engineering Research Group, Aragon Institute of Engineering Research (I3A), School of Engineering & Architecture, University of Zaragoza, 50018 Zaragoza, Aragon, Spain
- Aragon Institute for Health Research (IIS Aragon), Miguel Servet University Hospital, 50009 Zaragoza, Aragon, Spain
| | - Elena García-Gareta
- Multiscale in Mechanical & Biological Engineering Research Group, Aragon Institute of Engineering Research (I3A), School of Engineering & Architecture, University of Zaragoza, 50018 Zaragoza, Aragon, Spain
- Aragon Institute for Health Research (IIS Aragon), Miguel Servet University Hospital, 50009 Zaragoza, Aragon, Spain
- Division of Biomaterials & Tissue Engineering, UCL Eastman Dental Institute, University College London, London NW3 2PF, UK
| |
Collapse
|
4
|
Ouyang Y, Tang X, Zhao Y, Zuo X, Ren X, Wang J, Zou L, Lu J. Disruption of Bacterial Thiol-Dependent Redox Homeostasis by Magnolol and Honokiol as an Antibacterial Strategy. Antioxidants (Basel) 2023; 12:1180. [PMID: 37371909 DOI: 10.3390/antiox12061180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
Some traditional Chinese medicines (TCMs) possess various redox-regulation properties, but whether the redox regulation contributes to antibacterial mechanisms is not known. Here, ginger juice processed Magnoliae officinalis cortex (GMOC) was found to show strong antibacterial activities against some Gram-positive bacteria, but not Gram-negative bacteria including E. coli, while the redox-related transcription factor oxyR deficient E. coli mutant was sensitive to GMOC. In addition, GMOC and its main ingredients, magnolol and honokiol, exhibited inhibitory effects on the bacterial thioredoxin (Trx) system, a major thiol-dependent disulfide reductase system in bacteria. The effects of magnolol and honokiol on cellular redox homeostasis were further verified by elevation of the intracellular ROS levels. The therapeutic efficacies of GMOC, magnolol and honokiol were further verified in S. aureus-caused mild and acute peritonitis mouse models. Treatments with GMOC, magnolol and honokiol significantly reduced the bacterial load, and effectively protected the mice from S. aureus-caused peritonitis infections. Meanwhile, magnolol and honokiol produced synergistic effects when used in combination with several classic antibiotics. These results strongly suggest that some TCMs may exert their therapeutic effects via targeting the bacterial thiol-dependent redox system.
Collapse
Affiliation(s)
- Yanfang Ouyang
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education (Southwest University), College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Xuewen Tang
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education (Southwest University), College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Ying Zhao
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education (Southwest University), College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Xin Zuo
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education (Southwest University), College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Xiaoyuan Ren
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jun Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang 443002, China
| | - Lili Zou
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang 443002, China
| | - Jun Lu
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education (Southwest University), College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| |
Collapse
|
5
|
Gaire S, Fabian RL, Adhikari R, Tuma PL, Pegg IL, Sarkar A. Micromechanical Study of Hyperacetylated Nucleosomes Using Single Molecule Transverse Magnetic Tweezers. Int J Mol Sci 2023; 24:ijms24076188. [PMID: 37047156 PMCID: PMC10094661 DOI: 10.3390/ijms24076188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Nucleosomes are stable complexes of DNA and histone proteins that are essential for the proper functioning of the genome. These structures must be unwrapped and disassembled for processes such as gene expression, replication, and repair. Histone post-translational modifications (PTMs) are known to play a significant role in regulating the structural changes of nucleosomes. However, the underlying mechanisms by which these modifications function remain unclear. In this study, we report the results of single molecule micromanipulation experiments on DNA–protein complexes composed of hyperacetylated histone proteins using transverse magnetic tweezers. The experiments were conducted by pre-extending λ-DNA with a force less than 4 pN before introducing hyperacetylated histones into the sample chamber. The DNA shortened as the histones formed complexes with it and the nucleosome arrays were then exposed to increasing tension, resulting in quantized changes in the DNA’s extension with step sizes of (integral multiples of) ~50 nm. We also compared results of experiments using PTM histones and native histones with data collected for both types of histones for the same force ranges (2–80 pN) and loading rates. Our data show that hyperacetylated nucleosomes require an unbinding force of around ~2.5 pN, which is similar to that required for native histones. Moreover, we identified clear differences between the step-size distributions of native and hyperacetylated histones and found that in contrast to tethers reconstituted with native histones, the majority of nucleosomes in tethers compacted with hyperacetylated histones underwent disassembly at forces significantly lower than 6 pN.
