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Castillo-Velasquez C, Matamala E, Becerra D, Orio P, Brauchi SE. Optical recordings of organellar membrane potentials and the components of membrane conductance in lysosomes. J Physiol 2024; 602:1637-1654. [PMID: 38625711 DOI: 10.1113/jp283825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 03/20/2024] [Indexed: 04/17/2024] Open
Abstract
The eukaryotic cell is highly compartmentalized with organelles. Owing to their function in transporting metabolites, metabolic intermediates and byproducts of metabolic activity, organelles are important players in the orchestration of cellular function. Recent advances in optical methods for interrogating the different aspects of organellar activity promise to revolutionize our ability to dissect cellular processes with unprecedented detail. The transport activity of organelles is usually coupled to the transport of charged species; therefore, it is not only associated with the metabolic landscape but also entangled with membrane potentials. In this context, the targeted expression of fluorescent probes for interrogating organellar membrane potential (Ψorg) emerges as a powerful approach, offering less-invasive conditions and technical simplicity to interrogate cellular signalling and metabolism. Different research groups have made remarkable progress in adapting a variety of optical methods for measuring and monitoring Ψorg. These approaches include using potentiometric dyes, genetically encoded voltage indicators, hybrid fluorescence resonance energy transfer sensors and photoinduced electron transfer systems. These studies have provided consistent values for the resting potential of single-membrane organelles, such as lysosomes, the Golgi and the endoplasmic reticulum. We can foresee the use of dynamic measurements of Ψorg to study fundamental problems in organellar physiology that are linked to serious cellular disorders. Here, we present an overview of the available techniques, a survey of the resting membrane potential of internal membranes and, finally, an open-source mathematical model useful to interpret and interrogate membrane-bound structures of small volume by using the lysosome as an example.
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Affiliation(s)
- Cristian Castillo-Velasquez
- Department of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile
| | - Ella Matamala
- Department of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile
| | - Diego Becerra
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
| | - Patricio Orio
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
- Instituto de Neurociencias, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Sebastian E Brauchi
- Department of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile
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2
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Park SY, Choi DH, Song J, Lakshmanan M, Richelle A, Yoon S, Kontoravdi C, Lewis NE, Lee DY. Driving towards digital biomanufacturing by CHO genome-scale models. Trends Biotechnol 2024:S0167-7799(24)00065-9. [PMID: 38548556 DOI: 10.1016/j.tibtech.2024.03.001] [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: 01/01/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 05/20/2024]
Abstract
Genome-scale metabolic models (GEMs) of Chinese hamster ovary (CHO) cells are valuable for gaining mechanistic understanding of mammalian cell metabolism and cultures. We provide a comprehensive overview of past and present developments of CHO-GEMs and in silico methods within the flux balance analysis (FBA) framework, focusing on their practical utility in rational cell line development and bioprocess improvements. There are many opportunities for further augmenting the model coverage and establishing integrative models that account for different cellular processes and data for future applications. With supportive collaborative efforts by the research community, we envisage that CHO-GEMs will be crucial for the increasingly digitized and dynamically controlled bioprocessing pipelines, especially because they can be successfully deployed in conjunction with artificial intelligence (AI) and systems engineering algorithms.
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Affiliation(s)
- Seo-Young Park
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Dong-Hyuk Choi
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Jinsung Song
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Meiyappan Lakshmanan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, and Centre for Integrative Biology and Systems Medicine (IBSE), Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India
| | - Anne Richelle
- Sartorius Corporate Research, Avenue Ariane 5, 1200 Brussels, Belgium
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01850, USA
| | - Cleo Kontoravdi
- Department of Chemical Engineering and Chemical Technology, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Nathan E Lewis
- Departments of Pediatrics and Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea.
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Abalymov AA, Anisimov RA, Demina PA, Kildisheva VA, Kalinova AE, Serdobintsev AA, Novikova NG, Petrenko DB, Sadovnikov AV, Voronin DV, Lomova MV. Time-Delayed Anticancer Effect of an Extremely Low Frequency Alternating Magnetic Field and Multimodal Protein-Tannin-Mitoxantrone Carriers with Brillouin Microspectroscopy Visualization In Vitro. Biomedicines 2024; 12:443. [PMID: 38398045 PMCID: PMC10887239 DOI: 10.3390/biomedicines12020443] [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: 12/04/2023] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The effect of an extremely low frequency alternating magnetic field (ELF AMF) at frequencies of 17, 48, and 95 Hz at 100 mT on free and internalized 4T1 breast cancer cell submicron magnetic mineral carriers with an anticancer drug, mitoxantrone, was shown. The alternating magnetic field (100 mT; 17, 48, 95 Hz; time of treatment-10.5 min with a 30 s delay) does not lead to the significant destruction of carrier shells and release of mitoxantrone or bovine serum albumin from them according to the data of spectrophotometry, or the heating of carriers in the process of exposure to magnetic fields. The most optimal set of factors that would lead to the suppression of proliferation and survival of cells with anticancer drug carriers on the third day (in comparison with the control and first day) is exposure to an alternating magnetic field of 100 mT in a pulsed mode with a frequency of 95 Hz. The presence of magnetic nanocarriers in cell lines was carried out by a direct label-free method, space-resolved Brillouin light scattering (BLS) spectrometry, which was realized for the first time. The analysis of the series of integrated BLS spectra showed an increase in the magnetic phase in cells with a growth in the number of particles per cell (from 10 to 100) after their internalization. The safety of magnetic carriers in the release of their constituent ions has been evaluated using atomic absorption spectrometry.
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Affiliation(s)
- Anatolii A. Abalymov
- Science Medical Centre, Saratov State University, 83 Astrakhanskayast, Saratov 410012, Russia
| | - Roman A. Anisimov
- Science Medical Centre, Saratov State University, 83 Astrakhanskayast, Saratov 410012, Russia
| | - Polina A. Demina
- Science Medical Centre, Saratov State University, 83 Astrakhanskayast, Saratov 410012, Russia
- Institute of Chemistry, Saratov State University, 83 Astrakhanskayast, Saratov 410012, Russia
| | - Veronika A. Kildisheva
- Science Medical Centre, Saratov State University, 83 Astrakhanskayast, Saratov 410012, Russia
| | - Alexandra E. Kalinova
- Institute of Physics, Saratov State University, 83 Astrakhanskayast, Saratov 410012, Russia
| | - Alexey A. Serdobintsev
- Institute of Physics, Saratov State University, 83 Astrakhanskayast, Saratov 410012, Russia
| | - Nadezhda G. Novikova
- Institute of Comprehensive Exploitation, Mineral Resources Russian Academy of Sciences, Moscow 111020, Russia
- The Core Shared Research Facility “Industrial Biotechnologies”, Aleksei Nikolayevich Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russia
| | - Dmitry B. Petrenko
- Geological Institute, Russian Academy of Sciences, Moscow 119017, Russia
- Faculty of Natural Sciences, Department of Theoretical and Applied Chemistry, Federal State University of Education, Mytischi 141014, Russia
| | - Alexandr V. Sadovnikov
- Institute of Physics, Saratov State University, 83 Astrakhanskayast, Saratov 410012, Russia
| | - Denis V. Voronin
- Department of Physical and Colloid Chemistry, National University of Oil and Gas “Gubkin University”, Moscow 119991, Russia
| | - Maria V. Lomova
- Science Medical Centre, Saratov State University, 83 Astrakhanskayast, Saratov 410012, Russia
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Schauenburg D, Weil T. Chemical Reactions in Living Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303396. [PMID: 37679060 PMCID: PMC10885656 DOI: 10.1002/advs.202303396] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/18/2023] [Indexed: 09/09/2023]
Abstract
The term "in vivo ("in the living") chemistry" refers to chemical reactions that take place in a complex living system such as cells, tissue, body liquids, or even in an entire organism. In contrast, reactions that occur generally outside living organisms in an artificial environment (e.g., in a test tube) are referred to as in vitro. Over the past decades, significant contributions have been made in this rapidly growing field of in vivo chemistry, but it is still not fully understood, which transformations proceed efficiently without the formation of by-products or how product formation in such complex environments can be characterized. Potential applications can be imagined that synthesize drug molecules directly within the cell or confer new cellular functions through controlled chemical transformations that will improve the understanding of living systems and develop new therapeutic strategies. The guiding principles of this contribution are twofold: 1) Which chemical reactions can be translated from the laboratory to the living system? 2) Which characterization methods are suitable for studying reactions and structure formation in complex living environments?
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Affiliation(s)
| | - Tanja Weil
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
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Munan S, Yadav R, Pareek N, Samanta A. Ratiometric fluorescent probes for pH mapping in cellular organelles. Analyst 2023; 148:4242-4262. [PMID: 37581493 DOI: 10.1039/d3an00960b] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
The intracellular pH (pHi) in organelles, including mitochondria, endoplasmic reticulum, lysosomes, and nuclei, differs from the cytoplasmic pH, and thus maintaining the pH of these organelles is crucial for cellular homeostasis. Alterations in the intracellular pH (ΔpHi) in organelles lead to the disruption of cell proliferation, ion transportation, cellular homeostasis, and even cell death. Hence, accurately mapping the pH of organelles is crucial. Accordingly, the development of fluorescence imaging probes for targeting specific organelles and monitoring their dynamics at the molecular level has become the forefront of research in the last three decades. Among them, ratiometric fluorescent probes minimize the interference from the excitation wavelength of light, auto-fluorescence from probe concentration, environmental fluctuations, and instrument sensitivity through self-correction compared to monochromatic fluorescent probes, which are known as turn-on/off fluorescent probes. Small-molecular ratiometric fluorescent probes for detecting ΔpHi are challenging yet demanding. To date, sixty-two ratiometric pH probes have been reported for monitoring internal pH alterations in cellular organelles. However, a critical review on organelle-specific ratiometric probes for pH mapping is still lacking. Thus, in the present review, we report the most recent advances in ratiometric pH probes and the previous data on the role of mapping the ΔpHi of cellular organelles. The development strategy, including ratiometric fluorescence with one reference signal (RFRS) and ratiometric fluorescence with two reversible signals (RFRvS), is systematically illustrated. Finally, we emphasize the major challenges in developing ratiometric probes that merit further research in the future.
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Affiliation(s)
- Subrata Munan
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar Institute of Eminence Deemed to be University, NH 91, Tehsil Dadri, Uttar Pradesh, India 201314.
| | - Rashmi Yadav
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar Institute of Eminence Deemed to be University, NH 91, Tehsil Dadri, Uttar Pradesh, India 201314.
| | - Niharika Pareek
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar Institute of Eminence Deemed to be University, NH 91, Tehsil Dadri, Uttar Pradesh, India 201314.
| | - Animesh Samanta
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar Institute of Eminence Deemed to be University, NH 91, Tehsil Dadri, Uttar Pradesh, India 201314.
