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Harmon DM, Cao Z, Sherman AM, Takanti N, Murati K, Wimsatt MM, Cousineau ML, Hwang Y, Taylor LS, Simpson GJ. Diffusion Mapping with Diffractive Optical Elements for Periodically Patterned Photobleaching. Anal Chem 2024; 96:10161-10169. [PMID: 38864607 DOI: 10.1021/acs.analchem.3c05728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Fourier transform-fluorescence recovery after photobleaching (FT-FRAP) using a diffractive optical element (DOE) is shown to support distance-dependent diffusion analysis in biologically relevant media. Integration of DOEs enables patterning of a dot array for parallel acquisition of point-bleach FRAP measurements at multiple locations across the field of view. In homogeneous media, the spatial harmonics of the dot array analyzed in the spatial Fourier transform domain yield diffusion recovery curves evaluated over specific well-defined distances. Relative distances for diffusive recovery in the spatial Fourier transform domain are directly connected to the 2D (h,k) Miller indices of the corresponding lattice lines. The distribution of the photobleach power across the entire field of view using a multidot array pattern greatly increases the overall signal power in the spatial FT-domain for signal-to-noise improvements. Derivations are presented for the mathematical underpinnings of FT-FRAP performed with 2D periodicity in the photobleach patterns. Retrofitting of FT-FRAP into instrumentation for high-throughput FRAP analysis (Formulatrix) supports automated analysis of robotically prepared 96-well plates for precise quantification of molecular mobility. Figures of merit are evaluated for FT-FRAP in analysis for both slow diffusion of fluorescent dyes in glassy polymer matrices spanning several days and model proteins and monoclonal antibodies within aqueous solutions recovering in matters of seconds.
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Affiliation(s)
- Dustin M Harmon
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ziyi Cao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Alex M Sherman
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nita Takanti
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kevin Murati
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Maura M Wimsatt
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Michelle L Cousineau
- Department of Industrial and Molecular Pharmaceutics, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yechan Hwang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lynne S Taylor
- Department of Industrial and Molecular Pharmaceutics, Purdue University, West Lafayette, Indiana 47907, United States
| | - Garth J Simpson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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2
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Tverdokhlebova A, Sterin I, Jayaweera TM, Darie CC, Katz E, Smutok O. Chemical modification of α-chymotrypsin enabling its release from alginate hydrogel by electrochemically generated local pH change. Int J Biol Macromol 2024; 273:133234. [PMID: 38897525 DOI: 10.1016/j.ijbiomac.2024.133234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/31/2024] [Accepted: 06/15/2024] [Indexed: 06/21/2024]
Abstract
This study investigates the controlled release of α-chymotrypsin from an alginate hydrogel matrix. When protein molecules entrapped in the hydrogel matrix have a size smaller than the hydrogel pores, their hold/release from the polymer matrix are controlled by the electrostatic interaction between the guest molecules and host polymer. α-Chymotrypsin, as a model protein, was chemically modified with negatively charged species to change its pI and to convert its attractive interaction with a negatively charged alginate hydrogel matrix to a repulsion interaction allowing its release by pH-triggered signal. Then, bulk pH changes and electrochemically controlled local pH changes resulting from oxygen reduction were used for the controlled release of the enzyme from the alginate hydrogel. Three batches of modified α-chymotrypsin with different linker/enzyme ratios were synthesized, and their release profiles were investigated. The activity of both unmodified and modified α-chymotrypsin was evaluated using a UV-visible spectrophotometer following the standard procedure for the enzymatic assay of α-chymotrypsin (EC 3.4.21.1) and compared across all batches. Direct infusion electrospray ionization mass spectrometry (DI ESI-MS) was used to analyze the protein modifications and their impact on the isoelectric point values.
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Affiliation(s)
- Anna Tverdokhlebova
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Ilya Sterin
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Taniya M Jayaweera
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA.
| | - Oleh Smutok
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA.
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3
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Kesharwani A, Gujrati V. Multimodal techniques and strategies for chemical and metabolic imaging at the single-cell level. Curr Opin Biotechnol 2024; 88:103149. [PMID: 38810301 DOI: 10.1016/j.copbio.2024.103149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Single-cell chemical and metabolic imaging technologies provide unprecedented insights into individual cell dynamics, advancing our understanding of cellular processes, molecular interactions, and metabolic activities. Advances in fluorescence, Raman, optoacoustic (photoacoustic), or mass spectrometry methods have paved the way to characterize metabolites, signaling molecules, and other moieties within individual cells. These modalities can also lead to single-cell imaging capabilities by targeting endogenous cell contrast or by employing exogenous contrast generation techniques, including contrast agents that target specific cell structure or function. In this review, we present key developments, summarize recent applications in single-cell interrogation and imaging, and illustrate their advantages, limitations, and outlook.
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Affiliation(s)
- Ajay Kesharwani
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Neuherberg, Germany; Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Vipul Gujrati
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Neuherberg, Germany; Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine and Health, Technical University of Munich, Munich, Germany.
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4
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Bercea M, Lupu A. Recent Insights into Glucose-Responsive Concanavalin A-Based Smart Hydrogels for Controlled Insulin Delivery. Gels 2024; 10:260. [PMID: 38667679 PMCID: PMC11048858 DOI: 10.3390/gels10040260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/24/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Many efforts are continuously undertaken to develop glucose-sensitive biomaterials able of controlling glucose levels in the body and self-regulating insulin delivery. Hydrogels that swell or shrink as a function of the environmental free glucose content are suitable systems for monitoring blood glucose, delivering insulin doses adapted to the glucose concentration. In this context, the development of sensors based on reversible binding to glucose molecules represents a continuous challenge. Concanavalin A (Con A) is a bioactive protein isolated from sword bean plants (Canavalia ensiformis) and contains four sugar-binding sites. The high affinity for reversibly and specifically binding glucose and mannose makes Con A as a suitable natural receptor for the development of smart glucose-responsive materials. During the last few years, Con A was used to develop smart materials, such as hydrogels, microgels, nanoparticles and films, for producing glucose biosensors or drug delivery devices. This review is focused on Con A-based materials suitable in the diagnosis and therapeutics of diabetes. A brief outlook on glucose-derived theranostics of cancer is also presented.