Collapse
|
6
|
Lostao A, Lim K, Pallarés MC, Ptak A, Marcuello C. Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy. Int J Biol Macromol 2023; 238:124089. [PMID: 36948336 DOI: 10.1016/j.ijbiomac.2023.124089] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.
Collapse
Affiliation(s)
- Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain; Fundación ARAID, Aragón, Spain.
| | - KeeSiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Ishikawa 920-1192, Japan
| | - María Carmen Pallarés
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Arkadiusz Ptak
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Poznan 60-925, Poland
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain.
| |
Collapse
|
7
|
Marcuello C, Chabbert B, Berzin F, Bercu NB, Molinari M, Aguié-Béghin V. Influence of Surface Chemistry of Fiber and Lignocellulosic Materials on Adhesion Properties with Polybutylene Succinate at Nanoscale. MATERIALS (BASEL, SWITZERLAND) 2023; 16:ma16062440. [PMID: 36984320 PMCID: PMC10056059 DOI: 10.3390/ma16062440] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 06/01/2023]
Abstract
The production of bio-based composites with enhanced characteristics constitutes a strategic action to minimize the use of fossil fuel resources. The mechanical performances of these materials are related to the specific properties of their components, as well as to the quality of the interface between the matrix and the fibers. In a previous research study, it was shown that the polarity of the matrix played a key role in the mechanisms of fiber breakage during processing, as well as on the final properties of the composite. However, some key questions remained unanswered, and new investigations were necessary to improve the knowledge of the interactions between a lignocellulosic material and a polar matrix. In this work, for the first time, atomic force microscopy based on force spectroscopy measurements was carried out using functionalized tips to characterize the intermolecular interactions at the single molecule level, taking place between poly(butylene succinate) and four different plant fibers. The efficiency of the tip functionalization was checked out by scanning electron microscopy and energy-dispersive X-ray spectroscopy, whereas the fibers chemistry was characterized by Fourier-transform infrared spectroscopy. Larger interactions at the nanoscale level were found between the matrix and hypolignified fibers compared to lignified ones, as in control experiments on single lignocellulosic polymer films. These results could significantly aid in the design of the most appropriate composite composition depending on its final use.
Collapse
Affiliation(s)
- Carlos Marcuello
- Université de Reims Champagne Ardenne, INRAE, FARE, 51097 Reims, France
| | - Brigitte Chabbert
- Université de Reims Champagne Ardenne, INRAE, FARE, 51097 Reims, France
| | - Françoise Berzin
- Université de Reims Champagne Ardenne, INRAE, FARE, 51097 Reims, France
| | | | | | | |
Collapse
|
8
|
Magazzù A, Marcuello C. Investigation of Soft Matter Nanomechanics by Atomic Force Microscopy and Optical Tweezers: A Comprehensive Review. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13060963. [PMID: 36985857 PMCID: PMC10053849 DOI: 10.3390/nano13060963] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 05/17/2023]
Abstract
Soft matter exhibits a multitude of intrinsic physico-chemical attributes. Their mechanical properties are crucial characteristics to define their performance. In this context, the rigidity of these systems under exerted load forces is covered by the field of biomechanics. Moreover, cellular transduction processes which are involved in health and disease conditions are significantly affected by exogenous biomechanical actions. In this framework, atomic force microscopy (AFM) and optical tweezers (OT) can play an important role to determine the biomechanical parameters of the investigated systems at the single-molecule level. This review aims to fully comprehend the interplay between mechanical forces and soft matter systems. In particular, we outline the capabilities of AFM and OT compared to other classical bulk techniques to determine nanomechanical parameters such as Young's modulus. We also provide some recent examples of nanomechanical measurements performed using AFM and OT in hydrogels, biopolymers and cellular systems, among others. We expect the present manuscript will aid potential readers and stakeholders to fully understand the potential applications of AFM and OT to soft matter systems.