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Soleymani S, Naghib SM. 3D and 4D printing hydroxyapatite-based scaffolds for bone tissue engineering and regeneration. Heliyon 2023; 9:e19363. [PMID: 37662765 PMCID: PMC10474476 DOI: 10.1016/j.heliyon.2023.e19363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/20/2023] [Accepted: 08/20/2023] [Indexed: 09/05/2023] Open
Abstract
The osseous tissue can be classified as a nanocomposite that encompasses a complex interweaving of organic and inorganic matrices. This intricate amalgamation consists of a collagen component and a mineral phase that are intricately arranged to form elaborate and perforated configurations. Hydroxyapatite, whether synthesized artificially or obtained from natural sources, has garnered considerable attention as a composite material in the field of bone tissue engineering due to its striking resemblance to bone in terms of structure and characteristics. Hydroxyapatite (HA) constitutes the predominant ceramic biomaterial for biomedical applications due to its ability to replicate the mineral composition of vertebrate bone. Nonetheless, it is noteworthy that the present biomimetic substance exhibits unfavorable mechanical characteristics, characterized by insufficient tensile and compressive strength, thus rendering it unsuitable for effective employment in the field of bone tissue engineering. Due to its beneficial attributes, hydroxyapatite (HA) is frequently employed in conjunction with various polymers and crosslinkers as composites to enhance mechanical properties and overall efficacy of implantable biomaterials engineered. The restoration of skeletal defects through the use of customized replacements is an effective way to replace damaged or lost bone structures. This method not only restores the bones' original functions but also reinstates their initial aesthetic appearance. The utilization of hydroxyapatite-polymer composites within 3D-printed grafts necessitates meticulous optimization of both mechanical and biological properties, in order to ensure their suitability for employment in medical devices. The utilization of 3D-printing technology represents an innovative approach in the manufacturing of HA-based scaffolds, which offers advantageous prospects for personalized bone regeneration. The expeditious prototyping method, with emphasis on the application of 3D printing, presents a viable approach in the development of bespoke prosthetic implants, grounded on healthcare data sets. 4D printing approach is an evolved form of 3D printing that utilizes programmable materials capable of altering the intended shape of printed structures, contingent upon single or dual stimulating factors. These factors include aspects such as pH level, temperature, humidity, crosslinking degree, and leaching factors.
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Affiliation(s)
- Sina Soleymani
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran, Iran
| | - Seyed Morteza Naghib
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran, Iran
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7
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He Y, Vasilev K, Zilm P. pH-Responsive Biomaterials for the Treatment of Dental Caries-A Focussed and Critical Review. Pharmaceutics 2023; 15:1837. [PMID: 37514024 PMCID: PMC10385394 DOI: 10.3390/pharmaceutics15071837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Dental caries is a common and costly multifactorial biofilm disease caused by cariogenic bacteria that ferment carbohydrates to lactic acid, demineralizing the inorganic component of teeth. Therefore, low pH (pH 4.5) is a characteristic signal of the localised carious environment, compared to a healthy oral pH range (6.8 to 7.4). The development of pH-responsive delivery systems that release antibacterial agents in response to low pH has gained attention as a targeted therapy for dental caries. Release is triggered by high levels of acidogenic species and their reduction may select for the establishment of health-associated biofilm communities. Moreover, drug efficacy can be amplified by the modification of the delivery system to target adhesion to the plaque biofilm to extend the retention time of antimicrobial agents in the oral cavity. In this review, recent developments of different pH-responsive nanocarriers and their biofilm targeting mechanisms are discussed. This review critically discusses the current state of the art and innovations in the development and use of smart delivery materials for dental caries treatment. The authors' views for the future of the field are also presented.
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Affiliation(s)
- Yanping He
- Adelaide Dental School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Krasimir Vasilev
- College of Medicine and Public Health, Flinders University, Bedford Park, Adelaide, SA 5042, Australia
| | - Peter Zilm
- Adelaide Dental School, University of Adelaide, Adelaide, SA 5000, Australia
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8
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Kolen B, Borghans B, Kortzak D, Lugo V, Hannack C, Guzman RE, Ullah G, Fahlke C. Vesicular glutamate transporters are H +-anion exchangers that operate at variable stoichiometry. Nat Commun 2023; 14:2723. [PMID: 37169755 PMCID: PMC10175566 DOI: 10.1038/s41467-023-38340-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 04/26/2023] [Indexed: 05/13/2023] Open
Abstract
Vesicular glutamate transporters accumulate glutamate in synaptic vesicles, where they also function as a major Cl- efflux pathway. Here we combine heterologous expression and cellular electrophysiology with mathematical modeling to understand the mechanisms underlying this dual function of rat VGLUT1. When glutamate is the main cytoplasmic anion, VGLUT1 functions as H+-glutamate exchanger, with a transport rate of around 600 s-1 at -160 mV. Transport of other large anions, including aspartate, is not stoichiometrically coupled to H+ transport, and Cl- permeates VGLUT1 through an aqueous anion channel with unitary transport rates of 1.5 × 105 s-1 at -160 mV. Mathematical modeling reveals that H+ coupling is sufficient for selective glutamate accumulation in model vesicles and that VGLUT Cl- channel function increases the transport efficiency by accelerating glutamate accumulation and reducing ATP-driven H+ transport. In summary, we provide evidence that VGLUT1 functions as H+-glutamate exchanger that is partially or fully uncoupled by other anions.
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Affiliation(s)
- Bettina Kolen
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Bart Borghans
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Daniel Kortzak
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Victor Lugo
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Cora Hannack
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Raul E Guzman
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, FL, 33620, USA
| | - Christoph Fahlke
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, 52428, Jülich, Germany.
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9
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Wahl-Schott C, Freichel M, Hennis K, Philippaert K, Ottenheijm R, Tsvilovskyy V, Varbanov H. Characterization of Endo-Lysosomal Cation Channels Using Calcium Imaging. Handb Exp Pharmacol 2023; 278:277-304. [PMID: 36894791 DOI: 10.1007/164_2023_637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Endo-lysosomes are membrane-bound acidic organelles that are involved in endocytosis, recycling, and degradation of extracellular and intracellular material. The membranes of endo-lysosomes express several Ca2+-permeable cation ion channels, including two-pore channels (TPC1-3) and transient receptor potential mucolipin channels (TRPML1-3). In this chapter, we will describe four different state-of-the-art Ca2+ imaging approaches, which are well-suited to investigate the function of endo-lysosomal cation channels. These techniques include (1) global cytosolic Ca2+ measurements, (2) peri-endo-lysosomal Ca2+ imaging using genetically encoded Ca2+ sensors that are directed to the cytosolic endo-lysosomal membrane surface, (3) Ca2+ imaging of endo-lysosomal cation channels, which are engineered in order to redirect them to the plasma membrane in combination with approaches 1 and 2, and (4) Ca2+ imaging by directing Ca2+ indicators to the endo-lysosomal lumen. Moreover, we will review useful small molecules, which can be used as valuable tools for endo-lysosomal Ca2+ imaging. Rather than providing complete protocols, we will discuss specific methodological issues related to endo-lysosomal Ca2+ imaging.
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Affiliation(s)
- Christian Wahl-Schott
- Institut für Kardiovaskuläre Physiologie und Pathophysiologie, Lehrstuhl für Vegetative Physiologie, Biomedizinisches Zentrum, Ludwig-Maximilians-Universität München, München, Germany.
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany. .,DZHK (German Centre for Cardiovascular Research), Heidelberg/Mannheim, Germany.
| | - Konstantin Hennis
- Institut für Kardiovaskuläre Physiologie und Pathophysiologie, Lehrstuhl für Vegetative Physiologie, Biomedizinisches Zentrum, Ludwig-Maximilians-Universität München, München, Germany
| | - Koenraad Philippaert
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg/Mannheim, Germany
| | - Roger Ottenheijm
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg/Mannheim, Germany
| | - Volodymyr Tsvilovskyy
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg/Mannheim, Germany
| | - Hristo Varbanov
- Institut für Neurophysiologie, Medizinische Hochschule Hannover(MHH), Hannover, Germany
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10
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Subach OM, Vlaskina AV, Agapova YK, Korzhenevskiy DA, Nikolaeva AY, Varizhuk AM, Subach MF, Patrushev MV, Piatkevich KD, Boyko KM, Subach FV. cNTnC and fYTnC2, Genetically Encoded Green Calcium Indicators Based on Troponin C from Fast Animals. Int J Mol Sci 2022; 23:ijms232314614. [PMID: 36498942 PMCID: PMC9741049 DOI: 10.3390/ijms232314614] [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: 10/18/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
NTnC-like green fluorescent genetically encoded calcium indicators (GECIs) with two calcium ion binding sites were constructed using the insertion of truncated troponin C (TnC) from Opsanus tau into green fluorescent proteins (GFPs). These GECIs are small proteins containing the N- and C-termini of GFP; they exert a limited effect on the cellular free calcium ion concentration; and in contrast to calmodulin-based calcium indicators they lack undesired interactions with intracellular proteins in neurons. The available TnC-based NTnC or YTnC GECIs had either an inverted response and high brightness but a limited dynamic range or a positive response and fast kinetics in neurons but lower brightness and an enhanced but still limited dF/F dynamic range. Here, we solved the crystal structure of NTnC at 2.5 Å resolution. Based on this structure, we developed positive NTnC2 and inverted iNTnC2 GECIs with a large dF/F dynamic range in vitro but very slow rise and decay kinetics in neurons. To overcome their slow responsiveness, we swapped TnC from O. tau in NTnC2 with truncated troponin C proteins from the muscles of fast animals, namely, the falcon, hummingbird, cheetah, bat, rattlesnake, and ant, and then optimized the resulting constructs using directed molecular evolution. Characterization of the engineered variants using purified proteins, mammalian cells, and neuronal cultures revealed cNTnC GECI with truncated TnC from Calypte anna (hummingbird) to have the largest dF/F fluorescence response and fast dissociation kinetics in neuronal cultures. In addition, based on the insertion of truncated TnCs from fast animals into YTnC2, we developed fYTnC2 GECI with TnC from Falco peregrinus (falcon). The purified proteins cNTnC and fYTnC2 had 8- and 6-fold higher molecular brightness and 7- and 6-fold larger dF/F responses to the increase in Ca2+ ion concentration than YTnC, respectively. cNTnC GECI was also 4-fold more photostable than YTnC and fYTnC2 GECIs. Finally, we assessed the developed GECIs in primary mouse neuronal cultures stimulated with an external electric field; in these conditions, cNTnC had a 2.4-fold higher dF/F fluorescence response than YTnC and fYTnC2 and was the same or slightly slower (1.4-fold) than fYTnC2 and YTnC in the rise and decay half-times, respectively.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Yuliya K. Agapova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Dmitriy A. Korzhenevskiy
- Laboratory of Electrophysiology, Federal Center of Brain Research and Neurotechnologies, Ostrovityanova Str. 1, Bld. 10, Moscow 125367, Russia
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Anna M. Varizhuk
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str. 1a, Moscow 119435, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Maksim F. Subach
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Maxim V. Patrushev
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Kiryl D. Piatkevich
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow 119071, Russia
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
- Correspondence: ; Tel.: +7-499-196-7100-3389
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Kosmidis E, Shuttle CG, Preobraschenski J, Ganzella M, Johnson PJ, Veshaguri S, Holmkvist J, Møller MP, Marantos O, Marcoline F, Grabe M, Pedersen JL, Jahn R, Stamou D. Regulation of the mammalian-brain V-ATPase through ultraslow mode-switching. Nature 2022; 611:827-834. [PMID: 36418452 PMCID: PMC11212661 DOI: 10.1038/s41586-022-05472-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/21/2022] [Indexed: 11/24/2022]
Abstract
Vacuolar-type adenosine triphosphatases (V-ATPases)1-3 are electrogenic rotary mechanoenzymes structurally related to F-type ATP synthases4,5. They hydrolyse ATP to establish electrochemical proton gradients for a plethora of cellular processes1,3. In neurons, the loading of all neurotransmitters into synaptic vesicles is energized by about one V-ATPase molecule per synaptic vesicle6,7. To shed light on this bona fide single-molecule biological process, we investigated electrogenic proton-pumping by single mammalian-brain V-ATPases in single synaptic vesicles. Here we show that V-ATPases do not pump continuously in time, as suggested by observing the rotation of bacterial homologues8 and assuming strict ATP-proton coupling. Instead, they stochastically switch between three ultralong-lived modes: proton-pumping, inactive and proton-leaky. Notably, direct observation of pumping revealed that physiologically relevant concentrations of ATP do not regulate the intrinsic pumping rate. ATP regulates V-ATPase activity through the switching probability of the proton-pumping mode. By contrast, electrochemical proton gradients regulate the pumping rate and the switching of the pumping and inactive modes. A direct consequence of mode-switching is all-or-none stochastic fluctuations in the electrochemical gradient of synaptic vesicles that would be expected to introduce stochasticity in proton-driven secondary active loading of neurotransmitters and may thus have important implications for neurotransmission. This work reveals and emphasizes the mechanistic and biological importance of ultraslow mode-switching.
