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Sánchez-Vargas J, Valdés-Parada FJ, Peraza-Reyes L, Lasseux D, Trujillo-Roldán MA. Flow modeling and structural characterization in fungal pellets. J Theor Biol 2024; 590:111853. [PMID: 38768893 DOI: 10.1016/j.jtbi.2024.111853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/11/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024]
Abstract
Fungal pellets are hierarchical systems that can be found in an ample variety of applications. Modeling transport phenomena in this type of systems is a challenging but necessary task to provide knowledge-based processes that improve the outcome of their biotechnological applications. In this work, an upscaled model for total mass and momentum transport in fungal pellets is implemented and analyzed, using elements of the volume averaging and adjoint homogenization methods departing from the governing equations at the microscale in the intracellular and extracellular phases. The biomass is assumed to be composed of a non-Newtonian fluid and the organelles impervious to momentum transport are modeled as a rigid solid phase. The upscaled equations contain effective-medium coefficients, which are predicted from the solution of adjoint closure problems in a three-dimensional periodic domains representative of the microstructure. The construction of these domains was performed for Laccaria trichodermophora based on observations of actual biological structures. The upscaled model was validated with direct numerical simulations in homogeneous portions of the pellets core. It is shown that no significant differences are observed when the dolipores are open or closed to fluid flow. By comparing the predictions of the average velocity in the extracellular phase resulting from the upscaled model with those from the classical Darcy equation (i.e., assuming that the biomass is a solid phase) the contribution of the intracellular fluid phase was evidenced. This work sets the foundations for further studies dedicated to transport phenomena in this type of systems.
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Affiliation(s)
- J Sánchez-Vargas
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico; Posgrado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico
| | - F J Valdés-Parada
- División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, 09340, CDMX, Mexico
| | - L Peraza-Reyes
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico
| | - D Lasseux
- University of Bordeaux, CNRS, Bordeaux INP, I2M, UMR 5295, Bordeaux, F-33400, Talence, France
| | - M A Trujillo-Roldán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico; Departamento de Bionanotecnología, Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico.
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2
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Sleigh JN, Mattedi F, Richter S, Annuario E, Ng K, Steinmark IE, Ivanova I, Darabán IL, Joshi PP, Rhymes ER, Awale S, Yahioglu G, Mitchell JC, Suhling K, Schiavo G, Vagnoni A. Age-specific and compartment-dependent changes in mitochondrial homeostasis and cytoplasmic viscosity in mouse peripheral neurons. Aging Cell 2024:e14250. [PMID: 38881280 DOI: 10.1111/acel.14250] [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: 10/24/2023] [Revised: 04/26/2024] [Accepted: 05/20/2024] [Indexed: 06/18/2024] Open
Abstract
Mitochondria are dynamic bioenergetic hubs that become compromised with age. In neurons, declining mitochondrial axonal transport has been associated with reduced cellular health. However, it is still unclear to what extent the decline of mitochondrial transport and function observed during ageing are coupled, and if somal and axonal mitochondria display compartment-specific features that make them more susceptible to the ageing process. It is also not known whether the biophysical state of the cytoplasm, thought to affect many cellular functions, changes with age to impact mitochondrial trafficking and homeostasis. Focusing on the mouse peripheral nervous system, we show that age-dependent decline in mitochondrial trafficking is accompanied by reduction of mitochondrial membrane potential and intramitochondrial viscosity, but not calcium buffering, in both somal and axonal mitochondria. Intriguingly, we observe a specific increase in cytoplasmic viscosity in the neuronal cell body, where mitochondria are most polarised, which correlates with decreased cytoplasmic diffusiveness. Increasing cytoplasmic crowding in the somatic compartment of DRG neurons grown in microfluidic chambers reduces mitochondrial axonal trafficking, suggesting a mechanistic link between the regulation of cytoplasmic viscosity and mitochondrial dynamics. Our work provides a reference for studying the relationship between neuronal mitochondrial homeostasis and the viscoelasticity of the cytoplasm in a compartment-dependent manner during ageing.
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Affiliation(s)
- James N Sleigh
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
| | - Francesca Mattedi
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Sandy Richter
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Emily Annuario
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Kristal Ng
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - Iveta Ivanova
- Department of Physics, King's College London, London, UK
| | - István L Darabán
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Parth P Joshi
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Elena R Rhymes
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
| | - Shirwa Awale
- Department of Physics, King's College London, London, UK
| | - Gokhan Yahioglu
- Antikor Biopharma Ltd, Stevenage Bioscience Catalyst, Stevenage, UK
| | - Jacqueline C Mitchell
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Klaus Suhling
- Department of Physics, King's College London, London, UK
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
| | - Alessio Vagnoni
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MIA-Portugal, Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
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3
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Bernardi M, Cardarelli F. Phasor identifier: A cloud-based analysis of phasor-FLIM data on Python notebooks. BIOPHYSICAL REPORTS 2023; 3:100135. [PMID: 38053971 PMCID: PMC10694583 DOI: 10.1016/j.bpr.2023.100135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023]
Abstract
This paper introduces an innovative approach utilizing Google Colaboratory for the versatile analysis of phasor fluorescence lifetime imaging microscopy (FLIM) data collected from various samples (e.g., cuvette, cells, tissues) and in various input file formats. In fact, phasor-FLIM widespread adoption has been hampered by complex instrumentation and data analysis requirements. We mean to make advanced FLIM analysis more accessible to researchers through a cloud-based solution that 1) harnesses robust computational resources, 2) eliminates hardware limitations, and 3) supports both CPU and GPU processing. We envision a paradigm shift in FLIM data accessibility and potential, aligning with the evolving field of artificial intelligence-driven FLIM analysis. This approach simplifies FLIM data handling and opens doors for diverse applications, from studying cellular metabolism to investigating drug encapsulation, benefiting researchers across multiple domains. The comparative analysis of freely distributed FLIM tools highlights the unique advantages of this approach in terms of adaptability, scalability, and open-source nature.
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4
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Lin B, Li Z, Lin Y, Shu Y, Wang J. Evaluation of intracellular lipid droplets viscosity by a probe with high fluorescence quantum yield. Anal Chim Acta 2023; 1279:341776. [PMID: 37827674 DOI: 10.1016/j.aca.2023.341776] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Lipid droplets (LDs) are an important organelle as the main energy storage site in cells. LDs viscosity controls the material and energy exchange between it and other organelles. Furthermore, the LDs metabolic abnormalities, cell dysfunction, some diseases may be attributed to the singular LDs viscosity. Currently, the fluorescent probes for sensing the variations of LDs viscosity are still scarce and expose some drawbacks of low fluorescence quantum yield, low sensitivity and LDs polarity interference. Thus, the development of high performance probes is significant to detect LDs viscosity. RESULTS We hereby provide a lipophilic fluorescent probe (TPE-BET) with high fluorescence quantum yield (Φf, 0.91 in glycerol) for imaging LDs viscosity in living cells. With the increase of viscosity from 0.54 cp to 934 cp, the fluorescence at λex/λem = 405/520 nm and the fluorescence quantum yield of TPE-BET linearly increased by 64.9 and 128.5 folds, respectively. Meanwhile, the outstanding LDs staining capability of TPE-BET may provide a high spatial resolution for LDs imaging. The cell imaging of TPE-BET not only successfully observed the viscosity variations of LDs in cell stress models, e.g., ferroptosis, inflammation and mitophagy, but also revealed the increased viscosity and extracellular delivery of LDs in heavy metal cell injury models (Hg/As) for the first time, which may supply concrete evidence for understanding the structure and function of LDs. SIGNIFICANCE This represents a new fluorescent probe TPE-BET with high fluorescence quantum yield for imaging LDs viscosity, which may decrease the dose of probe and excitation light intensity along with the improvement on signal noise ratio (S/N). The imaging results of TPE-BET clarified that LDs viscosity may be an appraisal index on cell differentiation, state evaluation and drug screening.
