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Nowakowski P, Stumpf BH, Smith AS, Maciołek A. Demixing of homogeneous binary lipid membranes induced by protein inclusions. Phys Rev E 2023; 107:054120. [PMID: 37329062 DOI: 10.1103/physreve.107.054120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 04/17/2023] [Indexed: 06/18/2023]
Abstract
We study a model of a lipid bilayer membrane described by two order parameters: the chemical composition described using the Gaussian model and the spatial configuration described with the elastic deformation model of a membrane with a finite thickness or, equivalently, for an adherent membrane. We assume and explain on physical grounds the linear coupling between the two order parameters. Using the exact solution, we calculate the correlation functions and order parameter profiles. We also study the domains that form around inclusions on the membrane. We propose and compare six distinct ways to quantify the size of such domains. Despite its simplicity, the model has many interesting features like the Fisher-Widom line and two distinct critical regions.
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Affiliation(s)
- Piotr Nowakowski
- Max-Planck-Institut für Intelligente Systeme Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany; Institut für Theoretische Physik IV, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; and Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Bernd Henning Stumpf
- PULS Group, Institut für Theoretische Physik, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 3, 91058 Erlangen, Germany
| | - Ana-Sunčana Smith
- PULS Group, Institut für Theoretische Physik, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 3, 91058 Erlangen, Germany and Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Anna Maciołek
- Max-Planck-Institut für Intelligente Systeme Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany and Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Cerri DG, Rodrigues LC, Fermino ML, Papoti M, Cummings RD, Stowell SR, Dias-Baruffi M. Investigation of Galectins in Frozen Tissue and Mammalian Cell Culture Using Confocal Miccroscopy. Methods Mol Biol 2022; 2442:289-306. [PMID: 35320532 DOI: 10.1007/978-1-0716-2055-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Galectins are multifunctional glycan-binding proteins present in various tissues that participate in multiple physiological and pathological processes and are considered as not only biomarkers of human diseases but also molecular targets for treating cancer and inflammatory illnesses in many organs. In the glycobiology field, it is crucial to determine the pattern of galectin expression and location in cells and tissues. Confocal microscopy is a powerful imaging technology that represents a unique approach to investigate the expression and location of biomolecules in various tissues and cells. The confocal microscope acquires images of the specimen through the reflected or fluorescent light from the objective's focal plane, using laser light focused on a small spot inside the tissue or cell. This technique provides high-resolution and high-contrast images without artifacts generated by conventional microscopy and enables reconstruction of virtual tridimensional images by acquiring multiple sections from several focal planes, which makes it possible to obtain the precise spatial location of any cellular structure or molecule. Furthermore, confocal microscopy is a non-invasive tissue imaging strategy used in clinical practices. We describe herein the immunofluorescence confocal method for examining galectins in frozen tissue sections and mammalian cell culture.
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Affiliation(s)
- Daniel Giuliano Cerri
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas da Faculdade de Ciências Farmacênuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Lilian Cataldi Rodrigues
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas da Faculdade de Ciências Farmacênuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Marise Lopes Fermino
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas da Faculdade de Ciências Farmacênuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Marcelo Papoti
- Escola de Educação Física e Esporte de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Richard D Cummings
- Department of Surgery, National Center for Functional Glycomics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sean R Stowell
- Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Marcelo Dias-Baruffi
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas da Faculdade de Ciências Farmacênuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil.
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Ilangumaran Ponmalar I, Sarangi NK, Basu JK, Ayappa KG. Pore Forming Protein Induced Biomembrane Reorganization and Dynamics: A Focused Review. Front Mol Biosci 2021; 8:737561. [PMID: 34568431 PMCID: PMC8459938 DOI: 10.3389/fmolb.2021.737561] [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: 07/07/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Pore forming proteins are a broad class of pathogenic proteins secreted by organisms as virulence factors due to their ability to form pores on the target cell membrane. Bacterial pore forming toxins (PFTs) belong to a subclass of pore forming proteins widely implicated in bacterial infections. Although the action of PFTs on target cells have been widely investigated, the underlying membrane response of lipids during membrane binding and pore formation has received less attention. With the advent of superresolution microscopy as well as the ability to carry out molecular dynamics (MD) simulations of the large protein membrane assemblies, novel microscopic insights on the pore forming mechanism have emerged over the last decade. In this review, we focus primarily on results collated in our laboratory which probe dynamic lipid reorganization induced in the plasma membrane during various stages of pore formation by two archetypal bacterial PFTs, cytolysin A (ClyA), an α-toxin and listeriolysin O (LLO), a β-toxin. The extent of lipid perturbation is dependent on both the secondary structure of the membrane inserted motifs of pore complex as well as the topological variations of the pore complex. Using confocal and superresolution stimulated emission depletion (STED) fluorescence correlation spectroscopy (FCS) and MD simulations, lipid diffusion, cholesterol reorganization and deviations from Brownian diffusion are correlated with the oligomeric state of the membrane bound protein as well as the underlying membrane composition. Deviations from free diffusion are typically observed at length scales below ∼130 nm to reveal the presence of local dynamical heterogeneities that emerge at the nanoscale-driven in part by preferential protein binding to cholesterol and domains present in the lipid membrane. Interrogating the lipid dynamics at the nanoscale allows us further differentiate between binding and pore formation of β- and α-PFTs to specific domains in the membrane. The molecular insights gained from the intricate coupling that occurs between proteins and membrane lipids and receptors during pore formation are expected to improve our understanding of the virulent action of PFTs.
