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Paez‐Perez M, Kuimova MK. Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules. Angew Chem Int Ed Engl 2024; 63:e202311233. [PMID: 37856157 PMCID: PMC10952837 DOI: 10.1002/anie.202311233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Abstract
The viscosity and crowding of biological environment are considered vital for the correct cellular function, and alterations in these parameters are known to underly a number of pathologies including diabetes, malaria, cancer and neurodegenerative diseases, to name a few. Over the last decades, fluorescent molecular probes termed molecular rotors proved extremely useful for exploring viscosity, crowding, and underlying molecular interactions in biologically relevant settings. In this review, we will discuss the basic principles underpinning the functionality of these probes and will review advances in their use as sensors for lipid order, protein crowding and conformation, temperature and non-canonical nucleic acid structures in live cells and other relevant biological settings.
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Affiliation(s)
- Miguel Paez‐Perez
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
| | - Marina K. Kuimova
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
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do Amaral MJ, Mohapatra S, Passos AR, Lopes da Silva TS, Carvalho RS, da Silva Almeida M, Pinheiro AS, Wegmann S, Cordeiro Y. Copper drives prion protein phase separation and modulates aggregation. SCIENCE ADVANCES 2023; 9:eadi7347. [PMID: 37922348 PMCID: PMC10624353 DOI: 10.1126/sciadv.adi7347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/03/2023] [Indexed: 11/05/2023]
Abstract
Prion diseases are characterized by prion protein (PrP) transmissible aggregation and neurodegeneration, which has been linked to oxidative stress. The physiological function of PrP seems related to sequestering of redox-active Cu2+, and Cu2+ dyshomeostasis is observed in prion disease brain. It is unclear whether Cu2+ contributes to PrP aggregation, recently shown to be mediated by PrP condensation. This study indicates that Cu2+ promotes PrP condensation in live cells at the cell surface and in vitro through copartitioning. Molecularly, Cu2+ inhibited PrP β-structure and hydrophobic residues exposure. Oxidation, induced by H2O2, triggered liquid-to-solid transition of PrP:Cu2+ condensates and promoted amyloid-like PrP aggregation. In cells, overexpression of PrPC initially protected against Cu2+ cytotoxicity but led to PrPC aggregation upon extended copper exposure. Our data suggest that PrP condensates function as a buffer for copper that prevents copper toxicity but can transition into PrP aggregation at prolonged oxidative stress.
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Affiliation(s)
- Mariana Juliani do Amaral
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | | | - Aline Ribeiro Passos
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | | | | | - Marcius da Silva Almeida
- Plataforma Avançada de Biomoléculas, Centro Nacional de Biologia Estrutural e Bioimagem, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anderson Sá Pinheiro
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Susanne Wegmann
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Mora AK, Hundani PZ, Nath S. Contrasting complexation behaviour of zwitterionic amyloid probe, SYPRO orange with β-cyclodextrin and captisol. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2023.114712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Sarkar A, Namboodiri V, Kumbhakar M. Single-Molecule Orientation Imaging Reveals Two Distinct Binding Configurations on Amyloid Fibrils. J Phys Chem Lett 2023:4990-4996. [PMID: 37220418 DOI: 10.1021/acs.jpclett.3c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Fluorescence readouts for an amyloid fibril sensor critically depend on its molecular interaction and local environment offered by the available structural motifs. Here we employ polarized points accumulation for imaging in nanoscale topography with intramolecular charge transfer probes transiently bound to amyloid fibrils to investigate the organization of fibril nanostructures and probe binding configurations. Besides the in-plane (θ ≈ 90°) mode for binding on the fibril surface parallel to the long fibril axis, we also observed a sizable population of over 60% out-of-plane (θ < 60°) dipoles for rotor probes experiencing a varying degree of orientational mobility. Highly confined dipoles exhibiting an out-of-plane configuration probably reflect tightly bound dipoles in the inner channel grooves, while the weakly bound ones on amyloid enjoy rotational flexibility. Our observation of an out-of-plane binding mode emphasizes the pivotal role played by the electron donor amino group toward fluorescence detection and hence the emergence of anchored probes alongside conventional groove binders.
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Affiliation(s)
- Aranyak Sarkar
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Vinu Namboodiri
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
| | - Manoj Kumbhakar
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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Pauly T, Zhang T, Sternke-Hoffmann R, Nagel-Steger L, Willbold D. Differentiation of subnucleus-sized oligomers and nucleation-competent assemblies of the Aβ peptide. Biophys J 2023; 122:269-278. [PMID: 36529991 PMCID: PMC9892607 DOI: 10.1016/j.bpj.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
A significant feature of Alzheimer's disease is the formation of amyloid deposits in the brain consisting mainly of misfolded derivatives of proteolytic cleavage products of the amyloid precursor protein amyloid-β (Aβ) peptide. While high-resolution structures already exist for both the monomer and the amyloid fibril of the Aβ peptide, the mechanism of amyloid formation itself still defies precise characterization. In this study, low and high molecular weight oligomers (LMWOs and HMWOs) were identified by sedimentation velocity analysis, and for the first time, the temporal evolution of oligomer size distributions was correlated with the kinetics of amyloid formation as determined by thioflavin T-binding studies. LMWOs of subnucleus size contain fewer than seven monomer units and exist alongside a heterogeneous group of HMWOs with 20-160 monomer units that represent potential centers of nucleus formation due to high local monomer concentrations. These HMWOs already have slightly increased β-strand content and appear structurally similar regardless of size, as shown by examination with a range of fluorescent dyes. Once fibril nuclei are formed, the monomer concentration begins to decrease, followed by a decrease in oligomer concentration, starting with LMWOs, which are the least stable species. The observed behavior classifies the two LMWOs as off pathway. In contrast, we consider HMWOs to be on-pathway, prefibrillar intermediates, representing structures in which nucleated conformational conversion is facilitated by high local concentrations. Aβ40 and Aβ42 M35ox take much longer to form nuclei and enter the growth phase than Aβ42 under identical reaction conditions, presumably because both the size and the concentration of HMWOs formed are much smaller.