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Affiliation(s)
- Bo Lin
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Zhenru Li
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Yanna Lin
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Yang Shu
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China.
| | - Jianhua Wang
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China.
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5
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Shi Y, Liu J, Liu Y, Quan H, Li B, Lu H, Ding H, Yu Z, Han J. Detection of breast cancer cells by a near-infrared fluorescent probe targeting mitochondrial viscosity. Heliyon 2023; 9:e18704. [PMID: 37560648 PMCID: PMC10407741 DOI: 10.1016/j.heliyon.2023.e18704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/11/2023] Open
Abstract
Monitoring abnormal viscosity in biological systems is important for basic research and clinical applications. Fluorescence imaging technology is adaptable for the visualization of tumor tissues due to its comprehensive features. However, fluorescence detection of intracellular viscosity in clinical samples remains challenging. We developed a promising near-infrared fluorescent probe, M556, for viscosity measurement. M556, which targets mitochondria, was successfully applied to monitor the mitochondrial viscosity in living cells. Furthermore, M556 was demonstrated to effectively discriminate tumors from normal tissues in a mouse tumor model and in clinical specimens from breast cancer patients, thus indicating the potential perioperative use of this probe by clinicians to assist with biopsy procedures.
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Affiliation(s)
- Yu Shi
- Department of Breast Cancer, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Junjun Liu
- Department of Breast Cancer, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yingying Liu
- Department of Physiology and Pathophysiology, Health Science Center, Peking University, Beijing 100191, China
| | - Hong Quan
- Department of Breast Cancer, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Bo Li
- Department of Breast Cancer, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Haili Lu
- Department of Breast Cancer, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Hanzhi Ding
- Department of Breast Cancer, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Zuoren Yu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jing Han
- Department of Breast Cancer, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
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6
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Trosel Y, Gregory LP, Booth VK, Yethiraj A. Diffusion NMR and Rheology of a Model Polymer in Bacterial Cell Lysate Crowders. Biomacromolecules 2023. [PMID: 37216308 DOI: 10.1021/acs.biomac.2c01534] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The intracellular milieu is crowded and heterogeneous, and this can have profound consequences for biomolecule motions and biochemical kinetics. Macromolecular crowding has been traditionally studied in artificial crowders like Ficoll and dextran or globular proteins such as bovine serum albumin. It is, however, not clear if the effects of artificial crowders on such phenomena are the same as the crowding that is experienced in a heterogeneous biological environment. Bacterial cells, for example, are composed of heterogeneous biomolecules with different sizes, shapes, and charges. Using crowders composed of one of three different pretreatments of bacterial cell lysate (unmanipulated, ultracentrifuged, and anion exchanged), we examine the effects of crowding on the diffusivity of a model polymer. We measure the translational diffusivity, via diffusion NMR, of the test polymer polyethylene glycol (PEG) in these bacterial cell lysates. We show that the small (Rg ∼ 5 nm) test polymer shows a modest decrease in self-diffusivity with increasing crowder concentration for all lysate treatments. The corresponding self-diffusivity decrease in the artificial Ficoll crowder is much more pronounced. Moreover, a comparison of the rheological response of biological and artificial crowders shows that while the artificial crowder Ficoll exhibits a Newtonian response even at high concentrations, the bacterial cell lysate is markedly non-Newtonian; it behaves like a shear-thinning fluid with a yield stress. While at any concentration the rheological properties are sensitive to both lysate pretreatment and batch-to-batch variations, the PEG diffusivity is nearly unaffected by the type of lysate pretreatment.
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Affiliation(s)
- Yanitza Trosel
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada
| | - Liam P Gregory
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada
| | - Valerie K Booth
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada
| | - Anand Yethiraj
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada
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7
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Lee S, Jung I, Lee S, Shin J, Cho E, Jung S, Ih S, Kim YG, Hong S, Choi YL, Park S. Plasmonic-Magnetic Active Nanorheology for Intracellular Viscosity. NANO LETTERS 2023; 23:2031-2038. [PMID: 36695563 DOI: 10.1021/acs.nanolett.2c04761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We demonstrate active plasmonic systems where plasmonic signals are repeatedly modulated by changing the orientation of nanoprobes under an external magnetic field, which is a prerequisite for in situ active nanorheology in intracellular viscosity measurements. Au/Ni/Au nanorods act as "nanotransmitters", which transmit the mechanical motion of nanorods to an electromagnetic radiation signal as a periodic sine function. This fluctuating optical response is transduced to frequency peaks via Fourier transform surface plasmon resonance (FTSPR). As a driving frequency of the external magnetic field applied to the Au/Ni/Au nanorods increases and reaches above a critical threshold, there is a transition from the synchronous motion of nanorods to asynchronous responses, leading to the disappearance of the FTSPR peak, which allows us to measure the local viscosity of the complex fluids. Using this ensemble-based method with plasmonic functional nanomaterials, we measure the intracellular viscosity of cancer cells and normal cells in a reliable and reproducible manner.
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Affiliation(s)
- Sungwoo Lee
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
- Institute of Basic Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Insub Jung
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
- Institute of Basic Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Soohyun Lee
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Junghyun Shin
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University (SNU), Seoul 08826, Republic of Korea
| | - Eunbyeol Cho
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Sangbaek Jung
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Seongkeun Ih
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Yang-Gyun Kim
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Seunghun Hong
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University (SNU), Seoul 08826, Republic of Korea
| | - Yoon-La Choi
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University (SKKU), Seoul 06355, Republic of Korea
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Sungho Park
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
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8
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Kang YG, Canoy RJE, Jang Y, Santos ARMP, Son I, Kim BM, Park Y. Optical coherence microscopy with a split-spectrum image reconstruction method for temporal-dynamics contrast-based imaging of intracellular motility. BIOMEDICAL OPTICS EXPRESS 2023; 14:577-592. [PMID: 36874497 PMCID: PMC9979675 DOI: 10.1364/boe.478264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Biomedical researchers use optical coherence microscopy (OCM) for its high resolution in real-time label-free tomographic imaging. However, OCM lacks bioactivity-related functional contrast. We developed an OCM system that can measure changes in intracellular motility (indicating cellular process states) via pixel-wise calculations of intensity fluctuations from metabolic activity of intracellular components. To reduce image noise, the source spectrum is split into five using Gaussian windows with 50% of the full bandwidth. The technique verified that F-actin fiber inhibition by Y-27632 reduces intracellular motility. This finding could be used to search for other intracellular-motility-associated therapeutic strategies for cardiovascular diseases.