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Affiliation(s)
- Maria Bercea
- “Petru Poni” Institute of Macromolecular Chemistry, 41-A Grigore Ghica Voda Alley, 700487 Iasi, Romania
| | - Alexandra Lupu
- “Petru Poni” Institute of Macromolecular Chemistry, 41-A Grigore Ghica Voda Alley, 700487 Iasi, Romania
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Öberg R, Sil TB, Ohlin A, Andersson M, Malyshev D. Assessing CaDPA levels, metabolic activity, and spore detection through deuterium labeling. Analyst 2024; 149:1861-1871. [PMID: 38348676 DOI: 10.1039/d3an02162a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Many strains among spore-forming bacteria species are associated with food spoilage, foodborne disease, and hospital-acquired infections. Understanding the impact of environmental conditions and decontamination techniques on the metabolic activity, viability, and biomarkers of these spores is crucial for combatting them. To distinguish and track spores and to understand metabolic mechanisms, spores must be labeled. Staining or genetic modification are current methods for this, however, these methods can be time-consuming, and affect the viability and function of spore samples. In this work, we investigate the use of heavy water for permanent isotope labeling of spores and Raman spectroscopy for tracking sporulation/germination mechanisms. We also discuss the potential of this method in observing decontamination. We find that steady-state deuterium levels in the spore are achieved after only ∼48 h of incubation with 30% D2O-infused broth and sporulation, generating Raman peaks at cell silent region of 2200 and 2300 cm-1. These deuterium levels then decrease rapidly upon spore germination in non-deuterated media. We further find that unlike live spores, spores inactivated using various methods do not lose these Raman peaks upon incubation in growth media, suggesting these peaks may be used to indicate the viability of a spore sample. We further observe several Raman peaks exclusive to deuterated DPA, a spore-specific chemical biomarker, at e.g. 988 and 2300 cm-1, which can be used to track underlying changes in spores involving DPA. In conclusion, permanent spore labeling using deuterium offers a robust and non-invasive way of labeling bacterial spores for marking, viability determination, and characterising spore activity.
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Affiliation(s)
- Rasmus Öberg
- Department of Physics, Umeå University, 901 87, Umeå, Sweden.
- Swedish Defence Research Agency (FOI), Cementvägen 20, 906 21 Umeå, Sweden
| | - Timir Baran Sil
- Department of Physics, Umeå University, 901 87, Umeå, Sweden.
| | - André Ohlin
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | | | - Dmitry Malyshev
- Department of Physics, Umeå University, 901 87, Umeå, Sweden.
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Reja SI, Minoshima M, Hori Y, Kikuchi K. Recent advancements of fluorescent biosensors using semisynthetic probes. Biosens Bioelectron 2024; 247:115862. [PMID: 38147718 DOI: 10.1016/j.bios.2023.115862] [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: 07/15/2022] [Revised: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 12/28/2023]
Abstract
Fluorescent biosensors are crucial experimental tools for live-cell imaging and the quantification of different biological analytes. Fluorescent protein (FP)-based biosensors are widely used for imaging applications in living systems. However, the use of FP-based biosensors is hindered by their large size, poor photostability, and laborious genetic manipulations required to improve their properties. Recently, semisynthetic fluorescent biosensors have been developed to address the limitations of FP-based biosensors using chemically modified fluorescent probes and self-labeling protein tag/peptide tags or DNA/RNA-based hybrid systems. Semisynthetic biosensors have unique advantages, as they can be easily modified using different probes. Moreover, the self-labeling protein tag, which labels synthetically developed ligands via covalent bonds, has immense potential for biosensor development. This review discusses the recent progress in different types of fluorescent biosensors for metabolites, protein aggregation and degradation, DNA methylation, endocytosis and exocytosis, membrane tension, and cellular viscosity. Here, we explain in detail the design strategy and working principle of these biosensors. The information presented will help the reader to create new biosensors using self-labeling protein tags for various applications.
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Affiliation(s)
- Shahi Imam Reja
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masafumi Minoshima
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuichiro Hori
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kazuya Kikuchi
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan; Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
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7
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Veríssimo NVP, Mussagy CU, Bento HBS, Pereira JFB, Santos-Ebinuma VDC. Ionic liquids and deep eutectic solvents for the stabilization of biopharmaceuticals: A review. Biotechnol Adv 2024; 71:108316. [PMID: 38199490 DOI: 10.1016/j.biotechadv.2024.108316] [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: 08/16/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Biopharmaceuticals have allowed the control of previously untreatable diseases. However, their low solubility and stability still hinder their application, transport, and storage. Hence, researchers have applied different compounds to preserve and enhance the delivery of biopharmaceuticals, such as ionic liquids (ILs) and deep eutectic solvents (DESs). Although the biopharmaceutical industry can employ various substances for enhancing formulations, their effect will change depending on the properties of the target biomolecule and environmental conditions. Hence, this review organized the current state-of-the-art on the application of ILs and DESs to stabilize biopharmaceuticals, considering the properties of the biomolecules, ILs, and DESs classes, concentration range, types of stability, and effect. We also provided a critical discussion regarding the potential utilization of ILs and DESs in pharmaceutical formulations, considering the restrictions in this field, as well as the advantages and drawbacks of these substances for medical applications. Overall, the most applied IL and DES classes for stabilizing biopharmaceuticals were cholinium-, imidazolium-, and ammonium-based, with cholinium ILs also employed to improve their delivery. Interestingly, dilute and concentrated ILs and DESs solutions presented similar results regarding the stabilization of biopharmaceuticals. With additional investigation, ILs and DESs have the potential to overcome current challenges in biopharmaceutical formulation.
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Affiliation(s)
- Nathalia Vieira Porphirio Veríssimo
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil; Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences, São Paulo University, CEP: 14040-020 Ribeirão Preto, SP, Brazil.
| | - Cassamo Usemane Mussagy
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile.
| | - Heitor Buzetti Simões Bento
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil.
| | | | - Valéria de Carvalho Santos-Ebinuma
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil.