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Affiliation(s)
- Eleftherios Kosmidis
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Christopher G Shuttle
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Julia Preobraschenski
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute for Auditory Neuroscience, University Medical Center, Göttingen, Germany
- Multiscale Bioimaging Cluster of Excellence (MBExC), University of Göttingen, Göttingen, Germany
| | - Marcelo Ganzella
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Peter J Johnson
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Mathematics, University of Manchester, Manchester, UK
| | - Salome Veshaguri
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Novozymes A/S, Kgs Lyngby, Denmark
| | - Jesper Holmkvist
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Mads P Møller
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Orestis Marantos
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Frank Marcoline
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jesper L Pedersen
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Reinhard Jahn
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Dimitrios Stamou
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
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12
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Kakkar V, Narula P. Role of molecularly imprinted hydrogels in drug delivery - A current perspective. Int J Pharm 2022; 625:121883. [PMID: 35870667 DOI: 10.1016/j.ijpharm.2022.121883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/23/2022] [Accepted: 05/28/2022] [Indexed: 10/17/2022]
Abstract
Molecular imprinting in hydrogels crafts memory for template molecules in a flexible macromolecular structure. Molecular imprinting can control the pattern of the drug release via different mechanistic pathways which may involve swelling, which releases the drug via diffusion or receptive-swollen networks. Responsive hydrogels or smart hydrogels can be tailored to undergo a change in the network structure in response to a stimulus by inserting specific chemical or biological entities along their backbone polymer chains. The stimuli which can be either physical, chemical or biochemical in nature, may impact at various energy levels thereby initiating the molecular interactions at critical onset points. Conventional hydrogels lack in responding to an external stimuli in a swift manner, hence the molecular imprinting technology can significantly advance the therapeutic efficiency of the drugs with anticipated controlled release and targeting efficiency. Molecular imprinting in hydrogels is thus anticipated as a step towards establishment of drug delivery systems by providing improved delivery profiles or longer release times and deliver the drugs in a feedback regulated way. The review article focuses on the current scenario of molecularly imprinted hydrogels with emphasis on the imprinting strategies within hydrogels and challenges encountered, latent translational applications, and future perspectives.
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Affiliation(s)
- Vandita Kakkar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh- 5 160014, India.
| | - Priyanka Narula
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh- 5 160014, India
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13
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Klier PEZ, Gest AMM, Martin JG, Roo R, Navarro MX, Lesiak L, Deal PE, Dadina N, Tyson J, Schepartz A, Miller EW. Bioorthogonal, Fluorogenic Targeting of Voltage-Sensitive Fluorophores for Visualizing Membrane Potential Dynamics in Cellular Organelles. J Am Chem Soc 2022; 144:12138-12146. [PMID: 35776693 DOI: 10.1021/jacs.2c02664] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Electrical potential differences across lipid bilayers play foundational roles in cellular physiology. Plasma membrane voltage is the most widely studied; however, the bilayers of organelles like mitochondria, lysosomes, nuclei, and the endoplasmic reticulum (ER) also provide opportunities for ionic compartmentalization and the generation of transmembrane potentials. Unlike plasma membranes, organellar bilayers, cloistered within the cell, remain recalcitrant to traditional approaches like patch-clamp electrophysiology. To address the challenge of monitoring changes in organelle membrane potential, we describe the design, synthesis, and application of the LUnAR RhoVR (Ligation Unquenched for Activation and Redistribution Rhodamine-based Voltage Reporter) for optically monitoring membrane potential changes in the ER of living cells. We pair a tetrazine-quenched RhoVR for voltage sensing with a transcyclooctene (TCO)-conjugated ceramide (Cer-TCO) for targeting to the ER. Bright fluorescence is observed only at the coincidence of the LUnAR RhoVR and TCO in the ER, minimizing non-specific, off-target fluorescence. We show that the product of the LUnAR RhoVR and Cer-TCO is voltage-sensitive and that the LUnAR RhoVR can be targeted to an intact ER in living cells. Using the LUnAR RhoVR, we use two-color, ER-localized, fast voltage imaging coupled with cytosolic Ca2+ imaging to validate the electroneutrality of Ca2+ release from internal stores. Finally, we use the LUnAR RhoVR to directly visualize functional coupling between the plasma-ER membranes in patch clamped cell lines, providing the first direct evidence of the sign of the ER potential response to plasma membrane potential changes. We envision that the LUnAR RhoVR, along with other existing organelle-targeting TCO probes, could be applied widely for exploring organelle physiology.
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Affiliation(s)
- Pavel E Z Klier
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Anneliese M M Gest
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Julia G Martin
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ryan Roo
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Marisol X Navarro
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Lauren Lesiak
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Parker E Deal
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Neville Dadina
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jonathan Tyson
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, United States
| | - Evan W Miller
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, United States.,Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, United States
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14
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Seidel T. The Plant V-ATPase. FRONTIERS IN PLANT SCIENCE 2022; 13:931777. [PMID: 35845650 PMCID: PMC9280200 DOI: 10.3389/fpls.2022.931777] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/03/2022] [Indexed: 05/25/2023]
Abstract
V-ATPase is the dominant proton pump in plant cells. It contributes to cytosolic pH homeostasis and energizes transport processes across endomembranes of the secretory pathway. Its localization in the trans Golgi network/early endosomes is essential for vesicle transport, for instance for the delivery of cell wall components. Furthermore, it is crucial for response to abiotic and biotic stresses. The V-ATPase's rather complex structure and multiple subunit isoforms enable high structural flexibility with respect to requirements for different organs, developmental stages, and organelles. This complexity further demands a sophisticated assembly machinery and transport routes in cells, a process that is still not fully understood. Regulation of V-ATPase is a target of phosphorylation and redox-modifications but also involves interactions with regulatory proteins like 14-3-3 proteins and the lipid environment. Regulation by reversible assembly, as reported for yeast and the mammalian enzyme, has not be proven in plants but seems to be absent in autotrophic cells. Addressing the regulation of V-ATPase is a promising approach to adjust its activity for improved stress resistance or higher crop yield.
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15
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Yang L, Liu Y, Yue M, Li P, Liu Y, Ye F, Fu Y. A Multifunctional and Fast-Response Lysosome-Targetable Fluorescent Probe for Monitoring pH and Isoxaflutole. Int J Mol Sci 2022; 23:ijms23116256. [PMID: 35682934 PMCID: PMC9181397 DOI: 10.3390/ijms23116256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/13/2022] [Accepted: 05/30/2022] [Indexed: 12/10/2022] Open
Abstract
A new chemosensor, namely N-(2-morpholinoethyl)acetamide-4-morpholine-1,8-naphthimide (MMN), was designed and synthesized through an amidation reaction. MMN was fabricated as a multifunctional fluorescent probe for monitoring pH and isoxaflutole. MMN exhibited excellent stability in MeCN/H2O (v/v, 9/1), with an obvious "off-on" fluorescence response toward pH changes due to intramolecular charge transfer (ICT), where the linear response ranges of MMN in the weakly acidic system were from 4.2 to 5.0 and from 5.0 to 6.0 with apparent pKa = 4.62 ± 0.02 and 5.43 ± 0.02. Based on morpholine as the lysosome targetable unit, MMN could selectively locate lysosomes in live cells. MMN also successfully detected the presence of H+ in test papers. Finally, MMN could specifically recognize isoxaflutole at a detection limit of 0.88 μM. A possible sensing mechanism was identified based on density function theory calculations. These results indicate that MMN could be a superior potential chemosensor for detecting pH and isoxaflutole selectively and sensitively and could be used in real sample detection.
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Affiliation(s)
| | | | | | | | | | - Fei Ye
- Correspondence: (F.Y.); (Y.F.)
| | - Ying Fu
- Correspondence: (F.Y.); (Y.F.)
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16
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García-Soriano D, Milán-Rois P, Lafuente-Gómez N, Navío C, Gutiérrez L, Cussó L, Desco M, Calle D, Somoza Á, Salas G. Iron oxide-manganese oxide nanoparticles with tunable morphology and switchable MRI contrast mode triggered by intracellular conditions. J Colloid Interface Sci 2022; 613:447-460. [DOI: 10.1016/j.jcis.2022.01.070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/24/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022]
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17
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Tivony R, Fletcher M, Keyser UF. Quantifying proton-induced membrane polarization in single biomimetic giant vesicles. Biophys J 2022; 121:2223-2232. [DOI: 10.1016/j.bpj.2022.05.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 11/25/2022] Open
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18
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Karsten L, Goett-Zink L, Schmitz J, Hoffrogge R, Grünberger A, Kottke T, Müller KM. Genetically Encoded Ratiometric pH Sensors for the Measurement of Intra- and Extracellular pH and Internalization Rates. BIOSENSORS 2022; 12:bios12050271. [PMID: 35624572 PMCID: PMC9138566 DOI: 10.3390/bios12050271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
Abstract
pH-sensitive fluorescent proteins as genetically encoded pH sensors are promising tools for monitoring intra- and extracellular pH. However, there is a lack of ratiometric pH sensors, which offer a good dynamic range and can be purified and applied extracellularly to investigate uptake. In our study, the bright fluorescent protein CoGFP_V0 was C-terminally fused to the ligand epidermal growth factor (EGF) and retained its dual-excitation and dual-emission properties as a purified protein. The tandem fluorescent variants EGF-CoGFP-mTagBFP2 (pK′ = 6.6) and EGF-CoGFP-mCRISPRed (pK′ = 6.1) revealed high dynamic ranges between pH 4.0 and 7.5. Using live-cell fluorescence microscopy, both pH sensor molecules permitted the conversion of fluorescence intensity ratios to detailed intracellular pH maps, which revealed pH gradients within endocytic vesicles. Additionally, extracellular binding of the pH sensors to cells expressing the EGF receptor (EGFR) enabled the tracking of pH shifts inside cultivation chambers of a microfluidic device. Furthermore, the dual-emission properties of EGF-CoGFP-mCRISPRed upon 488 nm excitation make this pH sensor a valuable tool for ratiometric flow cytometry. This high-throughput method allowed for the determination of internalization rates, which represents a promising kinetic parameter for the in vitro characterization of protein–drug conjugates in cancer therapy.
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Affiliation(s)
- Lennard Karsten
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Lukas Goett-Zink
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Julian Schmitz
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Raimund Hoffrogge
- Cell Culture Technology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
- Correspondence:
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19
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Cabot M, Kiessling V, White JM, Tamm LK. Endosomes supporting fusion mediated by vesicular stomatitis virus glycoprotein have distinctive motion and acidification. Traffic 2022; 23:221-234. [PMID: 35147273 PMCID: PMC10621750 DOI: 10.1111/tra.12836] [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: 11/05/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 11/28/2022]
Abstract
Most enveloped viruses infect cells by binding receptors at the cell surface and undergo trafficking through the endocytic pathway to a compartment with the requisite conditions to trigger fusion with a host endosomal membrane. Broad categories of compartments in the endocytic pathway include early and late endosomes, which can be further categorized into subpopulations with differing rates of maturation and motility characteristics. Endocytic compartments have varying protein and lipid components, luminal ionic conditions and pH that provide uniquely hospitable environments for specific viruses to fuse. In order to characterize compartments that permit fusion, we studied the trafficking and fusion of viral particles pseudotyped with the vesicular stomatitis virus glycoprotein (VSV-G) on their surface and equipped with a novel pH sensor and a fluorescent content marker to measure pH, motion and fusion at the single particle level in live cells. We found that the VSV-G particles fuse predominantly from more acidic and more motile endosomes, and that a significant fraction of particles is trafficked to more static and less acidic endosomes that do not support their fusion. Moreover, the fusion-supporting endosomes undergo directed motion.