Collapse
Affiliation(s)
- Alessandro Magazzù
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, 98158 Mesina, Italy
- NLHT-Lab, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
- Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
- Correspondence: ; Tel.: +34-876555357
| |
Collapse
|
9
|
Yu L, Zhang M, Chen H, Xiao B, Chang S. Measurements of single-molecule electromechanical properties based on atomic force microscopy fixed-junction technique. NANOSCALE 2023; 15:4277-4281. [PMID: 36751974 DOI: 10.1039/d2nr06074d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A hybrid technique combining atomic force microscopy and the fixed-junction technique is developed to simultaneously probe the electrical and mechanical characteristics of a single-molecule junction.
Collapse
Affiliation(s)
- Lei Yu
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.
- The Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Mingyang Zhang
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.
- The Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Haijian Chen
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.
- The Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Bohuai Xiao
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.
- The Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.
- The Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| |
Collapse
|
10
|
Nanoscale Prognosis of Colorectal Cancer Metastasis from AFM Image Processing of Histological Sections. Cancers (Basel) 2023; 15:cancers15041220. [PMID: 36831563 PMCID: PMC9953928 DOI: 10.3390/cancers15041220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Early ascertainment of metastatic tumour phases is crucial to improve cancer survival, formulate an accurate prognostic report of disease advancement, and, most importantly, quantify the metastatic progression and malignancy state of primary cancer cells with a universal numerical indexing system. This work proposes an early improvement to metastatic cancer detection with 97.7 nm spatial resolution by indexing the metastatic cancer phases from the analysis of atomic force microscopy images of human colorectal cancer histological sections. The procedure applies variograms of residuals of Gaussian filtering and theta statistics of colorectal cancer tissue image settings. This methodology elucidates the early metastatic progression at the nanoscale level by setting metastatic indexes and critical thresholds based on relatively large histological sections and categorising the malignancy state of a few suspicious cells not identified with optical image analysis. In addition, we sought to detect early tiny morphological differentiations indicating potential cell transition from epithelial cell phenotypes of low metastatic potential to those of high metastatic potential. This metastatic differentiation, which is also identified in higher moments of variograms, sets different hierarchical levels for metastatic progression dynamics.
Collapse
|
11
|
Kwon S. Structural Insight into the Working Mechanism of the FAD Synthetase from the Human Pathogen Streptococcus pneumoniae: A Molecular Docking Simulation Study. Int J Mol Sci 2023; 24:ijms24043121. [PMID: 36834532 PMCID: PMC9962085 DOI: 10.3390/ijms24043121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Flavin adenine dinucleotide synthetases (FADSs) catalyze FAD biosynthesis through two consecutive catalytic reactions, riboflavin (RF) phosphorylation and flavin mononucleotide (FMN) adenylylation. Bacterial FADSs have RF kinase (RFK) and FMN adenylyltransferase (FMNAT) domains, whereas the two domains are separated into two independent enzymes in human FADSs. Bacterial FADSs have attracted considerable attention as drug targets due to the fact that they differ from human FADSs in structure and domain combinations. In this study, we analyzed the putative FADS structure from the human pathogen Streptococcus pneumoniae (SpFADS) determined by Kim et al., including conformational changes of key loops in the RFK domain upon substrate binding. Structural analysis and comparisons with a homologous FADS structure revealed that SpFADS corresponds to a hybrid between open and closed conformations of the key loops. Surface analysis of SpFADS further revealed its unique biophysical properties for substrate attraction. In addition, our molecular docking simulations predicted possible substrate-binding modes at the active sites of the RFK and FMNAT domains. Our results provide a structural basis to understand the catalytic mechanism of SpFADS and develop novel SpFADS inhibitors.