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Inavalli VVGK, Puente Muñoz V, Draffin JE, Tønnesen J. Fluorescence microscopy shadow imaging for neuroscience. Front Cell Neurosci 2024; 18:1330100. [PMID: 38425431 PMCID: PMC10902105 DOI: 10.3389/fncel.2024.1330100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Fluorescence microscopy remains one of the single most widely applied experimental approaches in neuroscience and beyond and is continuously evolving to make it easier and more versatile. The success of the approach is based on synergistic developments in imaging technologies and fluorophore labeling strategies that have allowed it to greatly diversify and be used across preparations for addressing structure as well as function. Yet, while targeted labeling strategies are a key strength of fluorescence microscopy, they reciprocally impose general limitations on the possible types of experiments and analyses. One recent development that overcomes some of these limitations is fluorescence microscopy shadow imaging, where membrane-bound cellular structures remain unlabeled while the surrounding extracellular space is made to fluoresce to provide a negative contrast shadow image. When based on super-resolution STED microscopy, the technique in effect provides a positive image of the extracellular space geometry and entire neuropil in the field of view. Other noteworthy advantages include the near elimination of the adverse effects of photobleaching and toxicity in live imaging, exhaustive and homogeneous labeling across the preparation, and the ability to apply and adjust the label intensity on the fly. Shadow imaging is gaining popularity and has been applied on its own or combined with conventional positive labeling to visualize cells and synaptic proteins in their parenchymal context. Here, we highlight the inherent limitations of fluorescence microscopy and conventional labeling and contrast these against the pros and cons of recent shadow imaging approaches. Our aim is to describe the brief history and current trajectory of the shadow imaging technique in the neuroscience field, and to draw attention to its ease of application and versatility.
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Affiliation(s)
| | - Virginia Puente Muñoz
- Department of Neurosciences, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Jonathan E. Draffin
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
- Aligning Science Across Parkinson’s (ASAP), Collaborative Research Network, Chevy Chase, MD, United States
| | - Jan Tønnesen
- Department of Neurosciences, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
- Aligning Science Across Parkinson’s (ASAP), Collaborative Research Network, Chevy Chase, MD, United States
- Instituto Biofisika (CSIC/UPV), Leioa, Spain
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Akkaya M, Al Souz J, Williams D, Kamdar R, Kamenyeva O, Kabat J, Shevach E, Akkaya B. Illuminating T cell-dendritic cell interactions in vivo by FlAsHing antigens. eLife 2024; 12:RP91809. [PMID: 38236633 PMCID: PMC10945603 DOI: 10.7554/elife.91809] [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] [Indexed: 01/19/2024] Open
Abstract
Delineating the complex network of interactions between antigen-specific T cells and antigen presenting cells (APCs) is crucial for effective precision therapies against cancer, chronic infections, and autoimmunity. However, the existing arsenal for examining antigen-specific T cell interactions is restricted to a select few antigen-T cell receptor pairs, with limited in situ utility. This lack of versatility is largely due to the disruptive effects of reagents on the immune synapse, which hinder real-time monitoring of antigen-specific interactions. To address this limitation, we have developed a novel and versatile immune monitoring strategy by adding a short cysteine-rich tag to antigenic peptides that emits fluorescence upon binding to thiol-reactive biarsenical hairpin compounds. Our findings demonstrate the specificity and durability of the novel antigen-targeting probes during dynamic immune monitoring in vitro and in vivo. This strategy opens new avenues for biological validation of T-cell receptors with newly identified epitopes by revealing the behavior of previously unrecognized antigen-receptor pairs, expanding our understanding of T cell responses.
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Affiliation(s)
- Munir Akkaya
- Department of Internal Medicine, Division of Rheumatology and Immunology, The College of Medicine, The Ohio State UniversityColumbusUnited States
- Microbial Infection and Immunity, The Ohio State University Wexner Medical CenterColumbusUnited States
- Pelotonia Institute for Immuno-Oncology, The Ohio State UniversityColumbusUnited States
| | - Jafar Al Souz
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Daniel Williams
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Rahul Kamdar
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Olena Kamenyeva
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Juraj Kabat
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Ethan Shevach
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Billur Akkaya
- Pelotonia Institute for Immuno-Oncology, The Ohio State UniversityColumbusUnited States
- Department of Neurology, The Ohio State University Wexner Medical CenterColumbusUnited States
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10
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Lucidi M, Capecchi G, Visaggio D, Gasperi T, Parisi M, Cincotti G, Rampioni G, Visca P, Kolmakov K. Expanding the microbiologist toolbox via new far-red-emitting dyes suitable for bacterial imaging. Microbiol Spectr 2024; 12:e0369023. [PMID: 38095476 PMCID: PMC10782969 DOI: 10.1128/spectrum.03690-23] [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: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE By harnessing the versatility of fluorescence microscopy and super-resolution imaging, bacteriologists explore critical aspects of bacterial physiology and resolve bacterial structures sized beyond the light diffraction limit. These techniques are based on fluorophores with profitable photochemical and tagging properties. The paucity of available far-red (FR)-emitting dyes for bacterial imaging strongly limits the multicolor choice of bacteriologists, hindering the possibility of labeling multiple structures in a single experiment. The set of FR fluorophores characterized in this study expands the palette of dyes useful for microbiologists, as they can be used for bacterial LIVE/DEAD staining and for tagging the membranes of viable Escherichia coli and Bacillus subtilis cells. The absence of toxicity makes these dyes suitable for live-cell imaging and allows monitoring of bacterial membrane biogenesis. Moreover, a newly synthesized FR-fluorophore can be employed for imaging bacterial membranes with stimulated emission depletion microscopy, a super-resolution technique capable of increasing the resolving power of conventional microscopes.