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Affiliation(s)
| | - Nirod K. Sarangi
- School of Chemical Science, Dublin City University, Dublin, Ireland
| | - Jaydeep K. Basu
- Department of Physics, Indian Institute of Science, Bangalore, India
| | - K. Ganapathy Ayappa
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
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Abstract
Recent advances in super-resolution (sub-diffraction limited) microscopy have yielded remarkable insights into the nanoscale architecture and behavior of cells. In addition to the capacity to provide sub 100 nm resolution, these technologies offer unique quantitative opportunities with particular relevance to platelet and megakaryocyte biology. In this review, we provide a short introduction to modern super-resolution microscopy, its applications in the field of platelet and megakaryocyte biology, and emerging quantitative approaches which will allow for unprecedented insights into the biology of these unique cell types.
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Affiliation(s)
- Abdullah O Khan
- Institute of Cardiovascular Sciences, College of Medical and Dental Science, University of Birmingham , Birmingham, UK
| | - Jeremy A Pike
- Institute of Cardiovascular Sciences, College of Medical and Dental Science, University of Birmingham , Birmingham, UK.,Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham , UK
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Sharma R, Singh M, Sharma R. Recent advances in STED and RESOLFT super-resolution imaging techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 231:117715. [PMID: 31748155 DOI: 10.1016/j.saa.2019.117715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/15/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
Stimulated emission depletion (STED) and reversible saturable optical fluorescence transition (RESOLFT) microscopy are the super-resolution imaging techniques that can acquire nanoscale spatial resolution. The spatial resolution of the other far-field optical microscopic techniques is bound by diffraction limit, however, STED/RESOLFT techniques eliminate the diffraction barrier. These microscopic techniques have taken the limits of optical image resolution down to the nanometer scale and opened new paths for biomedical and nanophosphor research. In this paper, we review the recent advancements of these techniques in the field of nanoscopy using continuous wave (CW) laser sources. Further, we discuss the main limitation of the STED microscopy in terms of essential requirements of higher depletion beam power and photobleaching issues. The RESOLFT microscopic technique can be considered as an alternate technique to overcome limitations of existing STED microscopy. Moreover, the Bessel and Gaussian-Bessel beam STED microscopic techniques are also reviewed to produce deep images with faster scanning of the samples. The organic molecules as well as the fluorescent doped nanoparticles like ZnSe:Mn having characteristics of excited state absorption can be investigated using RESOLFT microscopy.
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Affiliation(s)
- Reena Sharma
- Department of Physics, University Institute of Sciences, Chandigarh University, Mohali, Punjab, 140413, India
| | - Manjot Singh
- Department of Physics, University Institute of Sciences, Chandigarh University, Mohali, Punjab, 140413, India
| | - Rajesh Sharma
- Department of Physics, University Institute of Sciences, Chandigarh University, Mohali, Punjab, 140413, India.
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Man Z, Lv Z, Xu Z, Cui H, Liao Q, Zheng L, Jin X, He Q, Fu H. Organic nanoparticles with ultrahigh stimulated emission depletion efficiency for low-power STED nanoscopy. NANOSCALE 2019; 11:12990-12996. [PMID: 31264678 DOI: 10.1039/c9nr02781e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Stimulated emission depletion (STED) nanoscopy is a powerful sub-diffraction imaging tool to probe subcellular structures and organelles. Conventional organic dyes require high STED power (PSTED) to obtain sub-diffraction resolution, leading to serious photo-bleaching. Herein, this study demonstrates highly emissive silica-coated core-shell organic nanoparticles (CSONPs) as a new type of photostable probe with ultrahigh stimulated emission depletion efficiency for low-power super-resolution STED nanoscopy. The CSONPs offer (i) efficient red emission with high solid-state fluorescence quantum yields around 0.6, (ii) large Stokes shift of 150 nm and (iii) high photostability owing to silica shell protection. The stimulated emission depletion efficiency (η) of CSONPs was extremely high up to η = 99% (the highest value reported so far) with a saturation intensity as low as Isat = 0.18 MW cm-2. Moreover, this research demonstrates the super-resolution imaging of living HeLa cells stained using CSONPs with a lateral spatial resolution of 63 nm at an extremely low depletion power of ISTED = 0.89 MW cm-2 and a long-term stability >600 s at η = 80% without obvious fatigue. The excellent and comprehensive performances of the CSONPs are promising for super-resolution imaging in biological applications.