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Affiliation(s)
- Maya Cabot
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Volker Kiessling
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Judith M. White
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Lukas K. Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22903, USA
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20
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Egashira Y, Katsurabayashi S, Takamori S. Quantitative Analysis of Presynaptic Vesicle Luminal pH in Cultured Neurons. Methods Mol Biol 2022; 2417:45-58. [PMID: 35099790 DOI: 10.1007/978-1-0716-1916-2_4] [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: 06/14/2023]
Abstract
Newly generated synaptic vesicles (SVs) are re-acidified by the activity of the vacuolar-type H+-ATPases. Since H+ gradient across SV membrane drives neurotransmitter uptake into SVs, precise measurements of steady-state vesicular pH and dynamics of re-acidification process will provide important information concerning the H+-driven neurotransmitter uptake. Indeed, we recently demonstrated distinct features of steady state and dynamics of vesicular pH between glutamatergic vesicles and GABAergic vesicles in cultured hippocampal neurons. In this article, we focus on an experimental protocol and setup required to determine steady-state luminal pH of SVs in living neurons. This protocol is composed of efficient expression of a pH-sensitive fluorescent protein in the lumen of SVs in cultured neurons, and recordings of its fluorescence changes under a conventional fluorescent microscope during local applications of acidic buffer and ionophores-containing solution at a given pH. The method described here can be easily applied for measuring luminal pH of different types of secretory organelles and other acidic organelles such as lysosomes and endosomes in cultured cell preparations.
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Affiliation(s)
- Yoshihiro Egashira
- Laboratory of Neural Membrane Biology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan.
- Department of Physiology, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan.
| | - Shutaro Katsurabayashi
- Department of Neuropharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Shigeo Takamori
- Laboratory of Neural Membrane Biology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan.
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21
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Peters JT, Wechsler ME, Peppas NA. Advanced biomedical hydrogels: molecular architecture and its impact on medical applications. Regen Biomater 2021; 8:rbab060. [PMID: 34925879 PMCID: PMC8678442 DOI: 10.1093/rb/rbab060] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/22/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Hydrogels are cross-linked polymeric networks swollen in water, physiological aqueous solutions or biological fluids. They are synthesized by a wide range of polymerization methods that allow for the introduction of linear and branched units with specific molecular characteristics. In addition, they can be tuned to exhibit desirable chemical characteristics including hydrophilicity or hydrophobicity. The synthesized hydrogels can be anionic, cationic, or amphiphilic and can contain multifunctional cross-links, junctions or tie points. Beyond these characteristics, hydrogels exhibit compatibility with biological systems, and can be synthesized to render systems that swell or collapse in response to external stimuli. This versatility and compatibility have led to better understanding of how the hydrogel's molecular architecture will affect their physicochemical, mechanical and biological properties. We present a critical summary of the main methods to synthesize hydrogels, which define their architecture, and advanced structural characteristics for macromolecular/biological applications.
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Affiliation(s)
- Jonathan T Peters
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, 200 E. Dean Keeton, Austin, TX 78712, USA
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, 107 W. Dean Keeton, Austin, TX 78712, USA
| | - Marissa E Wechsler
- Department of Biomedical Engineering and Chemical Engineering, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Nicholas A Peppas
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, 200 E. Dean Keeton, Austin, TX 78712, USA
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, 107 W. Dean Keeton, Austin, TX 78712, USA
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton, Austin, TX 78712, USA
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, 107 W. Dean Keeton, Austin, TX 78712, USA
- Department of Surgery and Perioperative Care, and Department of Pediatrics, Dell Medical School, The University of Texas at Austin, 1601 Trinity St., Bldg. B, Austin, TX 78712, USA
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22
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Baumrucker CR, Macrina AL, Bruckmaier RM. Colostrogenesis: Role and Mechanism of the Bovine Fc Receptor of the Neonate (FcRn). J Mammary Gland Biol Neoplasia 2021; 26:419-453. [PMID: 35080749 DOI: 10.1007/s10911-021-09506-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 12/10/2021] [Indexed: 11/28/2022] Open
Abstract
Colostrogenesis is a separate and unique phase of mammary epithelial cell activity occurring in the weeks before parturition and rather abruptly ending after birth in the bovine. It has been the focus of research to define what controls this process and how it produces high concentrations of specific biologically active components important for the neonate. In this review we consider colostrum composition and focus upon components that appear in first milked colostrum in concentrations exceeding that in blood serum. The Fc Receptor of the Neonate (FcRn) is recognized as the major immunoglobulin G (IgG) and albumin binding protein that accounts for the proteins' long half-lives. We integrate the action of the pinocytotic (fluid phase) uptake of extracellular components and merge them with FcRn in sorting endosomes. We define and explore the means of binding, sorting, and the transcytotic delivery of IgG1 while recycling IgG2 and albumin. We consider the means of releasing the ligands from the receptor within the endosome and describe a new secretion mechanism of cargo release into colostrum without the appearance of FcRn itself in colostrum. We integrate the insulin-like growth factor family, some of which are highly concentrated bioactive components of colostrum, with the mechanisms related to FcRn endosome action. In addition to secretion, we highlight the recent findings of a role of the FcRn in phagocytosis and antigen presentation and relate its significant and abrupt change in cellular location after parturition to a role in the prevention and resistance to mastitis infections.
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Affiliation(s)
- Craig R Baumrucker
- Department of Animal Science, Penn State University, University Park, PA, 16802, USA.
- Veterinary Physiology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland.
| | - Ann L Macrina
- Department of Animal Science, Penn State University, University Park, PA, 16802, USA
| | - Rupert M Bruckmaier
- Veterinary Physiology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
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23
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Subach OM, Vlaskina AV, Agapova YK, Dorovatovskii PV, Nikolaeva AY, Ivashkina OI, Popov VO, Piatkevich KD, Khrenova MG, Smirnova TA, Boyko KM, Subach FV. LSSmScarlet, dCyRFP2s, dCyOFP2s and CRISPRed2s, Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift. Int J Mol Sci 2021; 22:12887. [PMID: 34884694 PMCID: PMC8657457 DOI: 10.3390/ijms222312887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/20/2021] [Accepted: 11/24/2021] [Indexed: 11/24/2022] Open
Abstract
Genetically encoded red fluorescent proteins with a large Stokes shift (LSSRFPs) can be efficiently co-excited with common green FPs both under single- and two-photon microscopy, thus enabling dual-color imaging using a single laser. Recent progress in protein development resulted in a great variety of novel LSSRFPs; however, the selection of the right LSSRFP for a given application is hampered by the lack of a side-by-side comparison of the LSSRFPs' performance. In this study, we employed rational design and random mutagenesis to convert conventional bright RFP mScarlet into LSSRFP, called LSSmScarlet, characterized by excitation/emission maxima at 470/598 nm. In addition, we utilized the previously reported LSSRFPs mCyRFP1, CyOFP1, and mCRISPRed as templates for directed molecular evolution to develop their optimized versions, called dCyRFP2s, dCyOFP2s and CRISPRed2s. We performed a quantitative assessment of the developed LSSRFPs and their precursors in vitro on purified proteins and compared their brightness at 488 nm excitation in the mammalian cells. The monomeric LSSmScarlet protein was successfully utilized for the confocal imaging of the structural proteins in live mammalian cells and multicolor confocal imaging in conjugation with other FPs. LSSmScarlet was successfully applied for dual-color two-photon imaging in live mammalian cells. We also solved the X-ray structure of the LSSmScarlet protein at the resolution of 1.4 Å that revealed a hydrogen bond network supporting excited-state proton transfer (ESPT). Quantum mechanics/molecular mechanics molecular dynamic simulations confirmed the ESPT mechanism of a large Stokes shift. Structure-guided mutagenesis revealed the role of R198 residue in ESPT that allowed us to generate a variant with improved pH stability. Finally, we showed that LSSmScarlet protein is not appropriate for STED microscopy as a consequence of LSSRed-to-Red photoconversion with high-power 775 nm depletion light.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Yuliya K. Agapova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Pavel V. Dorovatovskii
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
| | - Olga I. Ivashkina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir O. Popov
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kiryl D. Piatkevich
- School of Life Sciences, Westlake University, Hangzhou 310024, China;
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Tatiana A. Smirnova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
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Hernández-Juárez C, Flores-Cruz R, Jiménez-Sánchez A. Fluorescent probe for early mitochondrial voltage dynamics. Chem Commun (Camb) 2021; 57:5526-5529. [PMID: 33956917 DOI: 10.1039/d1cc01944a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mitochondrial voltage dynamics plays a crucial role in cell healthy and disease. Here, a new fluorescent probe to monitor mitochondrial early voltage variations is described. The slowly permeant probe is retained in mitochondria during measurements to avoid interferences from natural membrane potential by incorporating an hydrolizable ester function. Voltage, local polarity, pH parameters and transmembrane dynamics were found to be deeply correlated opening a approach in mitochondrial sensing.
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Affiliation(s)
- Cinthia Hernández-Juárez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n, De. Coyoacán 04510, Ciudad de México, Mexico.
| | - Ricardo Flores-Cruz
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n, De. Coyoacán 04510, Ciudad de México, Mexico.
| | - Arturo Jiménez-Sánchez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n, De. Coyoacán 04510, Ciudad de México, Mexico.
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25
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Savizi ISP, Motamedian E, E Lewis N, Jimenez Del Val I, Shojaosadati SA. An integrated modular framework for modeling the effect of ammonium on the sialylation process of monoclonal antibodies produced by CHO cells. Biotechnol J 2021; 16:e2100019. [PMID: 34021707 DOI: 10.1002/biot.202100019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Monoclonal antibodies (mABs) have emerged as one of the most important therapeutic recombinant proteins in the pharmaceutical industry. Their immunogenicity and therapeutic efficacy are influenced by post-translational modifications, specifically the glycosylation process. Bioprocess conditions can influence the intracellular process of glycosylation. Among all the process conditions that have been recognized to affect the mAB glycoforms, the detailed mechanism underlying how ammonium could perturb glycosylation remains to be fully understood. It was shown that ammonium induces heterogeneity in protein glycosylation by altering the sialic acid content of glycoproteins. Hence, understanding this mechanism would aid pharmaceutical manufacturers to ensure consistent protein glycosylation. METHODS Three different mechanisms have been proposed to explain how ammonium influences the sialylation process. In the first, the inhibition of CMP-sialic acid transporter, which transports CMP-sialic acid (sialylation substrate) into the Golgi, by an increase in UDP-GlcNAc content that is brought about by the augmented incorporation of ammonium into glucosamine formation. In the second, ammonia diffuses into the Golgi and raises its pH, thereby decreasing the sialyltransferase enzyme activity. In the third, the reduction of sialyltransferase enzyme expression level in the presence of ammonium. We employed these mechanisms in a novel integrated modular platform to link dynamic alteration in mAB sialylation process with extracellular ammonium concentration to elucidate how ammonium alters the sialic acid content of glycoproteins. RESULTS Our results show that the sialylation reaction rate is insensitive to the first mechanism. At low ammonium concentration, the second mechanism is the controlling mechanism in mAB sialylation and by increasing the ammonium level (< 8 mM) the third mechanism becomes the controlling mechanism. At higher ammonium concentrations (> 8 mM) the second mechanism becomes predominant again. CONCLUSION The presented model in this study provides a connection between extracellular ammonium and the monoclonal antibody sialylation process. This computational tool could help scientists to develop and formulate cell culture media. The model illustrated here can assist the researchers to select culture media that ensure consistent mAB sialylation.