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Affiliation(s)
- Massimiliano Lucidi
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | | | - Daniela Visaggio
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Tecla Gasperi
- Department of Science, Roma Tre University, Rome, Italy
| | - Miranda Parisi
- Department of Engineering, University Roma Tre, Rome, Italy
| | | | - Giordano Rampioni
- Department of Science, Roma Tre University, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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11
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Alfonso C, Sobrinos-Sanguino M, Luque-Ortega JR, Zorrilla S, Monterroso B, Nuero OM, Rivas G. Studying Macromolecular Interactions of Cellular Machines by the Combined Use of Analytical Ultracentrifugation, Light Scattering, and Fluorescence Spectroscopy Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:89-107. [PMID: 38507202 DOI: 10.1007/978-3-031-52193-5_7] [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: 03/22/2024]
Abstract
Cellular machines formed by the interaction and assembly of macromolecules are essential in many processes of the living cell. These assemblies involve homo- and hetero-associations, including protein-protein, protein-DNA, protein-RNA, and protein-polysaccharide associations, most of which are reversible. This chapter describes the use of analytical ultracentrifugation, light scattering, and fluorescence-based methods, well-established biophysical techniques, to characterize interactions leading to the formation of macromolecular complexes and their modulation in response to specific or unspecific factors. We also illustrate, with several examples taken from studies on bacterial processes, the advantages of the combined use of subsets of these techniques as orthogonal analytical methods to analyze protein oligomerization and polymerization, interactions with ligands, hetero-associations involving membrane proteins, and protein-nucleic acid complexes.
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Affiliation(s)
- Carlos Alfonso
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Marta Sobrinos-Sanguino
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Juan Román Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Silvia Zorrilla
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Begoña Monterroso
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Oscar M Nuero
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Germán Rivas
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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12
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Scribano FJ, Engevik KA, Gebert JT, Hyser JM. Live-Cell Fluorescence Imaging for Virus-Host Interactions. Methods Mol Biol 2024; 2751:33-46. [PMID: 38265708 DOI: 10.1007/978-1-0716-3617-6_3] [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] [Indexed: 01/25/2024]
Abstract
Recent technological advances in microscopy have facilitated novel approaches to investigate host-pathogen interactions. In particular, improvements in both microscope hardware and engineered biosensors have helped to overcome barriers to live-cell imaging with fluorescence microscopy. Live fluorescent microscopy allows for the detection of discrete signaling events and protein localization, improving our ability to assess the effects of pharmacologic agents, microbes, or infection with high temporal resolution. Here we describe a protocol for long-term live-cell fluorescence imaging of virus infected cell lines.
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Affiliation(s)
- Francesca J Scribano
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kristen A Engevik
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - J Thomas Gebert
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph M Hyser
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA.
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13
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Akkaya M, Al Souz J, Williams D, Kamdar R, Kamenyeva O, Kabat J, Shevach EM, Akkaya B. Illuminating T cell-dendritic cell interactions in vivo by FlAsHing antigens. RESEARCH SQUARE 2023:rs.3.rs-3193191. [PMID: 37546912 PMCID: PMC10402196 DOI: 10.21203/rs.3.rs-3193191/v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Delineating the complex network of interactions between antigen-specific T cells and antigen presenting cells (APCs) is crucial for effective precision therapies against cancer, chronic infections, and autoimmunity. However, the existing arsenal for examining antigen-specific T cell interactions is restricted to a select few antigen-T cell receptor pairs, with limited in situ utility. This lack of versatility is largely due to the disruptive effects of reagents on the immune synapse, which hinder real-time monitoring of antigen-specific interactions. To address this limitation, we have developed a novel and versatile immune monitoring strategy by adding a short cysteine-rich tag to antigenic peptides that emits fluorescence upon binding to thiol-reactive biarsenical hairpin compounds. Our findings demonstrate the specificity and durability of the novel antigen-targeting probes during dynamic immune monitoring in vitro and in vivo. This strategy opens new avenues for biological validation of T-cell receptors with newly identified epitopes by revealing the behavior of previously unrecognized antigen-receptor pairs, expanding our understanding of T cell responses.
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Affiliation(s)
- Munir Akkaya
- Department of Internal Medicine, Division of Rheumatology and Immunology, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Jafar Al Souz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Williams
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rahul Kamdar
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Olena Kamenyeva
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Juraj Kabat
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ethan M. Shevach
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Billur Akkaya
- Department of Neurology, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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14
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Akkaya M, Al Souz J, Williams D, Kamdar R, Kamenyeva O, Kabat J, Shevach EM, Akkaya B. Illuminating T cell-dendritic cell interactions in vivo by FlAsHing antigens. RESEARCH SQUARE 2023:rs.3.rs-3193191. [PMID: 37546912 PMCID: PMC10402196 DOI: 10.21203/rs.3.rs-3193191/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Delineating the complex network of interactions between antigen-specific T cells and antigen presenting cells (APCs) is crucial for effective precision therapies against cancer, chronic infections, and autoimmunity. However, the existing arsenal for examining antigen-specific T cell interactions is restricted to a select few antigen-T cell receptor pairs, with limited in situ utility. This lack of versatility is largely due to the disruptive effects of reagents on the immune synapse, which hinder real-time monitoring of antigen-specific interactions. To address this limitation, we have developed a novel and versatile immune monitoring strategy by adding a short cysteine-rich tag to antigenic peptides that emits fluorescence upon binding to thiol-reactive biarsenical hairpin compounds. Our findings demonstrate the specificity and durability of the novel antigen-targeting probes during dynamic immune monitoring in vitro and in vivo. This strategy opens new avenues for biological validation of T-cell receptors with newly identified epitopes by revealing the behavior of previously unrecognized antigen-receptor pairs, expanding our understanding of T cell responses.
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Affiliation(s)
- Munir Akkaya
- Department of Internal Medicine, Division of Rheumatology and Immunology, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Jafar Al Souz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Williams
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rahul Kamdar
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Olena Kamenyeva
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Juraj Kabat
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ethan M. Shevach
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Billur Akkaya
- Department of Neurology, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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15
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Malakoutikhah M, Mahran R, Gooran N, Masoumi A, Lundell K, Liljeblad A, Guiley K, Dai S, Zheng Q, Zhu L, Shokat KM, Kopra K, Härmä H. Nanomolar Protein Thermal Profiling with Modified Cyanine Dyes. Anal Chem 2023; 95:18344-18351. [PMID: 38060502 PMCID: PMC10733900 DOI: 10.1021/acs.analchem.3c02844] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023]
Abstract
Protein properties and interactions have been widely investigated by using external labels. However, the micromolar sensitivity of the current dyes limits their applicability due to the high material consumption and assay cost. In response to this challenge, we synthesized a series of cyanine5 (Cy5) dye-based quencher molecules to develop an external dye technique to probe proteins at the nanomolar protein level in a high-throughput one-step assay format. Several families of Cy5 dye-based quenchers with ring and/or side-chain modifications were designed and synthesized by introducing organic small molecules or peptides. Our results showed that steric hindrance and electrostatic interactions are more important than hydrophobicity in the interaction between the luminescent negatively charged europium-chelate-labeled peptide (Eu-probe) and the quencher molecules. The presence of substituents on the quencher indolenine rings reduces their quenching property, whereas the increased positive charge on the indolenine side chain improved the interaction between the quenchers and the luminescent compound. The designed quencher structures entirely altered the dynamics of the Eu-probe (protein-probe) for studying protein stability and interactions, as we were able to reduce the quencher concentration 100-fold. Moreover, the new quencher molecules allowed us to conduct the experiments using neutral buffer conditions, known as the peptide-probe assay. These improvements enabled us to apply the method in a one-step format for nanomolar protein-ligand interaction and protein profiling studies instead of the previously developed two-step protocol. These improvements provide a faster and simpler method with lower material consumption.