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Affiliation(s)
- Yong Guk Kang
- BK21 Four Institute of Precision Public Health, Korea University, Seoul 02841, Republic of Korea
- These authors contributed equally to this work
| | - Raymart Jay E. Canoy
- Department of Biomicro System Technology, College of Engineering, Korea University, Seoul 02841, Republic of Korea
- These authors contributed equally to this work
| | - Yongjun Jang
- Department of Biomedical Science, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Ana Rita M. P. Santos
- Department of Biomedical Science, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Inwoo Son
- Department of Biomedical Science, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Beop-Min Kim
- BK21 Four Institute of Precision Public Health, Korea University, Seoul 02841, Republic of Korea
- Department of Biomedical Engineering, College of Health Science, Korea University, Seoul 02841, Republic of Korea
| | - Yongdoo Park
- Department of Biomedical Science, College of Medicine, Korea University, Seoul 02841, Republic of Korea
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9
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Mondal S, Das S, Swamy MJ. Macromolecular Crowding Significantly Affects the Conformational Features and Carbohydrate Binding Properties of CIA17, a PP2-Type Lectin from Coccinia indica. Biochemistry 2022; 61:2344-2357. [PMID: 36200563 DOI: 10.1021/acs.biochem.2c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of macromolecular crowding on the conformational features and carbohydrate binding properties of CIA17, a PP2-type lectin, was investigated employing polymeric dextrans D6, D40, and D70 (Mr ∼ 6, 40, and 70 kDa, respectively) as crowders. While the secondary structure of CIA17 was significantly affected by D6, with a considerable decrease in the number of β-sheets and β-turns with a corresponding increase in the number of unordered structures, relatively smaller changes were induced by D40 and D70. However, differential scanning calorimetry (DSC) studies revealed that the thermal stability of the protein remains unchanged in the presence of crowders. While the larger dextrans, D70 and D40, induced modest quenching (∼10%) of the protein fluorescence by a static pathway, the smaller D6 induced a higher degree of quenching (37%), which involved both static and collisional quenching processes. The results of fluorescence correlation spectroscopy measurements together with DSC studies suggested that CIA17 forms larger oligomers in the presence of D40 and D70 but D6 prevents the formation of higher-order oligomers. The association constant for the CIA17-chitooligosaccharide interaction increased by ∼30% and 160% in the presence of D40 and D70, respectively, but decreased by ∼30% in the presence of D6. The higher binding affinity can be attributed to the excluded volume effect, i.e., an increased effective concentration of the protein in the presence of D40 and D70, whereas D6, being smaller, possibly penetrates into the protein interior, disrupting the water structure around the protein and also inducing conformational changes, resulting in weaker binding. These observations demonstrate that molecular crowding significantly affects the carbohydrate binding characteristics of lectins, which can modulate their physiological function.
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Affiliation(s)
- Saradamoni Mondal
- School of Chemistry, University of Hyderabad, Hyderabad500 046, India
| | - Somnath Das
- School of Chemistry, University of Hyderabad, Hyderabad500 046, India
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad500 046, India
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10
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Semenov AN, Gvozdev DA, Zlenko DV, Protasova EA, Khashimova AR, Parshina EY, Baizhumanov AA, Lotosh NY, Kim EE, Kononevich YN, Pakhomov AA, Selishcheva AA, Sluchanko NN, Shirshin EA, Maksimov EG. Modulation of Membrane Microviscosity by Protein-Mediated Carotenoid Delivery as Revealed by Time-Resolved Fluorescence Anisotropy. MEMBRANES 2022; 12:905. [PMID: 36295665 PMCID: PMC9609150 DOI: 10.3390/membranes12100905] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Carotenoids are potent antioxidants with a wide range of biomedical applications. However, their delivery into human cells is challenging and relatively inefficient. While the use of natural water-soluble carotenoproteins capable to reversibly bind carotenoids and transfer them into membranes is promising, the quantitative estimation of the delivery remains unclear. In the present work, we studied echinenone (ECN) delivery by cyanobacterial carotenoprotein AnaCTDH (C-terminal domain homolog of the Orange Carotenoid Protein from Anabaena), into liposome membranes labelled with BODIPY fluorescent probe. We observed that addition of AnaCTDH-ECN to liposomes led to the significant changes in the fast-kinetic component of the fluorescence decay curve, pointing on the dipole-dipole interactions between the probe and ECN within the membrane. It may serve as an indirect evidence of ECN delivery into membrane. To study the delivery in detail, we carried out molecular dynamics modeling of the localization of ECN within the lipid bilayer and calculate its orientation factor. Next, we exploited FRET to assess concentration of ECN delivered by AnaCTDH. Finally, we used time-resolved fluorescence anisotropy to assess changes in microviscosity of liposomal membranes. Incorporation of liposomes with β-carotene increased membrane microviscosity while the effect of astaxanthin and its mono- and diester forms was less pronounced. At temperatures below 30 °C addition of AnaCTDH-ECN increased membrane microviscosity in a concentration-dependent manner, supporting the protein-mediated carotenoid delivery mechanism. Combining all data, we propose FRET-based analysis and assessment of membrane microviscosity as potent approaches to characterize the efficiency of carotenoids delivery into membranes.
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Affiliation(s)
- Alexey N. Semenov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Danil A. Gvozdev
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Dmitry V. Zlenko
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Elena A. Protasova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Anastasia R. Khashimova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Evgenia Yu. Parshina
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Adil A. Baizhumanov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
| | - Natalia Yu. Lotosh
- National Research Center “Kurchatov Institute”, 1 Acad. Kurchatov Sq., Moscow 123182, Russia
| | - Eleonora E. Kim
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
| | - Yuriy N. Kononevich
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey A. Pakhomov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
- M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alla A. Selishcheva
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
- National Research Center “Kurchatov Institute”, 1 Acad. Kurchatov Sq., Moscow 123182, Russia
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology, Russian Academy of Sciences, 33 Leninsky Prospect, Moscow 119071, Russia
| | - Evgeny A. Shirshin
- Faculty of Physics, M.V. Lomonosov Moscow State University, 1-2 Leninskie Gory St., Moscow 119991, Russia
- Laboratory of Clinical Biophotonics, Biomedical Science and Technology Park, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, Moscow 119991, Russia
- Institute of Spectroscopy, Russian Academy of Sciences, 5 Fizicheskaya Str., Troitsk, Moscow 108840, Russia
| | - Eugene G. Maksimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory St., Moscow 119991, Russia
- Faculty of Physics, M.V. Lomonosov Moscow State University, 1-2 Leninskie Gory St., Moscow 119991, Russia
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11
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Śmigiel WM, Mantovanelli L, Linnik DS, Punter M, Silberberg J, Xiang L, Xu K, Poolman B. Protein diffusion in Escherichia coli cytoplasm scales with the mass of the complexes and is location dependent. SCIENCE ADVANCES 2022; 8:eabo5387. [PMID: 35960807 PMCID: PMC9374337 DOI: 10.1126/sciadv.abo5387] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/28/2022] [Indexed: 05/30/2023]
Abstract
We analyze the structure of the cytoplasm by performing single-molecule displacement mapping on a diverse set of native cytoplasmic proteins in exponentially growing Escherichia coli. We evaluate the method for application in small compartments and find that confining effects of the cell membrane affect the diffusion maps. Our analysis reveals that protein diffusion at the poles is consistently slower than in the center of the cell, i.e., to an extent greater than the confining effect of the cell membrane. We also show that the diffusion coefficient scales with the mass of the used probes, taking into account the oligomeric state of the proteins, while parameters such as native protein abundance or the number of protein-protein interactions do not correlate with the mobility of the proteins. We argue that our data paint the prokaryotic cytoplasm as a compartment with subdomains in which the diffusion of macromolecules changes with the perceived viscosity.