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Affiliation(s)
- Iman Shahidi Pour Savizi
- Faculty of Chemical Engineering, Biotechnology Department, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Motamedian
- Faculty of Chemical Engineering, Biotechnology Department, Tarbiat Modares University, Tehran, Iran
| | - Nathan E Lewis
- Department of Bioengineering, University of California, La Jolla, California, USA.,School of Medicine, Novo Nordisk Foundation Center for Biosustainability at the University of California, La Jolla, California, USA.,Department of Pediatrics, School of Medicine, University of California, La Jolla, California, USA
| | | | - Seyed Abbas Shojaosadati
- Faculty of Chemical Engineering, Biotechnology Department, Tarbiat Modares University, Tehran, Iran
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26
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Ruan S, Zhou Y, Jiang X, Gao H. Rethinking CRITID Procedure of Brain Targeting Drug Delivery: Circulation, Blood Brain Barrier Recognition, Intracellular Transport, Diseased Cell Targeting, Internalization, and Drug Release. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004025. [PMID: 33977060 PMCID: PMC8097396 DOI: 10.1002/advs.202004025] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/03/2020] [Indexed: 05/06/2023]
Abstract
The past decades have witnessed great progress in nanoparticle (NP)-based brain-targeting drug delivery systems, while their therapeutic potentials are yet to be fully exploited given that the majority of them are lost during the delivery process. Rational design of brain-targeting drug delivery systems requires a deep understanding of the entire delivery process along with the issues that they may encounter. Herein, this review first analyzes the typical delivery process of a systemically administrated NPs-based brain-targeting drug delivery system and proposes a six-step CRITID delivery cascade: circulation in systemic blood, recognizing receptor on blood-brain barrier (BBB), intracellular transport, diseased cell targeting after entering into parenchyma, internalization by diseased cells, and finally intracellular drug release. By dissecting the entire delivery process into six steps, this review seeks to provide a deep understanding of the issues that may restrict the delivery efficiency of brain-targeting drug delivery systems as well as the specific requirements that may guarantee minimal loss at each step. Currently developed strategies used for troubleshooting these issues are reviewed and some state-of-the-art design features meeting these requirements are highlighted. The CRITID delivery cascade can serve as a guideline for designing more efficient and specific brain-targeting drug delivery systems.
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Affiliation(s)
- Shaobo Ruan
- Key laboratory of Drug Targeting and Drug Delivery Systems of the Education MinistrySichuan Engineering Laboratory for Plant‐sourced Drug and Sichuan Research Center for Drug Precision Industrial TechnologyWest China School of PharmacySichuan UniversityChengdu610041China
- Department of PharmaceuticsCollege of PharmacyUniversity of FloridaGainesvilleFlorida32610USA
| | - Yang Zhou
- Key laboratory of Drug Targeting and Drug Delivery Systems of the Education MinistrySichuan Engineering Laboratory for Plant‐sourced Drug and Sichuan Research Center for Drug Precision Industrial TechnologyWest China School of PharmacySichuan UniversityChengdu610041China
| | - Xinguo Jiang
- Key laboratory of Smart Drug DeliveryMinistry of EducationSchool of PharmacyFudan UniversityShanghai201203China
| | - Huile Gao
- Key laboratory of Drug Targeting and Drug Delivery Systems of the Education MinistrySichuan Engineering Laboratory for Plant‐sourced Drug and Sichuan Research Center for Drug Precision Industrial TechnologyWest China School of PharmacySichuan UniversityChengdu610041China
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27
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Castro M, Lythe G, Smit J, Molina-París C. Fusion and fission events regulate endosome maturation and viral escape. Sci Rep 2021; 11:7845. [PMID: 33846408 PMCID: PMC8041880 DOI: 10.1038/s41598-021-86877-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023] Open
Abstract
Endosomes are intracellular vesicles that mediate the communication of the cell with its extracellular environment. They are an essential part of the cell’s machinery regulating intracellular trafficking via the endocytic pathway. Many viruses, which in order to replicate require a host cell, attach themselves to the cellular membrane; an event which usually initiates uptake of a viral particle through the endocytic pathway. In this way viruses hijack endosomes for their journey towards intracellular sites of replication and avoid degradation without host detection by escaping the endosomal compartment. Recent experimental techniques have defined the role of endosomal maturation in the ability of enveloped viruses to release their genetic material into the cytoplasm. Endosome maturation depends on a family of small hydrolase enzymes (or GTPases) called Rab proteins, arranged on the cytoplasmic surface of its membrane. Here, we model endosomes as intracellular compartments described by two variables (its levels of active Rab5 and Rab7 proteins) and which can undergo coagulation (or fusion) and fragmentation (or fission). The key element in our approach is the “per-cell endosomal distribution” and its dynamical (Boltzmann) equation. The Boltzmann equation allows us to derive the dynamics of the total number of endosomes in a cell, as well as the mean and the standard deviation of its active Rab5 and Rab7 levels. We compare our mathematical results with experiments of Dengue viral escape from endosomes. The relationship between endosomal active Rab levels and pH suggests a mechanism that can account for the observed variability in viral escape times, which in turn regulate the viability of a viral intracellular infection.
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Affiliation(s)
- Mario Castro
- Grupo Interdisciplinar de Sistemas Complejos (GISC) and Instituto de Investigación Tecnológica (IIT), Universidad Pontificia Comillas, Madrid, Spain.
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
| | - Jolanda Smit
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, The Netherlands
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK. .,Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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28
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Matamala E, Castillo C, Vivar JP, Rojas PA, Brauchi SE. Imaging the electrical activity of organelles in living cells. Commun Biol 2021; 4:389. [PMID: 33758369 PMCID: PMC7988155 DOI: 10.1038/s42003-021-01916-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 02/24/2021] [Indexed: 12/25/2022] Open
Abstract
Eukaryotic cells are complex systems compartmentalized in membrane-bound organelles. Visualization of organellar electrical activity in living cells requires both a suitable reporter and non-invasive imaging at high spatiotemporal resolution. Here we present hVoSorg, an optical method to monitor changes in the membrane potential of subcellular membranes. This method takes advantage of a FRET pair consisting of a membrane-bound voltage-insensitive fluorescent donor and a non-fluorescent voltage-dependent acceptor that rapidly moves across the membrane in response to changes in polarity. Compared to the currently available techniques, hVoSorg has advantages including simple and precise subcellular targeting, the ability to record from individual organelles, and the potential for optical multiplexing of organellar activity. Matamala et al. adapt a hybrid-FRET voltage sensor to enable the recording of resting membrane potential of different organelle compartments in living cells. Their approach allows simple and precise subcellular targeting, the ability to record from individual organelles, and the potential for optical multiplexing of organellar activity.
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Affiliation(s)
- Ella Matamala
- Physiology Institute, Universidad Austral de Chile, Valdivia, Chile.,Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile
| | - Cristian Castillo
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile
| | - Juan P Vivar
- Physiology Institute, Universidad Austral de Chile, Valdivia, Chile
| | - Patricio A Rojas
- Laboratory of Neuroscience, Faculty of Chemistry and Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Sebastian E Brauchi
- Physiology Institute, Universidad Austral de Chile, Valdivia, Chile. .,Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile. .,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, US.
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29
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Klier PEZ, Martin JG, Miller EW. Imaging Reversible Mitochondrial Membrane Potential Dynamics with a Masked Rhodamine Voltage Reporter. J Am Chem Soc 2021; 143:4095-4099. [PMID: 33710896 DOI: 10.1021/jacs.0c13110] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mitochondria are the site of aerobic respiration, producing ATP via oxidative phosphorylation as protons flow down their electrochemical gradient through ATP synthase. This negative membrane potential across the inner mitochondrial membrane (ΔΨm) represents a fundamental biophysical parameter central to cellular life. Traditional, electrode-based methods for recording membrane potential are impossible to implement on mitochondria within intact cells. Fluorescent ΔΨm indicators based on cationic, lipophilic dyes are a common alternative, but these indicators are complicated by concentration-dependent artifacts and the requirement to maintain dye in the extracellular solution to visualize reversible ΔΨm dynamics. Here, we report the first example of a fluorescent ΔΨm reporter that does not rely on ΔΨm-dependent accumulation. We redirected the localization of a photoinduced electron transfer (PeT)-based indicator, Rhodamine Voltage Reporter (RhoVR), to mitochondria by masking the carboxylate of RhoVR 1 as an acetoxymethyl (AM) ester. Once within mitochondria, esterases remove the AM ester, trapping RhoVR inside of the mitochondrial matrix, where it can incorporate within the inner membrane and reversibly report on changes in ΔΨm. We show that this Small molecule, Permeable, Internally Redistributing for Inner membrane Targeting Rhodamine Voltage Reporter, or SPIRIT RhoVR, localizes to mitochondria across a number of different cell lines and responds reversibly to changes in ΔΨm induced by exceptionally low concentrations of the uncoupler FCCP without the need for exogenous pools of dye (unlike traditional, accumulation-based rhodamine esters). SPIRIT RhoVR is compatible with multi-color imaging, enabling simultaneous, real-time observation of cytosolic Ca2+, plasma membrane potential, and reversible ΔΨm dynamics.
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30
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Kim A, Suzuki Y, Nagasaki Y. Molecular design of a high-performance polymeric carrier for delivery of a variety of boronic acid-containing drugs. Acta Biomater 2021; 121:554-565. [PMID: 33321218 DOI: 10.1016/j.actbio.2020.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 12/19/2022]
Abstract
Because of their many useful and unique properties, boronic acids are well suited for biomedical applications such as antitumor chemotherapy and boron neutron capture therapy (BNCT). Bortezomib, a boronic acid derivative, has drawn a lot of attention as a potent proteasome inhibitor. Nevertheless, because of rapid excretion and off-target effects, the clinical translation of boronic acid-containing drugs is limited. To this end, we employed a polymeric carrier to stably encapsulate boronic acid-containing drugs and achieve superior pharmacokinetics with an on-target drug release capability. Accordingly, to construct a supramolecular polymeric nanoparticle, we took advantage of the facile, stable, and pH-sensitive conjugation between boronic acids and diethanolamine-installed polymeric carriers. We demonstrated the feasibility of our molecular design by generating and applying bortezomib-loaded nanoparticles to a subcutaneous tumor-bearing mouse model. Stable encapsulation and pH-sensitive release of bortezomib facilitated antitumor efficacy and alleviated hepatotoxicity. We also verified the versatility of our approach through biological evaluations of the nanoparticles encapsulating benzo(b)thiophene-2-boronic acid, phenylboronic acid, and p-phenylene-diboronic acid.
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31
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Ban J, Li S, Zhan Q, Li X, Xing H, Chen N, Long L, Hou X, Zhao J, Yuan X. PMPC Modified PAMAM Dendrimer Enhances Brain Tumor-Targeted Drug Delivery. Macromol Biosci 2021; 21:e2000392. [PMID: 33506646 DOI: 10.1002/mabi.202000392] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/30/2020] [Indexed: 12/18/2022]
Abstract
The excellent biocompatibility drug delivery system for effective treatment of glioma is still greatly challenged by the existence of blood-brain barrier, blood-brain tumor barrier, and the tissue toxicity caused by chemotherapy drugs. In this study, poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) is used for the first time for modifying third-generation poly(amidoamine) (PAMAM) to enhance their brain tumor-targeted drug delivery ability as well as simultaneously reducing the toxicity of PAMAM dendrimers and the tissue toxicity of the loaded doxorubicin (DOX). The cytotoxicity, the therapeutic ability in vitro, and the brain tumor-targeted ability of the PMPC modified PAMAM nanoparticles are further studied. Results indicate that PMPC, as a dual-functional modifier, can significantly reduce the cytotoxicity of PAMAM dendrimers, while efficiently target the brain tumor. In addition, the therapeutic effect of DOX-loaded PAMAM-PMPC in mice inoculated with U-87 is also studied in vivo. In comparison with DOX solution, DOX-loaded PAMAM-PMPC alleviates weight loss of tumor-inoculated mice and reduces the cardiotoxicity of DOX. The tumor growth inhibition, in vivo, is significantly increased up to (80.76 ± 1.66)%. In conclusion, this strategy of PMPC dual-functional targeted nanocarrier provides a new method for the delivery of chemotherapeutic drugs to treat glioma.