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Affiliation(s)
| | - Randa Mahran
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Negin Gooran
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Ahmadreza Masoumi
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Katri Lundell
- Laboratory
of Synthetic Drug Chemistry, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Arto Liljeblad
- Laboratory
of Synthetic Drug Chemistry, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Keelan Guiley
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
- Current
address: Rezo Therapeutics, Inc., San Francisco, California 94158, United States
| | - Shizhong Dai
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
- Current
address: Department of Genetics, Stanford
University, Stanford, California 94305, United States
| | - Qinheng Zheng
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Lawrence Zhu
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Kevan M. Shokat
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Kari Kopra
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Harri Härmä
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
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16
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Szepesi Kovács D, Kontra B, Chiovini B, Müller D, Tóth EZ, Ábrányi-Balogh P, Wittner L, Várady G, Turczel G, Farkas Ö, Owen MC, Katona G, Győrffy B, Keserű GM, Mucsi Z, Rózsa BJ, Kovács E. Effective synthesis, development and application of a highly fluorescent cyanine dye for antibody conjugation and microscopy imaging. Org Biomol Chem 2023; 21:8829-8836. [PMID: 37917021 DOI: 10.1039/d3ob01471a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
An asymmetric cyanine-type fluorescent dye was designed and synthesized via a versatile, multi-step process, aiming to conjugate with an Her2+ receptor specific antibody by an azide-alkyne click reaction. The aromaticity and the excitation and relaxation energetics of the fluorophore were characterized by computational methods. The synthesized dye exhibited excellent fluorescence properties for confocal microscopy, offering efficient applicability in in vitro imaging due to its merits such as a high molar absorption coefficient (36 816 M-1 cm-1), excellent brightness, optimal wavelength (627 nm), larger Stokes shift (26 nm) and appropriate photostability compared to cyanines. The conjugated cyanine-trastuzumab was constructed via an effective, metal-free, strain-promoted azide-alkyne click reaction leading to a regulated number of dyes being conjugated. This novel cyanine-labelled antibody was successfully applied for in vitro confocal imaging and flow cytometry of Her2+ tumor cells.
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Affiliation(s)
- Dénes Szepesi Kovács
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Bence Kontra
- Brain Vision Center, H-1094 Budapest, Hungary
- Femtonics Ltd., H-1094 Budapest, Hungary
- Semmelweis University Doctoral School, H-1085 Budapest, Hungary
| | - Balázs Chiovini
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, H-1444 Budapest, Hungary
| | - Dalma Müller
- Semmelweis University Doctoral School, H-1085 Budapest, Hungary
- Oncology Biomarker Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Bioinformatics, Semmelweis University, H-1094, Budapest, Hungary
| | - Estilla Zsófia Tóth
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Semmelweis University Doctoral School, H-1085 Budapest, Hungary
- Integrative Neuroscience Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Lucia Wittner
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Integrative Neuroscience Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - György Várady
- Molecular Cell Biology Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Gábor Turczel
- NMR Research Laboratory, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Ödön Farkas
- Department of Organic Chemistry, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Michael C Owen
- Institute of Chemistry, University of Miskolc, Miskolc H-3515, Hungary
- Higher Education and Industrial Cooperation Centre, University of Miskolc, Miskolc H-3515, Hungary
| | - Gergely Katona
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, H-1444 Budapest, Hungary
| | - Balázs Győrffy
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Oncology Biomarker Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Bioinformatics, Semmelweis University, H-1094, Budapest, Hungary
| | - György Miklós Keserű
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Zoltán Mucsi
- Brain Vision Center, H-1094 Budapest, Hungary
- Femtonics Ltd., H-1094 Budapest, Hungary
- Institute of Chemistry, University of Miskolc, Miskolc H-3515, Hungary
| | - Balázs J Rózsa
- Brain Vision Center, H-1094 Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, H-1444 Budapest, Hungary
- Laboratory of 3D Functional Network and Dendritic Imaging, HUN-REN Institute of Experimental Medicine, H-1083 Budapest, Hungary
| | - Ervin Kovács
- Femtonics Ltd., H-1094 Budapest, Hungary
- Polymer Chemistry and Physics Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary.
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17
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Sviben I, Glavaš M, Erben A, Bachelart T, Pavlović Saftić D, Piantanida I, Basarić N. Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides. Molecules 2023; 28:7533. [PMID: 38005255 PMCID: PMC10672942 DOI: 10.3390/molecules28227533] [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: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Dipeptides 1 and 2 were synthesized from unnatural amino acids containing pyrene as a fluorescent label and polynucleotide binding unit, and modified tyrosine as a photochemically reactive unit. Photophysical properties of the peptides were investigated by steady-state and time-resolved fluorescence. Both peptides are fluorescent (Φf = 0.3-0.4) and do not show a tendency to form pyrene excimers in the concentration range < 10-5 M, which is important for their application in the fluorescent labeling of polynucleotides. Furthermore, both peptides are photochemically reactive and undergo deamination delivering quinone methides (QMs) (ΦR = 0.01-0.02), as indicated from the preparative photomethanolysis study of the corresponding N-Boc protected derivatives 7 and 8. Both peptides form stable complexes with polynucleotides (log Ka > 6) by noncovalent interactions and similar affinities, binding to minor grooves, preferably to the AT reach regions. Peptide 2 with a longer spacer between the fluorophore and the photo-activable unit undergoes a more efficient deamination reaction, based on the comparison with the N-Boc protected derivatives. Upon light excitation of the complex 2·oligoAT10, the photo-generation of QM initiates the alkylation, which results in the fluorescent labeling of the oligonucleotide. This study demonstrated, as a proof of principle, that small molecules can combine dual forms of fluorescent labeling of polynucleotides, whereby initial addition of the dye rapidly forms a reversible high-affinity noncovalent complex with ds-DNA/RNA, which can be, upon irradiation by light, converted to the irreversible (covalent) form. Such a dual labeling ability of a dye could have many applications in biomedicinal sciences.