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Affiliation(s)
- Wojciech M. Śmigiel
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Luca Mantovanelli
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Dmitrii S. Linnik
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Michiel Punter
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Jakob Silberberg
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Limin Xiang
- Department of Chemistry, UC Berkeley, Stanley Hall, Berkeley, CA 94720, USA
| | - Ke Xu
- Department of Chemistry, UC Berkeley, Stanley Hall, Berkeley, CA 94720, USA
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
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12
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Mayank, Sindhu J, Singh A, Nayak N, Garg N, Kaur N, Singh N. Excited-State Intramolecular Hydrogen-Bonding-Assisted Restricted Rotation: A Mechanism for Monitoring Intracellular Viscosity and Distinguishing Malignant, Differentiating, and Apoptotic Cancer Cells. ACS APPLIED BIO MATERIALS 2021; 4:7532-7541. [DOI: 10.1021/acsabm.1c00769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mayank
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM’s NMIMS University, Vile Parle, Mumbai 400056, India
| | - Jayant Sindhu
- Department of Chemistry, COBS&H, CCS Haryana Agricultural University, Hisar 125004, India
| | - Ashutosh Singh
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh 175005, India
| | - Namyashree Nayak
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh 175005, India
| | - Neha Garg
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh 175005, India
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Navneet Kaur
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Narinder Singh
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
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13
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Welte H, Sinn P, Kovermann M. Fluorine NMR Spectroscopy Enables to Quantify the Affinity Between DNA and Proteins in Cell Lysate. Chembiochem 2021; 22:2973-2980. [PMID: 34390111 PMCID: PMC8596521 DOI: 10.1002/cbic.202100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/30/2021] [Indexed: 11/12/2022]
Abstract
The determination of the binding affinity quantifying the interaction between proteins and nucleic acids is of crucial interest in biological and chemical research. Here, we have made use of site-specific fluorine labeling of the cold shock protein from Bacillus subtilis, BsCspB, enabling to directly monitor the interaction with single stranded DNA molecules in cell lysate. High-resolution 19 F NMR spectroscopy has been applied to exclusively report on resonance signals arising from the protein under study. We have found that this experimental approach advances the reliable determination of the binding affinity between single stranded DNA molecules and its target protein in this complex biological environment by intertwining analyses based on NMR chemical shifts, signal heights, line shapes and simulations. We propose that the developed experimental platform offers a potent approach for the identification of binding affinities characterizing intermolecular interactions in native surroundings covering the nano-to-micromolar range that can be even expanded to in cell applications in future studies.
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Affiliation(s)
- Hannah Welte
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
| | - Pia Sinn
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
| | - Michael Kovermann
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
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14
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Köhn B, Schwarz P, Wittung-Stafshede P, Kovermann M. Impact of crowded environments on binding between protein and single-stranded DNA. Sci Rep 2021; 11:17682. [PMID: 34480058 PMCID: PMC8417293 DOI: 10.1038/s41598-021-97219-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/20/2021] [Indexed: 11/09/2022] Open
Abstract
The concept of Molecular Crowding depicts the high density of diverse molecules present in the cellular interior. Here, we determine the impact of low molecular weight and larger molecules on binding capacity of single-stranded DNA (ssDNA) to the cold shock protein B (CspB). Whereas structural features of ssDNA-bound CspB are fully conserved in crowded environments as probed by high-resolution NMR spectroscopy, intrinsic fluorescence quenching experiments reveal subtle changes in equilibrium affinity. Kinetic stopped-flow data showed that DNA-to-protein association is significantly retarded independent of choice of the molecule that is added to the solution, but dissociation depends in a nontrivial way on its size and chemical characteristics. Thus, for this DNA-protein interaction, excluded volume effect does not play the dominant role but instead observed effects are dictated by the chemical properties of the crowder. We propose that surrounding molecules are capable of specific modification of the protein's hydration shell via soft interactions that, in turn, tune protein-ligand binding dynamics and affinity.
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Affiliation(s)
- Birgit Köhn
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Patricia Schwarz
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany. .,Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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15
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Vo TN, Malo Pueyo J, Wahni K, Ezeriņa D, Bolduc J, Messens J. Prdx1 Interacts with ASK1 upon Exposure to H 2O 2 and Independently of a Scaffolding Protein. Antioxidants (Basel) 2021; 10:antiox10071060. [PMID: 34209102 PMCID: PMC8300624 DOI: 10.3390/antiox10071060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 01/02/2023] Open
Abstract
Hydrogen peroxide (H2O2) is a key redox signaling molecule that selectively oxidizes cysteines on proteins. It can accomplish this even in the presence of highly efficient and abundant H2O2 scavengers, peroxiredoxins (Prdxs), as it is the Prdxs themselves that transfer oxidative equivalents to specific protein thiols on target proteins via their redox-relay functionality. The first evidence of a mammalian cytosolic Prdx-mediated redox-relay—Prdx1 with the kinase ASK1—was presented a decade ago based on the outcome of a co-immunoprecipitation experiment. A second such redox-relay—Prdx2:STAT3—soon followed, for which further studies provided insights into its specificity, organization, and mechanism. The Prdx1:ASK1 redox-relay, however, has never undergone such a characterization. Here, we combine cellular and in vitro protein–protein interaction methods to investigate the Prdx1:ASK1 interaction more thoroughly. We show that, contrary to the Prdx2:STAT3 redox-relay, Prdx1 interacts with ASK1 at elevated H2O2 concentrations, and that this interaction can happen independently of a scaffolding protein. We also provide evidence of a Prdx2:ASK1 interaction, and demonstrate that it requires a facilitator that, however, is not annexin A2. Our results reveal that cytosolic Prdx redox-relays can be organized in different ways and yet again highlight the differentiated roles of Prdx1 and Prdx2.
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Affiliation(s)
- Trung Nghia Vo
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Julia Malo Pueyo
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Khadija Wahni
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Daria Ezeriņa
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Jesalyn Bolduc
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Correspondence:
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16
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Zheng A, Liu H, Gao X, Xu K, Tang B. A Mitochondrial-Targeting Near-Infrared Fluorescent Probe for Revealing the Effects of Hydrogen Peroxide And Heavy Metal Ions on Viscosity. Anal Chem 2021; 93:9244-9249. [PMID: 34156833 DOI: 10.1021/acs.analchem.1c01511] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As an important cell organelle, the mitochondrion has special viscosities, while abnormal mitochondrial viscosity is closely related to many diseases. Hydrogen peroxide (H2O2) is an active molecule related to the cell microenvironment, and its influence on mitochondrial viscosity is still not clear, so further investigation is needed. In addition, since excessive accumulation of heavy metal ions would lead to cells' dysfunction, the study of effect of excessive heavy metal ions on mitochondrial viscosity has not been reported. Herein, we designed and synthesized a mitochondrial-targeting near-infrared fluorescent probe (Mito-NV) for real-time in situ imaging and analysis of mitochondrial viscosity. Furthermore, the probe revealed that H2O2 can raise mitochondrial viscosity, while heavy metal ions reduce the viscosity. This work is of great significance for understanding the execution of mitochondrial functions and the occurrence and development of related diseases.