Collapse
Affiliation(s)
- Sunghark Kwon
- Department of Biotechnology, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea;
- Research Institute for Biomedical & Health Science, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea
| |
Collapse
|
12
|
Dinarelli S, Longo G, Germanova-Taneva S, Todinova S, Krumova S, Girasole M. Surprising Structural and Functional Properties of Favism Erythrocytes Are Linked to Special Metabolic Regulation: A Cell Aging Study. Int J Mol Sci 2022; 24:ijms24010637. [PMID: 36614084 PMCID: PMC9820584 DOI: 10.3390/ijms24010637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022] Open
Abstract
Favism uniquely arises from a genetic defect of the Glucose-6 Phosphate Dehydrogenase (G6PD) enzyme and results in a severe reduction of erythrocytes' (RBCs) reducing power that impairs the cells' ability to respond to oxidative stresses. After exposure to fava beans or a few other drugs, the patients experience acute hemolytic anemia due to RBCs' lysis both intra and extra-vascularly. In the present paper, we compared selected biochemical, biophysical, and ultra-morphological properties of normal RBCs and cells from favism patients measured along cellular aging. Along the aging path, the cells' characteristics change, and their structural and functional properties degrade for both samples, but with different patterns and effectors that have been characterized in biophysical and biochemical terms. In particular, the analysis revealed distinct metabolic regulation in G6DP-deficient cells that determines important peculiarities in the cell properties during aging. Remarkably, the initial higher fragility and occurrence of structural/morphological alterations of favism cells develop, with longer aging times, into a stronger resistance to external stresses and higher general resilience. This surprisingly higher endurance against cell aging has been related to a special mechanism of metabolic regulation that permits lower energy consumption in environmental stress conditions. Our results provided a direct and coherent link between the RBCs' metabolic regulation and the cell properties that would not have been possible to establish without an investigation performed during aging. The consequences of this new knowledge, in particular, can be discussed in a more general context, such as understanding the role of the present findings in determining the characteristics of the favism pathology as a whole.
Collapse
Affiliation(s)
- Simone Dinarelli
- Italian National Research Council (CNR), Institute for the Structure of the Matter (ISM), Via fosso del Cavaliere 100, 00133 Rome, Italy
| | - Giovanni Longo
- Italian National Research Council (CNR), Institute for the Structure of the Matter (ISM), Via fosso del Cavaliere 100, 00133 Rome, Italy
| | - Stefka Germanova-Taneva
- Bulgarian Academy of Sciences (BAS), Institute of Biophysics and Biomedical Engineering, G. Bonchev Str. 21, 1113 Sofia, Bulgaria
| | - Svetla Todinova
- Bulgarian Academy of Sciences (BAS), Institute of Biophysics and Biomedical Engineering, G. Bonchev Str. 21, 1113 Sofia, Bulgaria
| | - Sashka Krumova
- Bulgarian Academy of Sciences (BAS), Institute of Biophysics and Biomedical Engineering, G. Bonchev Str. 21, 1113 Sofia, Bulgaria
| | - Marco Girasole
- Italian National Research Council (CNR), Institute for the Structure of the Matter (ISM), Via fosso del Cavaliere 100, 00133 Rome, Italy
- Correspondence:
| |
Collapse
|
13
|