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Affiliation(s)
| | | | | | | | | | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
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18
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Archipowa N, Wittmann L, Köckenberger J, Ertl FJ, Gleixner J, Keller M, Heinrich MR, Kutta RJ. Characterization of Fluorescent Dyes Frequently Used for Bioimaging: Photophysics and Photocatalytical Reactions with Proteins. J Phys Chem B 2023; 127:9532-9542. [PMID: 37903729 DOI: 10.1021/acs.jpcb.3c04484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Derivatives of the rhodamine-based dye 5-TAMRA (5-carboxy-tetramethylrhodamine) and the indocarbocyanine-type Cy3B (cyclized derivative of the cyanine dye Cy3), both representing important fluorophores frequently used for the labeling of biomolecules (proteins, nucleic acids) and bioactive compounds, such as receptor ligands, were photophysically investigated in aqueous solution, i.e., in neat phosphate-buffered saline (PBS) and in PBS supplemented with 1 wt % bovine serum albumin (BSA). The dyes exhibit comparable absorption (λabs,max: 550-569 nm) and emission wavelengths (λem,max: 580-582 nm), and similar S1 lifetimes (2.27-2.75 ns), and their excited state deactivation proceeds mainly via the lowest excited singlet state (triplet quantum yield ca. 1%). However, the probes show marked differences with respect to their fluorescence quantum yield and photostability. While 5-TAMRA shows a lower quantum yield (37-39%) than the Cy3B derivative (ca. 57%), its photostability is considerably higher compared to Cy3B. Generally, the impact of the protein on the photophysics is low. However, on prolonged illumination, both fluorescent dyes undergo a photocatalytic reaction with tryptophan residues of BSA mediated by sensitized singlet oxygen resulting in a tryptophan photoproduct with an absorption maximum around 330 nm. The overall results of this work will assist in choosing the right dye for the labeling of bioactive compounds, and the study demonstrates that experiments performed with 5-TAMRA or Cy3B-labeled compounds in a biological environment may be influenced by photochemical modification of experimentally relevant proteins at aromatic amino acid residues.
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Affiliation(s)
- Nataliya Archipowa
- Institute of Biophysics and Physical Biochemistry, Faculty of Biology and Preclinical Medicine, University of Regensburg, D-93053 Regensburg, Germany
| | - Lukas Wittmann
- Institute of Physical and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Johannes Köckenberger
- Department of Chemistry and Pharmacy, Molecular and Clinical Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Fabian J Ertl
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Jakob Gleixner
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy, Molecular and Clinical Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Roger Jan Kutta
- Institute of Physical and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
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19
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Molina M, Way LE, Ren Z, Liao Q, Guerra B, Shields B, Wang X, Kim H. A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments. CELL REPORTS METHODS 2023; 3:100614. [PMID: 37832544 PMCID: PMC10626211 DOI: 10.1016/j.crmeth.2023.100614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/28/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed an in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK tag substantially altered ParB's DNA compaction rates and its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. While it is typically assumed that short peptide tags minimally perturb protein function, our results urge researchers to carefully validate the use of tags for protein labeling. Our comprehensive analysis can be expanded and used as a guide to assess the impacts of other tags on DNA-binding proteins in single-molecule assays.
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Affiliation(s)
- Miranda Molina
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA; Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Lindsey E Way
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Qin Liao
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Bianca Guerra
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Brandon Shields
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Xindan Wang
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA.
| | - HyeongJun Kim
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA; Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA.
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20
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Richter D, Lakis E, Piel J. Site-specific bioorthogonal protein labelling by tetrazine ligation using endogenous β-amino acid dienophiles. Nat Chem 2023; 15:1422-1430. [PMID: 37400596 PMCID: PMC10533398 DOI: 10.1038/s41557-023-01252-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/24/2023] [Indexed: 07/05/2023]
Abstract
The tetrazine ligation is an inverse electron-demand Diels-Alder reaction widely used for bioorthogonal modifications due to its versatility, site specificity and fast reaction kinetics. A major limitation has been the incorporation of dienophiles in biomolecules and organisms, which relies on externally added reagents. Available methods require the incorporation of tetrazine-reactive groups by enzyme-mediated ligations or unnatural amino acid incorporation. Here we report a tetrazine ligation strategy, termed TyrEx (tyramine excision) cycloaddition, permitting autonomous dienophile generation in bacteria. It utilizes a unique aminopyruvate unit introduced by post-translational protein splicing at a short tag. Tetrazine conjugation occurs rapidly with a rate constant of 0.625 (15) M-1 s-1 and was applied to produce a radiolabel chelator-modified Her2-binding Affibody and intracellular, fluorescently labelled cell division protein FtsZ. We anticipate the labelling strategy to be useful for intracellular studies of proteins, as a stable conjugation method for protein therapeutics, as well as other applications.
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Affiliation(s)
- Daniel Richter
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Edgars Lakis
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.
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21
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Townsend JA, Marty MT. What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry. Methods 2023; 218:1-13. [PMID: 37482149 PMCID: PMC10529358 DOI: 10.1016/j.ymeth.2023.07.004] [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: 04/21/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.
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Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA.