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Affiliation(s)
- Aishan Zheng
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P. R. China
| | - Han Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P. R. China
| | - Xiaonan Gao
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P. R. China
| | - Kehua Xu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P. R. China
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17
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Nie L, Nusantara AC, Damle VG, Sharmin R, Evans EPP, Hemelaar SR, van der Laan KJ, Li R, Perona Martinez FP, Vedelaar T, Chipaux M, Schirhagl R. Quantum monitoring of cellular metabolic activities in single mitochondria. SCIENCE ADVANCES 2021; 7:7/21/eabf0573. [PMID: 34138746 PMCID: PMC8133708 DOI: 10.1126/sciadv.abf0573] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/17/2021] [Indexed: 05/08/2023]
Abstract
Free radicals play a vital role in all kinds of biological processes including immune responses. However, free radicals have short lifetimes and are highly reactive, making them difficult to measure using current methods. Here, we demonstrate that relaxometry measurement, or T1, inherited from the field of diamond magnetometry can be used to detect free radicals in living cells with subcellular resolution. This quantum sensing technique is based on defects in diamond, which convert a magnetic signal into an optical signal, allowing nanoscale magnetic resonance measurements. We functionalized fluorescent nanodiamonds (FNDs) to target single mitochondria within macrophage cells to detect the metabolic activity. In addition, we performed measurements on single isolated mitochondria. We were able to detect free radicals generated by individual mitochondria in either living cells or isolated mitochondria after stimulation or inhibition.
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Affiliation(s)
- L Nie
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - A C Nusantara
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - V G Damle
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - R Sharmin
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - E P P Evans
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - S R Hemelaar
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - K J van der Laan
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - R Li
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - F P Perona Martinez
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - T Vedelaar
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - M Chipaux
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - R Schirhagl
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV Groningen, Netherlands.
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18
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Chen F, Bian M, Nahmou M, Myung D, Goldberg JL. Fusogenic liposome-enhanced cytosolic delivery of magnetic nanoparticles. RSC Adv 2021; 11:35796-35805. [PMID: 35492766 PMCID: PMC9043121 DOI: 10.1039/d1ra03094a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/16/2021] [Indexed: 12/19/2022] Open
Abstract
Fusogenic liposomes facilitate MNPs passage into the cytosol and enable direct contact between MNPs and organelles other than endosomes.
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Affiliation(s)
- Fang Chen
- Department of Ophthalmology, Spencer Center for Vision Research, Byers Eye Institute at Stanford University, Palo Alto, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Minjuan Bian
- Department of Ophthalmology, Spencer Center for Vision Research, Byers Eye Institute at Stanford University, Palo Alto, CA, 94304, USA
| | - Michael Nahmou
- Department of Ophthalmology, Spencer Center for Vision Research, Byers Eye Institute at Stanford University, Palo Alto, CA, 94304, USA
| | - David Myung
- Department of Ophthalmology, Spencer Center for Vision Research, Byers Eye Institute at Stanford University, Palo Alto, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Jeffrey L. Goldberg
- Department of Ophthalmology, Spencer Center for Vision Research, Byers Eye Institute at Stanford University, Palo Alto, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
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19
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Liu X, Chi W, Gómez‐Infante ADJ, Peña‐Cabrera E, Liu X, Chang Y. A Systematic Study on the Relationship Between Viscosity Sensitivity and
Temperature Dependency
of
BODIPY
Rotors. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xiao Liu
- Department of Chemistry Pohang University of Science and Technology Pohang 37673 Republic of Korea
- Center for Self‐assembly and Complexity Institute for Basic Science (IBS) Pohang 37673 Republic of Korea
| | - Weijie Chi
- Fluorescence Research Group Singapore University of Technology and Design Singapore 487372 Singapore
| | | | - Eduardo Peña‐Cabrera
- Departamento de Quimica DCNE Campus Guanajuato, Universidad de Guanajuato Guanajuato 36050 Mexico
| | - Xiaogang Liu
- Fluorescence Research Group Singapore University of Technology and Design Singapore 487372 Singapore
| | - Young‐Tae Chang
- Department of Chemistry Pohang University of Science and Technology Pohang 37673 Republic of Korea
- Center for Self‐assembly and Complexity Institute for Basic Science (IBS) Pohang 37673 Republic of Korea
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20
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Subcellular Location of Tirapazamine Reduction Dramatically Affects Aerobic but Not Anoxic Cytotoxicity. Molecules 2020; 25:molecules25214888. [PMID: 33105798 PMCID: PMC7660101 DOI: 10.3390/molecules25214888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
Hypoxia is an adverse prognostic feature of solid cancers that may be overcome with hypoxia-activated prodrugs (HAPs). Tirapazamine (TPZ) is a HAP which has undergone extensive clinical evaluation in this context and stimulated development of optimized analogues. However the subcellular localization of the oxidoreductases responsible for mediating TPZ-dependent DNA damage remains unclear. Some studies conclude only nuclear-localized oxidoreductases can give rise to radical-mediated DNA damage and thus cytotoxicity, whereas others identify a broader role for endoplasmic reticulum and cytosolic oxidoreductases, indicating the subcellular location of TPZ radical formation is not a critical requirement for DNA damage. To explore this question in intact cells we engineered MDA-231 breast cancer cells to express the TPZ reductase human NADPH: cytochrome P450 oxidoreductase (POR) harboring various subcellular localization sequences to guide this flavoenzyme to the nucleus, endoplasmic reticulum, cytosol or inner surface of the plasma membrane. We show that all POR variants are functional, with differences in rates of metabolism reflecting enzyme expression levels rather than intracellular TPZ concentration gradients. Under anoxic conditions, POR expression in all subcellular compartments increased the sensitivity of the cells to TPZ, but with a fall in cytotoxicity per unit of metabolism (termed ‘metabolic efficiency’) when POR is expressed further from the nucleus. However, under aerobic conditions a much larger increase in cytotoxicity was observed when POR was directed to the nucleus, indicating very high metabolic efficiency. Consequently, nuclear metabolism results in collapse of hypoxic selectivity of TPZ, which was further magnified to the point of reversing O2 dependence (oxic > hypoxic sensitivity) by employing a DNA-affinic TPZ analogue. This aerobic hypersensitivity phenotype was partially rescued by cellular copper depletion, suggesting the possible involvement of Fenton-like chemistry in generating short-range effects mediated by the hydroxyl radical. In addition, the data suggest that under aerobic conditions reoxidation strictly limits the TPZ radical diffusion range resulting in site-specific cytotoxicity. Collectively these novel findings challenge the purported role of intra-nuclear reductases in orchestrating the hypoxia selectivity of TPZ.
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21
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Topology Challenge for the Assessment of Living Cell Deposits with Shear Bulk Acoustic Biosensor. NANOMATERIALS 2020; 10:nano10102079. [PMID: 33096764 PMCID: PMC7589984 DOI: 10.3390/nano10102079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023]
Abstract
Shear bulk acoustic type of resonant biosensors, such as the quartz crystal microbalance (QCM), give access to label-free in-liquid analysis of surface interactions. The general understanding of the sensing principles was inherited from past developments in biofilms measurements and applied to cells while keeping the same basic assumptions. Thus, the biosensor readouts are still quite often described using 'mass' related terminology. This contribution aims to show that assessment of cell deposits with acoustic biosensors requires a deep understanding of the sensor transduction mechanism. More specifically, the cell deposits should be considered as a structured viscoelastic load and the sensor response depends on both material and topological parameters of the deposits. This shifts the paradigm of acoustic biosensor away from the classical mass loading perspective. As a proof of the concept, we recorded QCM frequency shifts caused by blood platelet deposits on a collagen surface under different rheological conditions and observed the final deposit shape with atomic force microscopy (AFM). The results vividly demonstrate that the frequency shift is highly impacted by the platelet topology on the bio-interface. We support our findings with numerical simulations of viscoelastic unstructured and structured loads in liquid. Both experimental and theoretical studies underline the complexity behind the frequency shift interpretation when acoustic biosensing is used with cell deposits.