Ohkubo T, Shiina T, Kawaguchi K, Sasaki D, Inamasu R, Yang Y, Li Z, Taninaka K, Sakaguchi M, Fujimura S, Sekiguchi H, Kuramochi M, Arai T, Tsuda S, Sasaki YC, Mio K. Visualizing Intramolecular Dynamics of Membrane Proteins. Int J Mol Sci 2022; 23:ijms232314539. [PMID: 36498865 PMCID: PMC9736139 DOI: 10.3390/ijms232314539] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Membrane proteins play important roles in biological functions, with accompanying allosteric structure changes. Understanding intramolecular dynamics helps elucidate catalytic mechanisms and develop new drugs. In contrast to the various technologies for structural analysis, methods for analyzing intramolecular dynamics are limited. Single-molecule measurements using optical microscopy have been widely used for kinetic analysis. Recently, improvements in detectors and image analysis technology have made it possible to use single-molecule determination methods using X-rays and electron beams, such as diffracted X-ray tracking (DXT), X-ray free electron laser (XFEL) imaging, and cryo-electron microscopy (cryo-EM). High-speed atomic force microscopy (HS-AFM) is a scanning probe microscope that can capture the structural dynamics of biomolecules in real time at the single-molecule level. Time-resolved techniques also facilitate an understanding of real-time intramolecular processes during chemical reactions. In this review, recent advances in membrane protein dynamics visualization techniques were presented.
Collapse
Affiliation(s)
- Tatsunari Ohkubo
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takaaki Shiina
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
| | - Kayoko Kawaguchi
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
| | - Daisuke Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Rena Inamasu
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Yue Yang
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Zhuoqi Li
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Keizaburo Taninaka
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Masaki Sakaguchi
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Shoko Fujimura
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Hiroshi Sekiguchi
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5198, Japan
| | - Masahiro Kuramochi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Tatsuya Arai
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Sakae Tsuda
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Yuji C. Sasaki
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5198, Japan
| | - Kazuhiro Mio
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Correspondence:
| |
Collapse
|
14
|
Simonyan TR, Protasova EA, Mamontova AV, Shakhov AM, Lukyanov KA, Maksimov EG, Bogdanov AM. A Single Fluorescent Protein-Based Indicator with a Time-Resolved Fluorescence Readout for Precise pH Measurements in the Alkaline Range. Int J Mol Sci 2022; 23:12907. [PMID: 36361706 PMCID: PMC9658282 DOI: 10.3390/ijms232112907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 09/19/2023] Open
Abstract
The real-time monitoring of the intracellular pH in live cells with high precision represents an important methodological challenge. Although genetically encoded fluorescent indicators can be considered as a probe of choice for such measurements, they are hindered mostly by the inability to determine an absolute pH value and/or a narrow dynamic range of the signal, making them inefficient for recording the small pH changes that typically occur within cellular organelles. Here, we study the pH sensitivity of a green-fluorescence-protein (GFP)-based emitter (EGFP-Y145L/S205V) with the alkaline-shifted chromophore's pKa and demonstrate that, in the pH range of 7.5-9.0, its fluorescence lifetime changes by a factor of ~3.5 in a quasi-linear manner in mammalian cells. Considering the relatively strong lifetime response in a narrow pH range, we proposed the mitochondria, which are known to have a weakly alkaline milieu, as a target for live-cell pH measurements. Using fluorescence lifetime imaging microscopy (FLIM) to visualize the HEK293T cells expressing mitochondrially targeted EGFP-Y145L/S205V, we succeeded in determining the absolute pH value of the mitochondria and recorded the ETC-uncoupler-stimulated pH shift with a precision of 0.1 unit. We thus show that a single GFP with alkaline-shifted pKa can act as a high-precision indicator that can be used in a specific pH range.