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22
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Namitz KEW, Showalter SA, Cosgrove MS. Phase separation promotes a highly active oligomeric scaffold of the MLL1 core complex for regulation of histone H3K4 methylation. J Biol Chem 2023; 299:105204. [PMID: 37660926 PMCID: PMC10551905 DOI: 10.1016/j.jbc.2023.105204] [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: 07/05/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Enzymes that regulate the degree of histone H3 lysine 4 (H3K4) methylation are crucial for proper cellular differentiation and are frequently mutated in cancer. The Mixed lineage leukemia (MLL) family of enzymes deposit H3K4 mono-, di-, or trimethylation at distinct genomic locations, requiring precise spatial and temporal control. Despite evidence that the degree of H3K4 methylation is controlled in part by a hierarchical assembly pathway with key subcomplex components, we previously found that the assembled state of the MLL1 core complex is not favored at physiological temperature. To better understand this paradox, we tested the hypothesis that increasing the concentration of subunits in a biomolecular condensate overcomes this thermodynamic barrier via mass action. Here, we demonstrate that MLL1 core complex phase separation stimulates enzymatic activity up to 60-fold but not primarily by concentrating subunits into droplets. Instead, we found that stimulated activity is largely due to the formation of an altered oligomeric scaffold that greatly reduces substrate Km. We posit that phase separation-induced scaffolding of the MLL1 core complex is a potential "switch-like" mechanism for spatiotemporal control of H3K4 methylation through the rapid formation or dissolution of biomolecular condensates within RNA Pol II transcription factories.
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Affiliation(s)
- Kevin E W Namitz
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
| | - Scott A Showalter
- Department of Chemistry, Penn State University, University Park, Pennsylvania, USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA.
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23
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Coucke Q, Parveen N, Fernández GS, Qian C, Hofkens J, Debyser Z, Hendrix J. Particle-based phasor-FLIM-FRET resolves protein-protein interactions inside single viral particles. BIOPHYSICAL REPORTS 2023; 3:100122. [PMID: 37649577 PMCID: PMC10463199 DOI: 10.1016/j.bpr.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a popular modality to create additional contrast in fluorescence images. By carefully analyzing pixel-based nanosecond lifetime patterns, FLIM allows studying complex molecular populations. At the single-molecule or single-particle level, however, image series often suffer from low signal intensities per pixel, rendering it difficult to quantitatively disentangle different lifetime species, such as during Förster resonance energy transfer (FRET) analysis in the presence of a significant donor-only fraction. In this article we investigate whether an object localization strategy and the phasor approach to FLIM have beneficial effects when carrying out FRET analyses of single particles. Using simulations, we first showed that an average of ∼300 photons, spread over the different pixels encompassing single fluorescing particles and without background, is enough to determine a correct phasor signature (SD < 5% for a 4-ns lifetime). For immobilized single- or double-labeled dsDNA molecules, we next validated that particle-based phasor-FLIM-FRET readily allows estimating fluorescence lifetimes and FRET from single molecules. Thirdly, we applied particle-based phasor-FLIM-FRET to investigate protein-protein interactions in subdiffraction HIV-1 viral particles. To do this, we first quantitatively compared the fluorescence brightness, lifetime, and photostability of different popular fluorescent protein-based FRET probes when genetically fused to the HIV-1 integrase enzyme in viral particles, and conclude that eGFP, mTurquoise2, and mScarlet perform best. Finally, for viral particles coexpressing FRET-donor/acceptor-labeled IN, we determined the absolute FRET efficiency of IN oligomers. Available in a convenient open-source graphical user interface, we believe that particle-based phasor-FLIM-FRET is a promising tool to provide detailed insights in samples suffering from low overall signal intensities.
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Affiliation(s)
- Quinten Coucke
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Nagma Parveen
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Guillermo Solís Fernández
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- UFIEC, National Institute of Health Carlos III, Madrid, Spain
| | - Chen Qian
- Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science Munich (CIPSM), and Nanosystems Initiative Munich (NIM), Ludwig Maximilians-Universität München, Munich, Germany
| | - Johan Hofkens
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Hasselt, Belgium
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24
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van der Flier A, Hong V, Liu Z, Piepenhagen P, Ulinski G, Dumont JA, Orcutt KD, Goel A, Peters R, Salas J. Biodistribution of recombinant factor IX, extended half-life recombinant factor IX Fc fusion protein, and glycoPEGylated recombinant factor IX in hemophilia B mice. Blood Coagul Fibrinolysis 2023; 34:353-363. [PMID: 37577860 PMCID: PMC10481914 DOI: 10.1097/mbc.0000000000001230] [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: 04/15/2022] [Revised: 03/01/2023] [Accepted: 04/26/2023] [Indexed: 08/15/2023]
Abstract
Extended half-life recombinant FIX (rFIX) molecules have been generated to reduce the dosing burden and increase the protection of patients with hemophilia B. Clinical pharmacology studies with recombinant factor IX Fc fusion protein (rFIXFc) report a similar initial peak plasma recovery to that of rFIX, but with a larger volume of distribution. Although the pegylation of N9-GP results in a larger plasma recovery, there is a smaller volume of distribution, suggesting less extravasation of the latter drug. In this study, we set out to compare the biodistribution and tissue localization of rFIX, rFIXFc, and glycoPEGylated rFIX in a hemophilia B mouse model. Radiolabeled rFIX, rFIXFc, and rFIX-GP were employed in in vivo single-photon emission computed tomography imaging (SPECT/CT), microautoradiography (MARG), and histology to assess the distribution of FIX reagents over time. Immediately following injection, vascularized tissues demonstrated intense signal irrespective of FIX reagent. rFIX and rFIXFc were retained in joint and muscle areas through 5 half-lives, unlike rFIX-GP (assessed by SPECT). MARG and immunohistochemistry showed FIX agents localized at blood vessels among tissues, including liver, spleen, and kidney. Microautoradiographs, as well as fluorescent-labeled images of knee joint areas, demonstrated retention over time of FIX signal at the trabecular area of bone. Data indicate that rFIXFc is similar to rFIX in that it distributes outside the plasma compartment and is retained in certain tissues over time, while also retained at higher plasma levels. Overall, data suggest that Fc fusion does not impede the extravascular distribution of FIX.
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Affiliation(s)
| | | | | | | | | | | | - Kelly D. Orcutt
- Invicro LLC, A Konica Minolta Company, Boston, Massachusetts, USA
| | - Apollina Goel
- Invicro LLC, A Konica Minolta Company, Boston, Massachusetts, USA
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25
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Chu J, Romero A, Taulbee J, Aran K. Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300328. [PMID: 37226388 PMCID: PMC10524706 DOI: 10.1002/smll.202300328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Indexed: 05/26/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.