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Affiliation(s)
- Jiamin Ban
- Tianjin Nano-Biotechnology and Translational Medicine Lab School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Sidi Li
- Tianjin Nano-Biotechnology and Translational Medicine Lab School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China.,School of Environmental and Chemical Engineering, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Qi Zhan
- Tianjin Nano-Biotechnology and Translational Medicine Lab School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Xuepin Li
- Tianjin Nano-Biotechnology and Translational Medicine Lab School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Huike Xing
- Tianjin Nano-Biotechnology and Translational Medicine Lab School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Ning Chen
- Tianjin Nano-Biotechnology and Translational Medicine Lab School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Lixia Long
- Tianjin Nano-Biotechnology and Translational Medicine Lab School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Xin Hou
- Tianjin Nano-Biotechnology and Translational Medicine Lab School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Jin Zhao
- Tianjin Nano-Biotechnology and Translational Medicine Lab School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Xubo Yuan
- Tianjin Nano-Biotechnology and Translational Medicine Lab School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
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32
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Saminathan A, Devany J, Veetil AT, Suresh B, Pillai KS, Schwake M, Krishnan Y. A DNA-based voltmeter for organelles. NATURE NANOTECHNOLOGY 2021; 16:96-103. [PMID: 33139937 PMCID: PMC8513801 DOI: 10.1038/s41565-020-00784-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 09/21/2020] [Indexed: 05/16/2023]
Abstract
The role of membrane potential in most intracellular organelles remains unexplored because of the lack of suitable tools. Here, we describe Voltair, a fluorescent DNA nanodevice that reports the absolute membrane potential and can be targeted to organelles in live cells. Voltair consists of a voltage-sensitive fluorophore and a reference fluorophore for ratiometry, and acts as an endocytic tracer. Using Voltair, we could measure the membrane potential of different organelles in situ in live cells. Voltair can potentially guide the rational design of biocompatible electronics and enhance our understanding of how membrane potential regulates organelle biology.
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Affiliation(s)
- Anand Saminathan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - John Devany
- Department of Physics, The University of Chicago, Chicago, IL, USA
| | - Aneesh Tazhe Veetil
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - Bhavyashree Suresh
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | | | - Michael Schwake
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Biochemistry III/Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, Bielefeld, Germany
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA.
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Xiao Y, Hu F, Luo X, Zhao M, Sun Z, Qian X, Yang Y. Modulating the pKa Values of Hill-Type pH Probes for Biorelevant Acidic pH Range. ACS APPLIED BIO MATERIALS 2020; 4:2097-2103. [DOI: 10.1021/acsabm.0c01262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yansheng Xiao
- State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Fang Hu
- State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiao Luo
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Mingming Zhao
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine Chinese Academy of Medical Science, Beijing 100730, China
| | - Zhenglong Sun
- Suzhou Institute of Biomedical Engineering and Technology (SIBET), Chinese Academy of Sciences, Suzhou 215163, China
| | - Xuhong Qian
- State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Youjun Yang
- State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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34
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Chu H, Yang W, Sun L, Cai S, Yang R, Liang W, Yu H, Liu L. 4D Printing: A Review on Recent Progresses. MICROMACHINES 2020; 11:E796. [PMID: 32842588 PMCID: PMC7570144 DOI: 10.3390/mi11090796] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 11/25/2022]
Abstract
Since the late 1980s, additive manufacturing (AM), commonly known as three-dimensional (3D) printing, has been gradually popularized. However, the microstructures fabricated using 3D printing is static. To overcome this challenge, four-dimensional (4D) printing which defined as fabricating a complex spontaneous structure that changes with time respond in an intended manner to external stimuli. 4D printing originates in 3D printing, but beyond 3D printing. Although 4D printing is mainly based on 3D printing and become an branch of additive manufacturing, the fabricated objects are no longer static and can be transformed into complex structures by changing the size, shape, property and functionality under external stimuli, which makes 3D printing alive. Herein, recent major progresses in 4D printing are reviewed, including AM technologies for 4D printing, stimulation method, materials and applications. In addition, the current challenges and future prospects of 4D printing were highlighted.
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Affiliation(s)
- Honghui Chu
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China; (H.C.); (L.S.); (R.Y.)
| | - Wenguang Yang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China; (H.C.); (L.S.); (R.Y.)
| | - Lujing Sun
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China; (H.C.); (L.S.); (R.Y.)
| | - Shuxiang Cai
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China; (H.C.); (L.S.); (R.Y.)
| | - Rendi Yang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China; (H.C.); (L.S.); (R.Y.)
| | - Wenfeng Liang
- School of Mechanical Engineering, Shenyang Jianzhu University, Shenyang 110016, China;
| | - Haibo Yu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China; (H.Y.); (L.L.)
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China; (H.Y.); (L.L.)
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Banerjee S, Kane PM. Regulation of V-ATPase Activity and Organelle pH by Phosphatidylinositol Phosphate Lipids. Front Cell Dev Biol 2020; 8:510. [PMID: 32656214 PMCID: PMC7324685 DOI: 10.3389/fcell.2020.00510] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022] Open
Abstract
Luminal pH and the distinctive distribution of phosphatidylinositol phosphate (PIP) lipids are central identifying features of organelles in all eukaryotic cells that are also critical for organelle function. V-ATPases are conserved proton pumps that populate and acidify multiple organelles of the secretory and the endocytic pathway. Complete loss of V-ATPase activity causes embryonic lethality in higher animals and conditional lethality in yeast, while partial loss of V-ATPase function is associated with multiple disease states. On the other hand, many cancer cells increase their virulence by upregulating V-ATPase expression and activity. The pH of individual organelles is tightly controlled and essential for function, but the mechanisms for compartment-specific pH regulation are not completely understood. There is substantial evidence indicating that the PIP content of membranes influences organelle pH. We present recent evidence that PIPs interact directly with subunit isoforms of the V-ATPase to dictate localization of V-ATPase subpopulations and participate in their regulation. In yeast cells, which have only one set of organelle-specific V-ATPase subunit isoforms, the Golgi-enriched lipid PI(4)P binds to the cytosolic domain of the Golgi-enriched a-subunit isoform Stv1, and loss of PI(4)P binding results in mislocalization of Stv1-containing V-ATPases from the Golgi to the vacuole/lysosome. In contrast, levels of the vacuole/lysosome-enriched signaling lipid PI(3,5)P2 affect assembly and activity of V-ATPases containing the Vph1 a-subunit isoform. Mutations in the Vph1 isoform that disrupt the lipid interaction increase sensitivity to stress. These studies have decoded “zip codes” for PIP lipids in the cytosolic N-terminal domain of the a-subunit isoforms of the yeast V-ATPase, and similar interactions between PIP lipids and the V-ATPase subunit isoforms are emerging in higher eukaryotes. In addition to direct effects on the V-ATPase, PIP lipids are also likely to affect organelle pH indirectly, through interactions with other membrane transporters. We discuss direct and indirect effects of PIP lipids on organelle pH, and the functional consequences of the interplay between PIP lipid content and organelle pH.
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Affiliation(s)
- Subhrajit Banerjee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
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Subach OM, Sotskov VP, Plusnin VV, Gruzdeva AM, Barykina NV, Ivashkina OI, Anokhin KV, Nikolaeva AY, Korzhenevskiy DA, Vlaskina AV, Lazarenko VA, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Podgorny OV, Piatkevich KD, Boyden ES, Subach FV. Novel Genetically Encoded Bright Positive Calcium Indicator NCaMP7 Based on the mNeonGreen Fluorescent Protein. Int J Mol Sci 2020; 21:ijms21051644. [PMID: 32121243 PMCID: PMC7084697 DOI: 10.3390/ijms21051644] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/21/2022] Open
Abstract
Green fluorescent genetically encoded calcium indicators (GECIs) are the most popular tool for visualization of calcium dynamics in vivo. However, most of them are based on the EGFP protein and have similar molecular brightnesses. The NTnC indicator, which is composed of the mNeonGreen fluorescent protein with the insertion of troponin C, has higher brightness as compared to EGFP-based GECIs, but shows a limited inverted response with an ΔF/F of 1. By insertion of a calmodulin/M13-peptide pair into the mNeonGreen protein, we developed a green GECI called NCaMP7. In vitro, NCaMP7 showed positive response with an ΔF/F of 27 and high affinity (Kd of 125 nM) to calcium ions. NCaMP7 demonstrated a 1.7-fold higher brightness and similar calcium-association/dissociation dynamics compared to the standard GCaMP6s GECI in vitro. According to fluorescence recovery after photobleaching (FRAP) experiments, the NCaMP7 design partially prevented interactions of NCaMP7 with the intracellular environment. The NCaMP7 crystal structure was obtained at 1.75 Å resolution to uncover the molecular basis of its calcium ions sensitivity. The NCaMP7 indicator retained a high and fast response when expressed in cultured HeLa and neuronal cells. Finally, we successfully utilized the NCaMP7 indicator for in vivo visualization of grating-evoked and place-dependent neuronal activity in the visual cortex and the hippocampus of mice using a two-photon microscope and an NVista miniscope, respectively.
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Affiliation(s)
- Oksana M. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir P. Sotskov
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Viktor V. Plusnin
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna M. Gruzdeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Natalia V. Barykina
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Olga I. Ivashkina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Konstantin V. Anokhin
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Alena Y. Nikolaeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Dmitry A. Korzhenevskiy
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna V. Vlaskina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir A. Lazarenko
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia;
| | - Tatiana V. Rakitina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
| | - Anna M. Varizhuk
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Galina E. Pozmogova
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Oleg V. Podgorny
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- N.K. Koltzov Institute of Developmental Biology, RAS, Moscow 119334, Russia
| | - Kiryl D. Piatkevich
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
- School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Edward S. Boyden
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
| | - Fedor V. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Correspondence: ; Tel.: +07-499-196 7100-3389
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Gowrisankaran S, Milosevic I. Regulation of synaptic vesicle acidification at the neuronal synapse. IUBMB Life 2020; 72:568-576. [DOI: 10.1002/iub.2235] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 12/29/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Sindhuja Gowrisankaran
- European Neuroscience Institute (ENI)A Joint Initiative of the University Medical Center Göttingen and the Max Planck Society Göttingen Germany
| | - Ira Milosevic
- European Neuroscience Institute (ENI)A Joint Initiative of the University Medical Center Göttingen and the Max Planck Society Göttingen Germany
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Singh A, Marcoline FV, Veshaguri S, Kao AW, Bruchez M, Mindell JA, Stamou D, Grabe M. Protons in small spaces: Discrete simulations of vesicle acidification. PLoS Comput Biol 2019; 15:e1007539. [PMID: 31869334 PMCID: PMC6946529 DOI: 10.1371/journal.pcbi.1007539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 01/07/2020] [Accepted: 11/11/2019] [Indexed: 12/23/2022] Open
Abstract
The lumenal pH of an organelle is one of its defining characteristics and central to its biological function. Experiments have elucidated many of the key pH regulatory elements and how they vary from compartment-to-compartment, and continuum mathematical models have played an important role in understanding how these elements (proton pumps, counter-ion fluxes, membrane potential, buffering capacity, etc.) work together to achieve specific pH setpoints. While continuum models have proven successful in describing ion regulation at the cellular length scale, it is unknown if they are valid at the subcellular level where volumes are small, ion numbers may fluctuate wildly, and biochemical heterogeneity is large. Here, we create a discrete, stochastic (DS) model of vesicular acidification to answer this question. We used this simplified model to analyze pH measurements of isolated vesicles containing single proton pumps and compared these results to solutions from a continuum, ordinary differential equations (ODE)-based model. Both models predict similar parameter estimates for the mean proton pumping rate, membrane permeability, etc., but, as expected, the ODE model fails to report on the fluctuations in the system. The stochastic model predicts that pH fluctuations decrease during acidification, but noise analysis of single-vesicle data confirms our finding that the experimental noise is dominated by the fluorescent dye, and it reveals no insight into the true noise in the proton fluctuations. Finally, we again use the reduced DS model explore the acidification of large, lysosome-like vesicles to determine how stochastic elements, such as variations in proton-pump copy number and cycling between on and off states, impact the pH setpoint and fluctuations around this setpoint. Organelles harbor specific ion channels, transporters, and other molecular components that allow them to achieve specific intracellular ionic conditions required for their proper function. How all of these components work together to regulate these concentrations, such as maintaining a specific pH value, is complex, and continuum mathematical models have been helpful for evaluating different mechanisms and making quantitative predictions that can be tested experimentally. Nonetheless, organelles can be quite small and some contain only a handful of free protons—can continuum models accurately describe systems with so few molecules? We tested this by creating a discrete, stochastic (DS) model of vesicle acidification that tracks how all of these individual molecules in the vesicle change their state in time. When fitting experimental data, the DS model provides the same parameter estimates as a corresponding continuum model, indicating that both models are equally valid. However, the DS model additionally informs on the noise in the vesicle. When compared to the experimental noise in pH, we show that there is no agreement, because experimental fluctuations do not report on the true pH fluctuations, but rather they report on the fluctuations in reporter molecule protonation. Given experimental limitations, our result highlights the importance of DS models in predicting noise in organelles.