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22
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Michels L, Gorelova V, Harnvanichvech Y, Borst JW, Albada B, Weijers D, Sprakel J. Complete microviscosity maps of living plant cells and tissues with a toolbox of targeting mechanoprobes. Proc Natl Acad Sci U S A 2020; 117:18110-18118. [PMID: 32669427 PMCID: PMC7395454 DOI: 10.1073/pnas.1921374117] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mechanical patterns control a variety of biological processes in plants. The microviscosity of cellular structures effects the diffusion rate of molecules and organelles, thereby affecting processes such as metabolism and signaling. Spatial variations in local viscosity are also generated during fundamental events in the cell life cycle. While crucial to a complete understanding of plant mechanobiology, resolving subcellular microviscosity patterns in plants has remained an unsolved challenge. We present an imaging microviscosimetry toolbox of molecular rotors that yield complete microviscosity maps of cells and tissues, specifically targeting the cytosol, vacuole, plasma membrane, and wall of plant cells. These boron-dipyrromethene (BODIPY)-based molecular rotors are rigidochromic by means of coupling the rate of an intramolecular rotation, which depends on the mechanics of their direct surroundings, with their fluorescence lifetime. This enables the optical mapping of fluidity and porosity patterns in targeted cellular compartments. We show how apparent viscosity relates to cell function in the root, how the growth of cellular protrusions induces local tension, and how the cell wall is adapted to perform actuation surrounding leaf pores. These results pave the way to the noninvasive micromechanical mapping of complex tissues.
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Affiliation(s)
- Lucile Michels
- Physical Chemistry and Soft Matter, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Vera Gorelova
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Yosapol Harnvanichvech
- Physical Chemistry and Soft Matter, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
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23
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Abstract
The disaccharide trehalose is accumulated in the cytoplasm of some organisms in response to harsh environmental conditions. Trehalose biosynthesis and accumulation are important for the survival of such organisms by protecting the structure and function of proteins and membranes. Trehalose affects the dynamics of proteins and water molecules in the bulk and the protein hydration shell. Enzyme catalysis and other processes dependent on protein dynamics are affected by the viscosity generated by trehalose, as described by the Kramers’ theory of rate reactions. Enzyme/protein stabilization by trehalose against thermal inactivation/unfolding is also explained by the viscosity mediated hindering of the thermally generated structural dynamics, as described by Kramers’ theory. The analysis of the relationship of viscosity–protein dynamics, and its effects on enzyme/protein function and other processes (thermal inactivation and unfolding/folding), is the focus of the present work regarding the disaccharide trehalose as the viscosity generating solute. Finally, trehalose is widely used (alone or in combination with other compounds) in the stabilization of enzymes in the laboratory and in biotechnological applications; hence, considering the effect of viscosity on catalysis and stability of enzymes may help to improve the results of trehalose in its diverse uses/applications.
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Vaippully R, Ramanujan V, Bajpai S, Roy B. Measurement of viscoelastic properties of the cellular cytoplasm using optically trapped Brownian probes. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:235101. [PMID: 32059195 DOI: 10.1088/1361-648x/ab76ac] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Measurement of the viscoelastic properties of a cell using microscopic tracer particles has been complicated given that the medium viscosity is dependent upon the size of the measurement probe leading to reliability issues. Further, a technique for direct calibration of optically trapped particles in vivo has been elusive due to the frequency dependence and spatial inhomogeneity of the cytoplasmic viscosity, and the requirement of accurate knowledge of the medium refractive index. Here, we employ a recent extension of Jeffery's model of viscoelasticity in the microscopic domain to fit the passive motional power spectra of micrometer-sized optically trapped particles embedded in a viscoelastic medium. We find excellent agreement between the 0 Hz viscosity in MCF7 cells and the typical values of viscosity in literature, between 2 to 16 mPa sec expected for the typical concentration of proteins inside the cytoplasmic solvent. This bypasses the dependence on probe size by relying upon small thermal displacements. Our measurements of the relaxation time also match values reported with magnetic tweezers, at about 0.1 s. Finally, we calibrate the optical tweezers and demonstrate the efficacy of the technique to the study of in vivo translational motion.
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25
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Ling T, Boyle KC, Zuckerman V, Flores T, Ramakrishnan C, Deisseroth K, Palanker D. High-speed interferometric imaging reveals dynamics of neuronal deformation during the action potential. Proc Natl Acad Sci U S A 2020; 117:10278-10285. [PMID: 32341158 PMCID: PMC7229674 DOI: 10.1073/pnas.1920039117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neurons undergo nanometer-scale deformations during action potentials, and the underlying mechanism has been actively debated for decades. Previous observations were limited to a single spot or the cell boundary, while movement across the entire neuron during the action potential remained unclear. Here we report full-field imaging of cellular deformations accompanying the action potential in mammalian neuron somas (-1.8 to 1.4 nm) and neurites (-0.7 to 0.9 nm), using high-speed quantitative phase imaging with a temporal resolution of 0.1 ms and an optical path length sensitivity of <4 pm per pixel. The spike-triggered average, synchronized to electrical recording, demonstrates that the time course of the optical phase changes closely matches the dynamics of the electrical signal. Utilizing the spatial and temporal correlations of the phase signals across the cell, we enhance the detection and segmentation of spiking cells compared to the shot-noise-limited performance of single pixels. Using three-dimensional (3D) cellular morphology extracted via confocal microscopy, we demonstrate that the voltage-dependent changes in the membrane tension induced by ionic repulsion can explain the magnitude, time course, and spatial features of the phase imaging. Our full-field observations of the spike-induced deformations shed light upon the electromechanical coupling mechanism in electrogenic cells and open the door to noninvasive label-free imaging of neural signaling.
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Affiliation(s)
- Tong Ling
- Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305;
- Department of Ophthalmology, Stanford University, Stanford, CA 94305
| | - Kevin C Boyle
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305;
| | - Valentina Zuckerman
- Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305
| | - Thomas Flores
- Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305
| | | | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | - Daniel Palanker
- Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305;
- Department of Ophthalmology, Stanford University, Stanford, CA 94305
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26
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Liu X, Chi W, Qiao Q, Kokate SV, Cabrera EP, Xu Z, Liu X, Chang YT. Molecular Mechanism of Viscosity Sensitivity in BODIPY Rotors and Application to Motion-Based Fluorescent Sensors. ACS Sens 2020; 5:731-739. [PMID: 32072803 DOI: 10.1021/acssensors.9b01951] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Viscosity in the intracellular microenvironment shows a significant difference in various organelles and is closely related to cellular processes. Such microviscosity in live cells is often mapped and quantified with fluorescent molecular rotors. To enable the rational design of viscosity-sensitive molecular rotors, it is critical to understand their working mechanisms. Herein, we systematically synthesized and investigated two sets of BODIPY-based molecular rotors to study the relationship between intramolecular motions and viscosity sensitivity. Through experimental and computational studies, two conformations (i.e., the planar and butterfly conformations) are found to commonly exist in BODIPY rotors. We demonstrate that the transformation energy barrier from the planar conformation to the butterfly conformation is strongly affected by the molecular structures of BODIPY rotors and plays a critical role in viscosity sensitivity. These findings enable rational structure modifications of BODIPY molecular rotors for highly effective protein detection and recognition.