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Affiliation(s)
- Zhongwei Man
- Beijing Key Laboratory for Optical Materials and Photonic Devices, Capital Normal University, Beijing 100048, China.
| | - Zheng Lv
- Beijing Key Laboratory for Optical Materials and Photonic Devices, Capital Normal University, Beijing 100048, China.
| | - Zhenzhen Xu
- Beijing Key Laboratory for Optical Materials and Photonic Devices, Capital Normal University, Beijing 100048, China.
| | - Hongtu Cui
- Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, the Institute of Cardiovascular Sciences and Institute of Systems Biomedicine, Peking University Health Science Center, Beijing 100191, China.
| | - Qing Liao
- Beijing Key Laboratory for Optical Materials and Photonic Devices, Capital Normal University, Beijing 100048, China.
| | - Lemin Zheng
- Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, the Institute of Cardiovascular Sciences and Institute of Systems Biomedicine, Peking University Health Science Center, Beijing 100191, China.
| | - Xue Jin
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Institute of Molecular Plus, Tianjin Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China.
| | - Qihua He
- Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, the Institute of Cardiovascular Sciences and Institute of Systems Biomedicine, Peking University Health Science Center, Beijing 100191, China.
| | - Hongbing Fu
- Beijing Key Laboratory for Optical Materials and Photonic Devices, Capital Normal University, Beijing 100048, China. and Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Institute of Molecular Plus, Tianjin Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China.
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Combs CA, Sackett DL, Knutson JR. A simple empirical algorithm for optimising depletion power and resolution for dye and system specific STED imaging. J Microsc 2019; 274:168-176. [PMID: 31012103 DOI: 10.1111/jmi.12795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 11/28/2022]
Abstract
Here we show an easy method for determining an effective dye saturation factor ('PSTED ') for STED (Stimulated Emission Depletion) microscopy. We define PSTED to be a combined microscope system plus dye factor (analogous to the traditional ground truth Is measurement, which is microscope independent) that is functionally defined as the power in the depletion beam that provides a resolution enhancement of 41% compared to confocal, according to the modified Abbe's formula for STED resolution enhancement. We show that the determination of PSTED provides insight not only into the suitability of a particular dye and the best imaging parameters to be used for an experiment, but also sets the critical value for correctly determining the point spread function (PSF) used in deconvolution of STED images. PSTED can be a function of many experimental variables, both microscope and sample related. Here we show the utility of doing PSTED determinations by (1) exploiting the simple relationship between width and a threshold-defined area provided by a Gaussian PSF, for either linear or spherical objects and (2) linearising the normally inverse hyperbolic function of resolution versus power that can determine PSTED . We show that this rearrangement allows us to determine PSTED using only a few measurements: either at a few relatively low depletion powers, on traditional bead size measurements or by finding the total area of a naturally occurring sub-limit sized biological feature (in this case, microtubules). We show the derivation of these equations and methods and the utility of its use by characterising several dyes and a local imaging parameter relevant to STED microscopy. This information is used to predict the enhancement of resolution of the point spread function necessary for post-processing deconvolution. LAY DESCRIPTION: Stimulated Emission Depletion (STED) microscopy is a fluorescence imaging superresolution technique that achieves tens of nanometres resolution. This is done by utilising a depletion laser to effectively quench (deplete) fluorescence in a donut shape overlapping the normally excited fluorescence spot. The size of the remaining (undepleted) central fluorescence spot is power dependent allowing 'tunable' resolution with the power of the STED depletion laser. This depletion power versus resolution relationship is dye and instrument dependent. We have developed a method for quickly measuring this relationship to optimise experiments based on individual dyes and microscope specific parameters. This allows for quickly optimising microscope settings and for correctly postprocessing images.
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Affiliation(s)
- Christian A Combs
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Dan L Sackett
- NICHD Division of Basic and Translational Biophysics, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Jay R Knutson
- NHLBI Laboratory for Advanced Microscopy and Biophotonics, National Institutes of Health, Bethesda, Maryland, U.S.A
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Sarkar P, Chattopadhyay A. Exploring membrane organization at varying spatiotemporal resolutions utilizing fluorescence-based approaches: implications in membrane biology. Phys Chem Chem Phys 2019; 21:11554-11563. [DOI: 10.1039/c9cp02087j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Representative experimental approaches based on dynamic fluorescence microscopy to analyze organization and dynamics of membrane lipids and proteins.
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Affiliation(s)
- Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology
- Hyderabad 500 007
- India
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Wijesooriya CS, Nyamekye CKA, Smith EA. Optical Imaging of the Nanoscale Structure and Dynamics of Biological Membranes. Anal Chem 2018; 91:425-440. [DOI: 10.1021/acs.analchem.8b04755] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Charles K. A. Nyamekye
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- The Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
| | - Emily A. Smith
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- The Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
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