Collapse
Affiliation(s)
- Tatiana R. Simonyan
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Elena A. Protasova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anastasia V. Mamontova
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Aleksander M. Shakhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Semenov Federal Research Center for Chemical Physics, 119991 Moscow, Russia
| | | | - Eugene G. Maksimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| |
Collapse
|
15
|
First Case of a Cerebrocortical Ganglioglioma in a Dog. Vet Sci 2022; 9:vetsci9100514. [PMID: 36288127 PMCID: PMC9610530 DOI: 10.3390/vetsci9100514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/02/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Gangliogliomas are extremely rare tumors of the nervous system that contain a mixture of neoplastic glial and neuronal cells. The aim of the present paper is to describe the clinical presentation, magnetic resonance imaging findings and histopathological and immunophenotypical characteristics of a cerebral cortex ganglioglioma in a 7-year-old Border Collie. The dog presented an acute onset of tonic-clonic epileptic seizures. Magnetic resonance imaging revealed a well-defined large intra-axial mass located on the left forebrain, mainly affecting the frontal cortex. The histopathological examination of the mass revealed a diffuse proliferation of neoplastic glial cells mixed with anomalous neuronal bodies. Immunohistochemical analyses confirmed the presence of two different populations of neoplastic cells. Most neoplastic glial cells were immunoreactive to glial fibrillary acidic protein and the other subset of neoplastic cells were positive to neuronal markers such as PGP 9.5, synaptophysin and neuron-specific enolase, suggestive of neuronal cells. These findings confirmed the diagnosis of a cerebrocortical ganglioglioma. To the authors’ knowledge, this is the first description of a cerebral cortex ganglioglioma in a dog. Abstract Gangliogliomas are extremely rare tumors of the nervous system composed of neoplastic glial and neuronal cells. The aim of the present paper is to describe the clinical presentation, magnetic resonance imaging (MRI) findings and histopathological and immunophenotypical characteristics of a cerebral cortex ganglioglioma in a 7-year-old Border Collie. The dog presented an acute onset of tonic-clonic epileptic seizures. MRI revealed a well-defined large intra-axial mass located on the left forebrain, mainly affecting the frontal cortex. Following humane euthanasia, the histopathological examination of the mass revealed a diffuse proliferation of neoplastic glial cells mixed with anomalous neuronal bodies. Immunohistochemical analyses confirmed the presence of two different populations of neoplastic cells. Most neoplastic glial cells were immunoreactive to glial fibrillary acidic protein (GFAP) and the other subset of neoplastic cells were positive to neuronal markers such as PGP 9.5, synaptophysin (SYN) and neuron-specific enolase (NSE), suggestive of neuronal cells. These findings confirmed the diagnosis of a cerebrocortical ganglioglioma. To the authors knowledge, this is the first description of a ganglioglioma of the cerebral cortex in a dog.
Collapse
|
16
|
Protein Abundance of Drug Transporters in Human Hepatitis C Livers. Int J Mol Sci 2022; 23:ijms23147947. [PMID: 35887291 PMCID: PMC9317752 DOI: 10.3390/ijms23147947] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 11/17/2022] Open
Abstract
Transmembrane drug transport in hepatocytes is one of the major determinants of drug pharmacokinetics. In the present study, ABC transporters (P-gp, MRP1, MRP2, MRP3, MRP4, BCRP, and BSEP) and SLC transporters (MCT1, NTCP, OAT2, OATP1B1, OATP1B3, OATP2B1, OCT1, and OCT3) were quantified for protein abundance (LC-MS/MS) and mRNA levels (qRT-PCR) in hepatitis C virus (HCV)-infected liver samples from the Child–Pugh class A (n = 30), B (n = 21), and C (n = 7) patients. Protein levels of BSEP, MRP3, MCT1, OAT2, OATP1B3, and OCT3 were not significantly affected by HCV infection. P-gp, MRP1, BCRP, and OATP1B3 protein abundances were upregulated, whereas those of MRP2, MRP4, NTCP, OATP2B1, and OCT1 were downregulated in all HCV samples. The observed changes started to be seen in the Child–Pugh class A livers, i.e., upregulation of P-gp and MRP1 and downregulation of MRP2, MRP4, BCRP, and OATP1B3. In the case of NTCP, OATP2B1, and OCT1, a decrease in the protein levels was observed in the class B livers. In the class C livers, no other changes were noted than those in the class A and B patients. The results of the study demonstrate that drug transporter protein abundances are affected by the functional state of the liver in hepatitis C patients.