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Affiliation(s)
- Xiao Liu
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 37673, Republic of Korea
| | - Weijie Chi
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore
| | - Qinglong Qiao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Siddhant V. Kokate
- Departamento de Quimica DCNE, Campus Guanajuato, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Eduardo Peña Cabrera
- Departamento de Quimica DCNE, Campus Guanajuato, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Zhaochao Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 37673, Republic of Korea
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27
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Hornak I, Rieger H. Stochastic Model of T Cell Repolarization during Target Elimination I. Biophys J 2020; 118:1733-1748. [PMID: 32130873 DOI: 10.1016/j.bpj.2020.01.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/16/2022] Open
Abstract
Cytotoxic T lymphocytes (T) and natural killer cells are the main cytotoxic killer cells of the human body to eliminate pathogen-infected or tumorigenic cells (i.e., target cells). Once a natural killer or T cell has identified a target cell, they form a tight contact zone, the immunological synapse (IS). One then observes a repolarization of the cell involving the rotation of the microtubule (MT) cytoskeleton and a movement of the MT organizing center (MTOC) to a position that is just underneath the plasma membrane at the center of the IS. Concomitantly, a massive relocation of organelles attached to MTs is observed, including the Golgi apparatus, lytic granules, and mitochondria. Because the mechanism of this relocation is still elusive, we devise a theoretical model for the molecular-motor-driven motion of the MT cytoskeleton confined between plasma membrane and nucleus during T cell polarization. We analyze different scenarios currently discussed in the literature, the cortical sliding and capture-shrinkage mechanisms, and compare quantitative predictions about the spatiotemporal evolution of MTOC position and MT cytoskeleton morphology with experimental observations. The model predicts the experimentally observed biphasic nature of the repositioning due to an interplay between MT cytoskeleton geometry and motor forces and confirms the dominance of the capture-shrinkage over the cortical sliding mechanism when the MTOC and IS are initially diametrically opposed. We also find that the two mechanisms act synergistically, thereby reducing the resources necessary for repositioning. Moreover, it turns out that the localization of dyneins in the peripheral supramolecular activation cluster facilitates their interaction with the MTs. Our model also opens a way to infer details of the dynein distribution from the experimentally observed features of the MT cytoskeleton dynamics. In a subsequent publication, we will address the issue of general initial configurations and situations in which the T cell established two ISs.
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Affiliation(s)
- Ivan Hornak
- Center for Biophysics (ZBP) and Department of Theoretical Physics, Saarland University, Saarbrücken, Germany
| | - Heiko Rieger
- Center for Biophysics (ZBP) and Department of Theoretical Physics, Saarland University, Saarbrücken, Germany.
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28
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Das N, Sen P. Size-dependent macromolecular crowding effect on the thermodynamics of protein unfolding revealed at the single molecular level. Int J Biol Macromol 2019; 141:843-854. [DOI: 10.1016/j.ijbiomac.2019.09.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 11/29/2022]
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29
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Rodríguez‐Sevilla P, Sanz‐Rodríguez F, Peláez RP, Delgado‐Buscalioni R, Liang L, Liu X, Jaque D. Upconverting Nanorockers for Intracellular Viscosity Measurements During Chemotherapy. ACTA ACUST UNITED AC 2019; 3:e1900082. [DOI: 10.1002/adbi.201900082] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/22/2019] [Indexed: 11/06/2022]
Affiliation(s)
| | - Francisco Sanz‐Rodríguez
- Fluorescence Imaging Group Departamento de Biología Facultad de CienciasUniversidad Autónoma de Madrid 28049 Madrid Spain
- Nanobiology GroupInstituto Ramón y Cajal de Investigación Sanitaria Hospital Ramón y Cajal. Ctra. De Colmenar Viejo Km. 9100 28034 Madrid Spain
| | - Raúl P. Peláez
- Departamento de Física Teórica de la Materia Condensada Facultad de CienciasUniversidad Autónoma de Madrid 28049 Madrid Spain
| | - Rafael Delgado‐Buscalioni
- Departamento de Física Teórica de la Materia Condensada Facultad de CienciasUniversidad Autónoma de Madrid 28049 Madrid Spain
| | - Liangliang Liang
- Department of ChemistryNational University of Singapore Science Drive 3 Singapore 117543 Singapore
| | - Xiaogang Liu
- Department of ChemistryNational University of Singapore Science Drive 3 Singapore 117543 Singapore
| | - Daniel Jaque
- Nanobiology GroupInstituto Ramón y Cajal de Investigación Sanitaria Hospital Ramón y Cajal. Ctra. De Colmenar Viejo Km. 9100 28034 Madrid Spain
- Fluorescence Imaging Group Departamento de Fisica de MaterialesUniversidad Autónoma de Madrid 28049 Madrid Spain
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30
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31
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Puchkov EO. Quantitative Methods for Single-Cell Analysis of Microorganisms. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719010120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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32
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Oscillatory fluid flow drives scaling of contraction wave with system size. Proc Natl Acad Sci U S A 2018; 115:10612-10617. [PMID: 30282737 DOI: 10.1073/pnas.1805981115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Flows over remarkably long distances are crucial to the functioning of many organisms, across all kingdoms of life. Coordinated flows are fundamental to power deformations, required for migration or development, or to spread resources and signals. A ubiquitous mechanism to generate flows, particularly prominent in animals and amoebas, is actomyosin cortex-driven mechanical deformations that pump the fluid enclosed by the cortex. However, it is unclear how cortex dynamics can self-organize to give rise to coordinated flows across the largely varying scales of biological systems. Here, we develop a mechanochemical model of actomyosin cortex mechanics coupled to a contraction-triggering, soluble chemical. The chemical itself is advected with the flows generated by the cortex-driven deformations of the tubular-shaped cell. The theoretical model predicts a dynamic instability giving rise to stable patterns of cortex contraction waves and oscillatory flows. Surprisingly, simulated patterns extend beyond the intrinsic length scale of the dynamic instability-scaling with system size instead. Patterns appear randomly but can be robustly generated in a growing system or by flow-generating boundary conditions. We identify oscillatory flows as the key for the scaling of contraction waves with system size. Our work shows the importance of active flows in biophysical models of patterning, not only as a regulating input or an emergent output, but also as a full part of a self-organized machinery. Contractions and fluid flows are observed in all kinds of organisms, so this concept is likely to be relevant for a broad class of systems.
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33
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Das N, Sen P. Structural, Functional, and Dynamical Responses of a Protein in a Restricted Environment Imposed by Macromolecular Crowding. Biochemistry 2018; 57:6078-6089. [DOI: 10.1021/acs.biochem.8b00599] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208 016, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208 016, India
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34
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Chen E, Esquerra RM, Meléndez PA, Chandrasekaran SS, Kliger DS. Microviscosity in E. coli Cells from Time-Resolved Linear Dichroism Measurements. J Phys Chem B 2018; 122:11381-11389. [PMID: 30118225 DOI: 10.1021/acs.jpcb.8b07362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A protein's folding or function depends on its mobility through the viscous environment that is defined by the presence of macromolecules throughout the cell. The relevant parameter for this mobility is microviscosity-the viscosity on a time and distance scale that is important for protein folding/function movements. A quasi-null, ultrasensitive time-resolved linear dichroism (TRLD) spectroscopy is proving to be a useful tool for measurements of viscosity on this scale, with previous in vitro studies reporting on the microviscosities of crowded environments mimicked by high concentrations of different macromolecules. This study reports the microviscosity experienced by myoglobin in the E. coli cell's heterogeneous cytoplasm by using TRLD to measure rotational diffusion times. The results show that photolyzed deoxyMb ensembles randomize through environment-dependent rotational diffusion with a lifetime of 34 ± 6 ns. This value corresponds to a microviscosity of 2.82 ± 0.42 cP, which is consistent with previous reports of cytoplasmic viscosity in E. coli. The results of these TRLD studies in E. coli (1) provide a measurement of myoglobin mobility in the cytoplasm, (2) taken together with in vitro TRLD studies yield new insights into the nature of the cytoplasmic environment in cells, and (3) demonstrate the feasibility of TRLD as a probe of intracellular viscosity.