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Affiliation(s)
- Apeksha Singh
- College of Letters and Science, University of California Berkeley, Berkeley, California, United States of America
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Frank V. Marcoline
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (FVM); (MG)
| | - Salome Veshaguri
- Bionanotecnology and Nanomedicine Laboratory, University of Copenhagen, Copenhagen, Denmark
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Aimee W. Kao
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Marcel Bruchez
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Joseph A. Mindell
- Membrane Transport Biophysics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dimitrios Stamou
- Bionanotecnology and Nanomedicine Laboratory, University of Copenhagen, Copenhagen, Denmark
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (FVM); (MG)
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39
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Boyken SE, Benhaim MA, Busch F, Jia M, Bick MJ, Choi H, Klima JC, Chen Z, Walkey C, Mileant A, Sahasrabuddhe A, Wei KY, Hodge EA, Byron S, Quijano-Rubio A, Sankaran B, King NP, Lippincott-Schwartz J, Wysocki VH, Lee KK, Baker D. De novo design of tunable, pH-driven conformational changes. Science 2019; 364:658-664. [PMID: 31097662 DOI: 10.1126/science.aav7897] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/24/2019] [Indexed: 01/03/2023]
Abstract
The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.
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Affiliation(s)
- Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Mark A Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Florian Busch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Mengxuan Jia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Heejun Choi
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Jason C Klima
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Zibo Chen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA, USA
| | - Carl Walkey
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alexander Mileant
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA, USA
| | - Aniruddha Sahasrabuddhe
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Kathy Y Wei
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Edgar A Hodge
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Sarah Byron
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alfredo Quijano-Rubio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. .,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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40
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A General Workflow for Characterization of Nernstian Dyes and Their Effects on Bacterial Physiology. Biophys J 2019; 118:4-14. [PMID: 31810660 PMCID: PMC6950638 DOI: 10.1016/j.bpj.2019.10.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/08/2019] [Accepted: 10/18/2019] [Indexed: 12/22/2022] Open
Abstract
The electrical membrane potential (Vm) is one of the components of the electrochemical potential of protons across the biological membrane (proton motive force), which powers many vital cellular processes. Because Vm also plays a role in signal transduction, measuring it is of great interest. Over the years, a variety of techniques have been developed for the purpose. In bacteria, given their small size, Nernstian membrane voltage probes are arguably the favorite strategy, and their cytoplasmic accumulation depends on Vm according to the Nernst equation. However, a careful calibration of Nernstian probes that takes into account the tradeoffs between the ease with which the signal from the dye is observed and the dyes’ interactions with cellular physiology is rarely performed. Here, we use a mathematical model to understand such tradeoffs and apply the results to assess the applicability of the Thioflavin T dye as a Vm sensor in Escherichia coli. We identify the conditions in which the dye turns from a Vm probe into an actuator and, based on the model and experimental results, propose a general workflow for the characterization of Nernstian dye candidates.
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41
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Astaburuaga R, Quintanar Haro OD, Stauber T, Relógio A. A Mathematical Model of Lysosomal Ion Homeostasis Points to Differential Effects of Cl - Transport in Ca 2+ Dynamics. Cells 2019; 8:E1263. [PMID: 31623161 PMCID: PMC6848924 DOI: 10.3390/cells8101263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/11/2019] [Accepted: 10/13/2019] [Indexed: 12/20/2022] Open
Abstract
The establishment and maintenance of ion gradients between the interior of lysosomes and the cytosol are crucial for numerous cellular and organismal functions. Numerous ion transport proteins ensure the required variation in luminal concentrations of the different ions along the endocytic pathway to fit the needs of the organelles. Failures in keeping proper ion homeostasis have pathological consequences. Accordingly, several human diseases are caused by the dysfunction of ion transporters. These include osteopetrosis, caused by the dysfunction of Cl-/H+ exchange by the lysosomal transporter ClC-7. To better understand how chloride transport affects lysosomal ion homeostasis and how its disruption impinges on lysosomal function, we developed a mathematical model of lysosomal ion homeostasis including Ca2+ dynamics. The model recapitulates known biophysical properties of ClC-7 and enables the investigation of its differential activation kinetics on lysosomal ion homeostasis. We show that normal functioning of ClC-7 supports the acidification process, is associated with increased luminal concentrations of sodium, potassium, and chloride, and leads to a higher Ca2+ uptake and release. Our model highlights the role of ClC-7 in lysosomal acidification and shows the existence of differential Ca2+ dynamics upon perturbations of Cl-/H+ exchange and its activation kinetics, with possible pathological consequences.
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Affiliation(s)
- Rosario Astaburuaga
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, Corporate Member of the Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10115 Berlin, Germany.
- Medical Department of Hematology, Oncology and Tumor Immunology, Molekulares Krebsforschungzentrum (MKFZ), Charité-Universitätsmedizin Berlin, Corporate Member of the Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany.
| | - Orlando Daniel Quintanar Haro
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, Corporate Member of the Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10115 Berlin, Germany.
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, 14195 Berlin, Germany.
| | - Tobias Stauber
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, 14195 Berlin, Germany.
- Department of Human Medicine, Medical School Hamburg, 20457 Hamburg, Germany.
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, Corporate Member of the Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10115 Berlin, Germany.
- Medical Department of Hematology, Oncology and Tumor Immunology, Molekulares Krebsforschungzentrum (MKFZ), Charité-Universitätsmedizin Berlin, Corporate Member of the Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany.
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42
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Subach OM, Barykina NV, Anokhin KV, Piatkevich KD, Subach FV. Near-Infrared Genetically Encoded Positive Calcium Indicator Based on GAF-FP Bacterial Phytochrome. Int J Mol Sci 2019; 20:ijms20143488. [PMID: 31315229 PMCID: PMC6678319 DOI: 10.3390/ijms20143488] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 02/01/2023] Open
Abstract
A variety of genetically encoded calcium indicators are currently available for visualization of calcium dynamics in cultured cells and in vivo. Only one of them, called NIR-GECO1, exhibits fluorescence in the near-infrared region of the spectrum. NIR-GECO1 is engineered based on the near-infrared fluorescent protein mIFP derived from bacterial phytochromes. However, NIR-GECO1 has an inverted response to calcium ions and its excitation spectrum is not optimal for the commonly used 640 nm lasers. Using small near-infrared bacterial phytochrome GAF-FP and calmodulin/M13-peptide pair, we developed a near-infrared calcium indicator called GAF-CaMP2. In vitro, GAF-CaMP2 showed a positive response of 78% and high affinity (Kd of 466 nM) to the calcium ions. It had excitation and emission maxima at 642 and 674 nm, respectively. GAF-CaMP2 had a 2.0-fold lower brightness, 5.5-fold faster maturation and lower pH stability compared to GAF-FP in vitro. GAF-CaMP2 showed 2.9-fold higher photostability than smURFP protein. The GAF-CaMP2 fusion with sfGFP demonstrated a ratiometric response with a dynamic range of 169% when expressed in the cytosol of mammalian cells in culture. Finally, we successfully applied the ratiometric version of GAF-CaMP2 for the simultaneous visualization of calcium transients in three organelles of mammalian cells using four-color fluorescence microscopy.
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Affiliation(s)
- Oksana M Subach
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | | | - Konstantin V Anokhin
- P.K. Anokhin Institute of Normal Physiology, Moscow 125315, Russia
- Lomonosov Moscow State University, Moscow 119991, Russia
| | - Kiryl D Piatkevich
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Fedor V Subach
- National Research Center "Kurchatov Institute", Moscow 123182, Russia.
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43
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Slowly Reducible Genetically Encoded Green Fluorescent Indicator for In Vivo and Ex Vivo Visualization of Hydrogen Peroxide. Int J Mol Sci 2019; 20:ijms20133138. [PMID: 31252566 PMCID: PMC6650888 DOI: 10.3390/ijms20133138] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/19/2019] [Accepted: 06/25/2019] [Indexed: 12/16/2022] Open
Abstract
Hydrogen peroxide (H2O2) plays an important role in modulating cell signaling and homeostasis in live organisms. The HyPer family of genetically encoded indicators allows the visualization of H2O2 dynamics in live cells within a limited field of view. The visualization of H2O2 within a whole organism with a single cell resolution would benefit from a slowly reducible fluorescent indicator that integrates the H2O2 concentration over desired time scales. This would enable post hoc optical readouts in chemically fixed samples. Herein, we report the development and characterization of NeonOxIrr, a genetically encoded green fluorescent indicator, which rapidly increases fluorescence brightness upon reaction with H2O2, but has a low reduction rate. NeonOxIrr is composed of circularly permutated mNeonGreen fluorescent protein fused to the truncated OxyR transcription factor isolated from E. coli. When compared in vitro to a standard in the field, HyPer3 indicator, NeonOxIrr showed 5.9-fold higher brightness, 15-fold faster oxidation rate, 5.9-fold faster chromophore maturation, similar intensiometric contrast (2.8-fold), 2-fold lower photostability, and significantly higher pH stability both in reduced (pKa of 5.9 vs. ≥7.6) and oxidized states (pKa of 5.9 vs.≥ 7.9). When expressed in the cytosol of HEK293T cells, NeonOxIrr demonstrated a 2.3-fold dynamic range in response to H2O2 and a 44 min reduction half-time, which were 1.4-fold lower and 7.6-fold longer than those for HyPer3. We also demonstrated and characterized the NeonOxIrr response to H2O2 when the sensor was targeted to the matrix and intermembrane space of the mitochondria, nucleus, cell membranes, peroxisomes, Golgi complex, and endoplasmic reticulum of HEK293T cells. NeonOxIrr could reveal endogenous reactive oxygen species (ROS) production in HeLa cells induced with staurosporine but not with thapsigargin or epidermal growth factor. In contrast to HyPer3, NeonOxIrr could visualize optogenetically produced ROS in HEK293T cells. In neuronal cultures, NeonOxIrr preserved its high 3.2-fold dynamic range to H2O2 and slow 198 min reduction half-time. We also demonstrated in HeLa cells that NeonOxIrr preserves a 1.7-fold ex vivo dynamic range to H2O2 upon alkylation with N-ethylmaleimide followed by paraformaldehyde fixation. The same alkylation-fixation procedure in the presence of NP-40 detergent allowed ex vivo detection of H2O2 with 1.5-fold contrast in neuronal cultures and in the cortex of the mouse brain. The slowly reducible H2O2 indicator NeonOxIrr can be used for both the in vivo and ex vivo visualization of ROS. Expanding the family of fixable indicators may be a promising strategy to visualize biological processes at a single cell resolution within an entire organism.