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Affiliation(s)
- Thomas Pauly
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| | | | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany.
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
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A Near Infra-red Emitting Supramolecular Dye-Polymer Assembly as Promising Platform for Protamine Sensing. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Yoon Y, Kim HS, Yoon S, Yeon KM, Kim J. Precipitation-based microscale enzyme reactors coupled with porous and adhesive elastomer for effective bacterial decontamination and membrane antifouling on-demand. ENVIRONMENTAL RESEARCH 2022; 212:113407. [PMID: 35523281 DOI: 10.1016/j.envres.2022.113407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 06/14/2023]
Abstract
Bacterial contamination of water environments can cause various troubles in various areas. As one of potential solutions, we develop enzyme-immobilized elastomer, and demonstrate the uses of enzyme reactions on-demand for effective microbial decontamination and antifouling. Asymmetrically-structured elastomer is prepared by combining two polydimethylsiloxane (PDMS) layers with different degrees of crosslinking: highly-crosslinked and lightly-crosslinked PDMS layers. At the surface of highly-crosslinked PDMS layer, porous structure with average diameter of 842 nm is formed by dissolving pre-packed and entrapped latex beads. Lightly-crosslinked PDMS on the other side, due to its adhesive nature, enables iterative attachments on various materials under either dry or wet condition. Glucose oxidase (GOx) is immobilized by using the pores at the surface of highly-crosslinked PDMS matrix via a ship-in-a-bottle protocol of precipitation-based microscale enzyme reactor (p-MER), which consists of GOx adsorption, precipitation and chemical crosslinking (EAPC). As a result, crosslinked enzyme aggregates (CLEAs) of GOx not only are well entrapped within many pores of highly-crosslinked PDMS layer (ship-in-bottle) but also cover the external surface of matrix, both of which are well connected together. Highly-interconnected network of CLEAs themselves effectively prevents enzyme leaching, which shows the 25% residual activity of GOx under shaking at 200 rpm for 156 days after 48% initial drop of loosely-bound p-MER after 4 days. In presence of glucose, the underwater attachment of biocatalytic elastomer demonstrates the generation of hydrogen peroxide via p-MER-catalyzed glucose oxidation, exhibiting effective biocidal activities against both gram-positive S. aureus and gram-negative E. coli. Adhesion-induced GOx-catalyzed reaction also alleviates the biofouling of membrane, suggesting its extendibility to various engineering systems being suffered by biofouling. This study of biocatalytic elastomer has demonstrated its new opportunities for the facile and on-demand enzyme-catalyzed reactions in various environmental applications, such as bactericidal treatment, water treatment/purification, and pollutant degradation.
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Affiliation(s)
- YoungChul Yoon
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Han Sol Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Seji Yoon
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Kyung-Min Yeon
- Engineering Center, Samsung C&T Corporation, Tower B, 26, Sangil-ro, 6- gil, Gangdong-gu, Seoul, Republic of Korea.
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
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Sen A, Mora AK, Koli M, Mula S, Kundu S, Nath S. Sensing lysozyme fibrils by salicylaldimine substituted BODIPY dyes - A correlation with molecular structure. Int J Biol Macromol 2022; 220:901-909. [PMID: 35998856 DOI: 10.1016/j.ijbiomac.2022.08.112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022]
Abstract
Quick and efficient detection of protein fibrils has enormous impact on the diagnosis and treatment of amyloid related neurological diseases. Among several methods, fluorescence based techniques have garnered most importance in the detection of amyloid fibrils due to its high sensitivity and extreme simplicity. Among other classes of molecular probes, BODIPY derivatives have been employed extensively for the detection of amyloid fibrils. However, there are very few studies on the relationship between the molecular structure of BODIPY dyes and their amyloid sensing activity. Here in a BODIPY based salicylaldimine Schiff base and its corresponding boron complex have been evaluated for their ability to sense amyloid fibrils from hen-egg white lysozyme using steady state and time-resolved spectroscopic techniques. Both dyes show fluorescence enhancement as well as increase in their excited state lifetime upon their binding with lysozyme fibrils. However, the BODIPY derivative which shows more emission enhancement in fibrillar solution has much lower affinity towards amyloid fibrils as compared to other derivative. This contrasting behaviour in the emission enhancement and binding affinity has been explained on the basis of differences in their photophysical properties in water and amyloid fibril originating from the difference in their molecular structure. Such correlation between the amyloid sensitivity and the molecular structure of the probe can open up a new strategy for designing new efficient amyloid probes.
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Affiliation(s)
- Ayentika Sen
- Beam Technology Development Group, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| | - Aruna K Mora
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India.
| | - Mrunesh Koli
- Bio-Organic Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Soumyaditya Mula
- Bio-Organic Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| | - Soumitra Kundu
- Beam Technology Development Group, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India.
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