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Affiliation(s)
- Eefei Chen
- Department of Chemistry and Biochemistry , University of California , Santa Cruz , California 95064 , United States
| | - Raymond M Esquerra
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Philipp A Meléndez
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Sita S Chandrasekaran
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - David S Kliger
- Department of Chemistry and Biochemistry , University of California , Santa Cruz , California 95064 , United States
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35
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Chambers JE, Kubánková M, Huber RG, López-Duarte I, Avezov E, Bond PJ, Marciniak SJ, Kuimova MK. An Optical Technique for Mapping Microviscosity Dynamics in Cellular Organelles. ACS NANO 2018; 12:4398-4407. [PMID: 29648785 DOI: 10.1021/acsnano.8b00177] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Microscopic viscosity (microviscosity) is a key determinant of diffusion in the cell and defines the rate of biological processes occurring at the nanoscale, including enzyme-driven metabolism and protein folding. Here we establish a rotor-based organelle viscosity imaging (ROVI) methodology that enables real-time quantitative mapping of cell microviscosity. This approach uses environment-sensitive dyes termed molecular rotors, covalently linked to genetically encoded probes to provide compartment-specific microviscosity measurements via fluorescence lifetime imaging. ROVI visualized spatial and temporal dynamics of microviscosity with suborganellar resolution, reporting on a microviscosity difference of nearly an order of magnitude between subcellular compartments. In the mitochondrial matrix, ROVI revealed several striking findings: a broad heterogeneity of microviscosity among individual mitochondria, unparalleled resilience to osmotic stress, and real-time changes in microviscosity during mitochondrial depolarization. These findings demonstrate the use of ROVI to explore the biophysical mechanisms underlying cell biological processes.
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Affiliation(s)
- Joseph E Chambers
- Cambridge Institute for Medical Research (CIMR), Department of Medicine , University of Cambridge , Wellcome Trust/MRC Building, Hills Road , Cambridge , CB2 0XY , United Kingdom
| | - Markéta Kubánková
- Department of Chemistry , Imperial College London , South Kensington , London , SW7 2AZ , United Kingdom
| | - Roland G Huber
- Bioinformatics Institute (BII) , Agency for Science, Technology, and Research (A*STAR) , Matrix 07-01, 30 Biopolis Street , 138671 Singapore
| | - Ismael López-Duarte
- Department of Chemistry , Imperial College London , South Kensington , London , SW7 2AZ , United Kingdom
| | - Edward Avezov
- UK Dementia Research Institute at the University of Cambridge , Cambridge Biomedical Campus, Cambridge CB2 0AH , United Kingdom
| | - Peter J Bond
- Bioinformatics Institute (BII) , Agency for Science, Technology, and Research (A*STAR) , Matrix 07-01, 30 Biopolis Street , 138671 Singapore
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , 117543 Singapore
| | - Stefan J Marciniak
- Cambridge Institute for Medical Research (CIMR), Department of Medicine , University of Cambridge , Wellcome Trust/MRC Building, Hills Road , Cambridge , CB2 0XY , United Kingdom
| | - Marina K Kuimova
- Department of Chemistry , Imperial College London , South Kensington , London , SW7 2AZ , United Kingdom
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36
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Cattani J, Subramaniam V, Drescher M. Room-temperature in-cell EPR spectroscopy: alpha-Synuclein disease variants remain intrinsically disordered in the cell. Phys Chem Chem Phys 2018; 19:18147-18151. [PMID: 28696461 DOI: 10.1039/c7cp03432f] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human alpha-Synuclein (aS), implicated in Parkinson's disease, adopts a rich variety of different conformations depending on the macromolecular context. In order to unravel its pathophysiological role, monitoring its intracellular conformational state and identifying differences for the disease variants is crucial. Here, we present an intracellular spectroscopy approach based on a systematic spin-labeling site-scan in combination with intracellular electron paramagnetic resonance spectroscopy determining conformations on a molecular scale. A quantitative and model-based data analysis revealed that the vast majority of aS, be it wild-type or disease variants A30P or A53T, exists in the monomeric intrinsically disordered form in the cell.
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Affiliation(s)
- Julia Cattani
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
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37
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Model MA, Petruccelli JC. Intracellular Macromolecules in Cell Volume Control and Methods of Their Quantification. CURRENT TOPICS IN MEMBRANES 2018; 81:237-289. [DOI: 10.1016/bs.ctm.2018.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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38
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van den Berg J, Boersma AJ, Poolman B. Microorganisms maintain crowding homeostasis. Nat Rev Microbiol 2017; 15:309-318. [DOI: 10.1038/nrmicro.2017.17] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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39
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Malyan AN. The effect of medium viscosity on kinetics of ATP hydrolysis by the chloroplast coupling factor CF1. PHOTOSYNTHESIS RESEARCH 2016; 128:163-168. [PMID: 26754050 DOI: 10.1007/s11120-015-0213-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
The coupling factor CF1 is a catalytic part of chloroplast ATP synthase which is exposed to stroma whose viscosity is many-fold higher than that of reaction mixtures commonly used to measure kinetics of CF1-catalyzed ATP hydrolysis. This study is focused on the effect of medium viscosity modulated by sucrose or bovine serum albumin (BSA) on kinetics of Ca(2+)- and Mg(2+)-dependent ATP hydrolysis by CF1. These agents were shown to reduce the maximal rate of Ca(2+)-dependent ATPase without changing the apparent Michaelis constant (К m), thus supporting the hypothesis on viscosity dependence of CF1 activity. For the sulfite- and ethanol-stimulated Mg(2+)-dependent reaction, the presence of sucrose increased К m without changing the maximal rate that is many-fold as high as that of Ca(2+)-dependent hydrolysis. The hydrolysis reaction was shown to be stimulated by low concentrations of BSA and inhibited by its higher concentrations, with the increasing maximal reaction rate estimated by extrapolation. Sucrose- or BSA-induced inhibition of the Mg(2+)-dependent ATPase reaction is believed to result from diffusion-caused deceleration, while its BSA-induced stimulation is probably caused by optimization of the enzyme structure. Molecular mechanisms of the inhibitory effect of viscosity are discussed. Taking into account high protein concentrations in the chloroplast stroma, it was suggested that kinetic parameters of ATP hydrolysis, and probably those of ATP synthesis in vivo as well, must be quite different from measurements taken at a viscosity level close to that of water.
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Affiliation(s)
- Alexander N Malyan
- Institute of Basic Biological Problems Russian Academy of Sciences, Pushchino, Russia.
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40
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Contrasting relationship between macro- and microviscosity of the gelatin- and starch-based suspensions and gels. Polym Bull (Berl) 2016. [DOI: 10.1007/s00289-016-1664-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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