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Zhang X, Chen L, Lim KH, Gonuguntla S, Lim KW, Pranantyo D, Yong WP, Yam WJT, Low Z, Teo WJ, Nien HP, Loh QW, Soh S. The Pathway to Intelligence: Using Stimuli-Responsive Materials as Building Blocks for Constructing Smart and Functional Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1804540. [PMID: 30624820 DOI: 10.1002/adma.201804540] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/09/2018] [Indexed: 05/22/2023]
Abstract
Systems that are intelligent have the ability to sense their surroundings, analyze, and respond accordingly. In nature, many biological systems are considered intelligent (e.g., humans, animals, and cells). For man-made systems, artificial intelligence is achieved by massively sophisticated electronic machines (e.g., computers and robots operated by advanced algorithms). On the other hand, freestanding materials (i.e., not tethered to a power supply) are usually passive and static. Hence, herein, the question is asked: can materials be fabricated so that they are intelligent? One promising approach is to use stimuli-responsive materials; these "smart" materials use the energy supplied by a stimulus available from the surrounding for performing a corresponding action. After decades of research, many interesting stimuli-responsive materials that can sense and perform smart functions have been developed. Classes of functions discussed include practical functions (e.g., targeting and motion), regulatory functions (e.g., self-regulation and amplification), and analytical processing functions (e.g., memory and computing). The pathway toward creating truly intelligent materials can involve incorporating a combination of these different types of functions into a single integrated system by using stimuli-responsive materials as the basic building blocks.
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Affiliation(s)
- Xuan Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Linfeng Chen
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Kang Hui Lim
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Spandhana Gonuguntla
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Kang Wen Lim
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Dicky Pranantyo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wai Pong Yong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wei Jian Tyler Yam
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Zhida Low
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wee Joon Teo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Hao Ping Nien
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Qiao Wen Loh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Siowling Soh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
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Jennings ML. Carriers, exchangers, and cotransporters in the first 100 years of the Journal of General Physiology. J Gen Physiol 2018; 150:1063-1080. [PMID: 30030301 PMCID: PMC6080889 DOI: 10.1085/jgp.201812078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Jennings reviews the many contributions of JGP articles to our current understanding of solute transporter mechanisms. Transporters, pumps, and channels are proteins that catalyze the movement of solutes across membranes. The single-solute carriers, coupled exchangers, and coupled cotransporters that are collectively known as transporters are distinct from conductive ion channels, water channels, and ATP-hydrolyzing pumps. The main conceptual framework for studying transporter mechanisms is the alternating access model, which comprises substrate binding and release events on each side of the permeability barrier and translocation events involving conformational changes between inward-facing and outward-facing conformational states. In 1948, the Journal of General Physiology began to publish work that focused on the erythrocyte glucose transporter—the first transporter to be characterized kinetically—followed by articles on the rates, stoichiometries, asymmetries, voltage dependences, and regulation of coupled exchangers and cotransporters beginning in the 1960s. After the dawn of cDNA cloning and sequencing in the 1980s, heterologous expression systems and site-directed mutagenesis allowed identification of the functional roles of specific amino acid residues. In the past two decades, structures of transport proteins have made it possible to propose specific models for transporter function at the molecular level. Here, we review the contribution of JGP articles to our current understanding of solute transporter mechanisms. Whether the topic has been kinetics, energetics, regulation, mutagenesis, or structure-based modeling, a common feature of these articles has been a quantitative, mechanistic approach, leading to lasting insights into the functions of transporters.
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Affiliation(s)
- Michael L Jennings
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR
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Pardini FM, Faccia PA, Pardini OR, Amalvy JI. Thermal and pH dual responsive polyurethane/2-(diisopropylamino)ethyl methacrylate hybrids: Synthesis, characterization, and swelling behavior. INTERNATIONAL JOURNAL OF POLYMER ANALYSIS AND CHARACTERIZATION 2018. [DOI: 10.1080/1023666x.2017.1416998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Francisco M. Pardini
- Grupo (Nano) Materiales Poliméricos, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CCT La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Paula A. Faccia
- Grupo (Nano) Materiales Poliméricos, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CCT La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Oscar R. Pardini
- Grupo (Nano) Materiales Poliméricos, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CCT La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), La Plata, Argentina
| | - Javier I. Amalvy
- Grupo (Nano) Materiales Poliméricos, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CCT La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), La Plata, Argentina
- Facultad Regional La Plata, Centro de Investigación y Desarrollo en Ciencia y Tecnología de Materiales (CITEMA), Universidad Tecnológica Nacional, Berisso, Argentina
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Woldemichael T, Rosania GR. The physiological determinants of drug-induced lysosomal stress resistance. PLoS One 2017; 12:e0187627. [PMID: 29117253 PMCID: PMC5678708 DOI: 10.1371/journal.pone.0187627] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/03/2017] [Indexed: 01/01/2023] Open
Abstract
Many weakly basic, lipophilic drugs accumulate in lysosomes and exert complex, pleiotropic effects on organelle structure and function. Thus, modeling how perturbations of lysosomal physiology affect the maintenance of lysosomal ion homeostasis is necessary to elucidate the key factors which determine the toxicological effects of lysosomotropic agents, in a cell-type dependent manner. Accordingly, a physiologically-based mathematical modeling and simulation approach was used to explore the dynamic, multi-parameter phenomenon of lysosomal stress. With this approach, parameters that are either directly involved in lysosomal ion transportation or lysosomal morphology were transiently altered to investigate their downstream effects on lysosomal physiology reflected by the changes they induce in lysosomal pH, chloride, and membrane potential. In addition, combinations of parameters were simultaneously altered to assess which parameter was most critical for recovery of normal lysosomal physiology. Lastly, to explore the relationship between organelle morphology and induced stress, we investigated the effects of parameters controlling organelle geometry on the restoration of normal lysosomal physiology following a transient perturbation. Collectively, our results indicate a key, interdependent role of V-ATPase number and membrane proton permeability in lysosomal stress tolerance. This suggests that the cell-type dependent regulation of V-ATPase subunit expression and turnover, together with the proton permeability properties of the lysosomal membrane, is critical to understand the differential sensitivity or resistance of different cell types to the toxic effects of lysosomotropic drugs.
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Affiliation(s)
- Tehetina Woldemichael
- Biophysics Program, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gus R. Rosania
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Junghänel S, Karczewski S, Bäcker S, Knauer SK, Schmuck C. A Systematic Structure-Activity Study of a New Type of Small Peptidic Transfection Vector Reveals the Importance of a Special Oxo-Anion-Binding Motif for Gene Delivery. Chembiochem 2017; 18:2268-2279. [PMID: 28914486 DOI: 10.1002/cbic.201700433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 12/16/2022]
Abstract
We discovered a new class of artificial peptidic transfection vectors based on an artificial anion-binding motif, the guanidiniocarbonylpyrrole (GCP) cation. This new type of vector is surprisingly smaller than traditional systems, and our previous work suggested that the GCP group was important for promoting critical endosomal escape. We now present here a systematic comparison of similar DNA ligands featuring our GCP oxo-anion-binding motif with DNA ligands only consisting of naturally occurring amino acids. Structure-activity studies showed that the artificial binding motif clearly outperformed natural amino acids such as histidine, lysine, and arginine. It improved the ability to shuttle foreign genetic material into cells, yet successfully mediated endosomal escape. Also, plasmids that were complexed by our artificial ligands were stabilized against cytosolic degradation to some extent. This resulted in the successful expression of plasmid information (comparable to gold standards such as polyethyleneimine). Hence, our study clearly demonstrates the importance of the tailor-made GCP anion-binding site for efficient gene transfection.
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Affiliation(s)
- Sandra Junghänel
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Sarah Karczewski
- Institute of Molecular Biology, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Sandra Bäcker
- Institute of Molecular Biology, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Shirley K Knauer
- Institute of Molecular Biology, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
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Zhao Y, Houston ZH, Simpson JD, Chen L, Fletcher NL, Fuchs AV, Blakey I, Thurecht KJ. Using Peptide Aptamer Targeted Polymers as a Model Nanomedicine for Investigating Drug Distribution in Cancer Nanotheranostics. Mol Pharm 2017; 14:3539-3549. [DOI: 10.1021/acs.molpharmaceut.7b00560] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yongmei Zhao
- Centre for Advanced Imaging,
Australian Institute for Bioengineering and Nanotechnology, and ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Queensland, Brisbane, 4072, Australia
| | - Zachary H. Houston
- Centre for Advanced Imaging,
Australian Institute for Bioengineering and Nanotechnology, and ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Queensland, Brisbane, 4072, Australia
| | - Joshua D. Simpson
- Centre for Advanced Imaging,
Australian Institute for Bioengineering and Nanotechnology, and ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Queensland, Brisbane, 4072, Australia
| | - Liyu Chen
- Centre for Advanced Imaging,
Australian Institute for Bioengineering and Nanotechnology, and ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Queensland, Brisbane, 4072, Australia
| | - Nicholas L. Fletcher
- Centre for Advanced Imaging,
Australian Institute for Bioengineering and Nanotechnology, and ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Queensland, Brisbane, 4072, Australia
| | - Adrian V. Fuchs
- Centre for Advanced Imaging,
Australian Institute for Bioengineering and Nanotechnology, and ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Queensland, Brisbane, 4072, Australia
| | - Idriss Blakey
- Centre for Advanced Imaging,
Australian Institute for Bioengineering and Nanotechnology, and ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Queensland, Brisbane, 4072, Australia
| | - Kristofer J. Thurecht
- Centre for Advanced Imaging,
Australian Institute for Bioengineering and Nanotechnology, and ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Queensland, Brisbane, 4072, Australia
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50
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Zhao Y, Li X, Zhao X, Yang Y, Li H, Zhou X, Yuan W. Asymmetrical Polymer Vesicles for Drug delivery and Other Applications. Front Pharmacol 2017; 8:374. [PMID: 28676761 PMCID: PMC5476746 DOI: 10.3389/fphar.2017.00374] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/30/2017] [Indexed: 11/28/2022] Open
Abstract
Scientists have been attracted by polymersomes as versatile drug delivery systems since the last two decades. Polymersomes have the potential to be versatile drug delivery systems because of their tunable membrane formulations, stabilities in vivo, various physicochemical properties, controlled release mechanisms, targeting abilities, and capacities to encapsulate a wide range of drugs and other molecules. Asymmetrical polymersomes are nano- to micro-sized polymeric capsules with asymmetrical membranes, which means, they have different outer and inner coronas so that they can exhibit better endocytosis rate and endosomal escape ability than other polymeric systems with symmetrical membranes. Hence, asymmetrical polymersomes are highly promising as self-assembled nano-delivery systems in the future for in vivo therapeutics delivery and diagnostic imaging applications. In this review, we prepared a summary about recent research progresses of asymmetrical polymersomes in the following aspects: synthesis, preparation, applications in drug delivery and others.
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Affiliation(s)
- Yi Zhao
- School of Pharmacy, Shanghai Jiao Tong UniversityShanghai, China
| | - Xiaoming Li
- School of Pharmacy, Shanghai Jiao Tong UniversityShanghai, China
| | - Xiaotian Zhao
- School of Pharmacy, Shanghai Jiao Tong UniversityShanghai, China
| | - Yunqi Yang
- School of Pharmacy, Shanghai Jiao Tong UniversityShanghai, China
| | - Hui Li
- School of Medicine, University of California, San FranciscoSan Francisco, CA, United States
| | - Xinbo Zhou
- Laboratory of Computer-Aided Drug Design and Discovery, Beijing Institute of Pharmacology and ToxicologyBeijing, China
| | - Weien Yuan
- School of Pharmacy, Shanghai Jiao Tong UniversityShanghai, China
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