Collapse
|
17
|
Self-Assembled Inkjet Printer for Droplet Digital Loop-Mediated Isothermal Amplification. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10070247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Developing rapid and inexpensive diagnostic tools for molecular detection has been pushed forward by the advancements of technical aspects. However, attention has rarely been paid to the molecular detection methodology using inkjet printing technique. Herein, we developed an approach that employed a self-assembled inkjet printer as the enabling technology to realize droplet digital loop-mediated isothermal amplification in a low-cost and practical format. An inkjet printer is a self-assembled tool for the generation of discrete droplets in controllable volumes from a picoliter to a nanoliter. A microfluidic chip serves as a droplets reservoir to perform droplet digital LAMP assays. The inkjet printer approach successfully quantified the HPV16 from CaSki cells. This self-assembled and practical inkjet printer device may therefore become a promising tool for rapid molecular detection and can be extended to on-site analysis.
Collapse
|
18
|
Pérez-Domínguez S, Caballero-Mancebo S, Marcuello C, Martínez-Júlvez M, Medina M, Lostao A. Nanomechanical Study of Enzyme: Coenzyme Complexes: Bipartite Sites in Plastidic Ferredoxin-NADP+ Reductase for the Interaction with NADP+. Antioxidants (Basel) 2022; 11:antiox11030537. [PMID: 35326186 PMCID: PMC8944804 DOI: 10.3390/antiox11030537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/04/2022] Open
Abstract
Plastidic ferredoxin-NADP+ reductase (FNR) transfers two electrons from two ferredoxin or flavodoxin molecules to NADP+, generating NADPH. The forces holding the Anabaena FNR:NADP+ complex were analyzed by dynamic force spectroscopy, using WT FNR and three C-terminal Y303 variants, Y303S, Y303F, and Y303W. FNR was covalently immobilized on mica and NADP+ attached to AFM tips. Force–distance curves were collected for different loading rates and specific unbinding forces were analyzed under the Bell–Evans model to obtain the mechanostability parameters associated with the dissociation processes. The WT FNR:NADP+ complex presented a higher mechanical stability than that reported for the complexes with protein partners, corroborating the stronger affinity of FNR for NADP+. The Y303 mutation induced changes in the FNR:NADP+ interaction mechanical stability. NADP+ dissociated from WT and Y303W in a single event related to the release of the adenine moiety of the coenzyme. However, two events described the Y303S:NADP+ dissociation that was also a more durable complex due to the strong binding of the nicotinamide moiety of NADP+ to the catalytic site. Finally, Y303F shows intermediate behavior. Therefore, Y303, reported as crucial for achieving catalytically competent active site geometry, also regulates the concerted dissociation of the bipartite nucleotide moieties of the coenzyme.
Collapse
Affiliation(s)
- Sandra Pérez-Domínguez
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (S.P.-D.); (S.C.-M.); (C.M.)
| | - Silvia Caballero-Mancebo
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (S.P.-D.); (S.C.-M.); (C.M.)
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (S.P.-D.); (S.C.-M.); (C.M.)
- Laboratorio de Microscopías Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50018 Zaragoza, Spain;
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50018 Zaragoza, Spain;
- Correspondence: (M.M.); (A.L.); Tel.: +34-976762476 (M.M.); +34-876555357 (A.L.)
| | - Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (S.P.-D.); (S.C.-M.); (C.M.)
- Laboratorio de Microscopías Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
- Fundación ARAID, 50018 Zaragoza, Spain
- Correspondence: (M.M.); (A.L.); Tel.: +34-976762476 (M.M.); +34-876555357 (A.L.)
| |
Collapse
|