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Affiliation(s)
- Josephine Chu
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Andres Romero
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Jeffrey Taulbee
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kiana Aran
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Cardea, San Diego, CA, 92121, USA
- University of California Berkeley, Berkeley, CA, 94720, USA
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26
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De Silva ARI, Page RC. Ubiquitination detection techniques. Exp Biol Med (Maywood) 2023; 248:1333-1346. [PMID: 37787047 PMCID: PMC10625345 DOI: 10.1177/15353702231191186] [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] [Indexed: 10/04/2023] Open
Abstract
Ubiquitination is an intricately regulated post-translational modification that involves the covalent attachment of ubiquitin to a substrate protein. The complex dynamic nature of the ubiquitination process regulates diverse cellular functions including targeting proteins for degradation, cell cycle, deoxyribonucleic acid (DNA) damage repair, and numerous cell signaling pathways. Ubiquitination also serves as a crucial mechanism in protein quality control. Dysregulation in ubiquitination could result in lethal disease conditions such as cancers and neurodegenerative diseases. Therefore, the ubiquitination cascade has become an attractive target for therapeutic interventions. Enormous efforts have been made to detect ubiquitination involving different detection techniques to better grasp the underlying molecular mechanisms of ubiquitination. This review discusses a wide range of techniques stretching from the simplest assays to real-time assays. This includes western blotting/immunoblotting, fluorescence assays, chemiluminescence assays, spectrophotometric assays, and nanopore sensing assays. This review compares these applications, and the inherent advantages and limitations.
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Affiliation(s)
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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27
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Szepesi Kovács D, Chiovini B, Müller D, Tóth EZ, Fülöp A, Ábrányi-Balogh P, Wittner L, Várady G, Farkas Ö, Turczel G, Katona G, Győrffy B, Keserű GM, Mucsi Z, Rózsa BJ, Kovács E. Synthesis and Application of Two-Photon Active Fluorescent Rhodol Dyes for Antibody Conjugation and In Vitro Cell Imaging. ACS OMEGA 2023; 8:22836-22843. [PMID: 37396252 PMCID: PMC10308389 DOI: 10.1021/acsomega.3c01796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023]
Abstract
A novel family of julolidine-containing fluorescent rhodols equipped with a wide variety of substituents was synthesized in a versatile two-step process. The prepared compounds were fully characterized and exhibited excellent fluorescence properties for microscopy imaging. The best candidate was conjugated to the therapeutic antibody trastuzumab through a copper-free strain-promoted azide-alkyne click reaction. The rhodol-labeled antibody was successfully applied for in vitro confocal and two-photon microscopy imaging of Her2+ cells.
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Affiliation(s)
- Dénes Szepesi Kovács
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Budapest
University of Technology and Economics, H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Balázs Chiovini
- Faculty
of Information Technology and Bionics, Pázmány
Péter Catholic University, H-1444 Budapest, Hungary
| | - Dalma Müller
- Oncology
Biomarker Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
- Department
of Bioinformatics, Semmelweis University, H-1094 Budapest, Hungary
- Semmelweis
University Doctoral School, H-1085 Budapest Hungary
| | - Estilla Zsófia Tóth
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Semmelweis
University Doctoral School, H-1085 Budapest Hungary
- Integrative
Neuroscience Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
| | - Anna Fülöp
- Femtonics
Ltd., H-1094 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Budapest
University of Technology and Economics, H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Lucia Wittner
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Integrative
Neuroscience Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
| | - György Várady
- Molecular
Cell Biology Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
| | - Ödön Farkas
- Department
of Organic Chemistry, Eötvös
Loránd University, H-1117 Budapest, Hungary
| | - Gábor Turczel
- NMR
Research Laboratory, Research Centre for
Natural Sciences, H-1117 Budapest, Hungary
| | - Gergely Katona
- Faculty
of Information Technology and Bionics, Pázmány
Péter Catholic University, H-1444 Budapest, Hungary
| | - Balázs Győrffy
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Oncology
Biomarker Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
- Department
of Bioinformatics, Semmelweis University, H-1094 Budapest, Hungary
- Department
of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
| | - György Miklós Keserű
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Budapest
University of Technology and Economics, H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Zoltán Mucsi
- Brain Vision Center, H-1094 Budapest, Hungary
- Faculty
of Materials and Chemical Sciences, University
of Miskolc, Miskolc H-3515, Hungary
| | - Balázs J. Rózsa
- Faculty
of Information Technology and Bionics, Pázmány
Péter Catholic University, H-1444 Budapest, Hungary
- Brain Vision Center, H-1094 Budapest, Hungary
- Laboratory of 3D Functional Network and Dendritic Imaging, Institute of Experimental Medicine, H-1083 Budapest, Hungary
| | - Ervin Kovács
- Femtonics
Ltd., H-1094 Budapest, Hungary
- Polymer
Chemistry and Physics Research Group, Research
Centre for Natural Sciences, H-1117 Budapest, Hungary
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28
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Bailey MLP, Pratt SE, Hinrichsen M, Zhang Y, Bewersdorf J, Regan LJ, Mochrie SGJ. Uncovering diffusive states of the yeast membrane protein, Pma1, and how labeling method can change diffusive behavior. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:42. [PMID: 37294385 PMCID: PMC10369454 DOI: 10.1140/epje/s10189-023-00301-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
We present and analyze video-microscopy-based single-particle-tracking measurements of the budding yeast (Saccharomyces cerevisiae) membrane protein, Pma1, fluorescently labeled either by direct fusion to the switchable fluorescent protein, mEos3.2, or by a novel, light-touch, labeling scheme, in which a 5 amino acid tag is directly fused to the C-terminus of Pma1, which then binds mEos3.2. The track diffusivity distributions of these two populations of single-particle tracks differ significantly, demonstrating that labeling method can be an important determinant of diffusive behavior. We also applied perturbation expectation maximization (pEMv2) (Koo and Mochrie in Phys Rev E 94(5):052412, 2016), which sorts trajectories into the statistically optimum number of diffusive states. For both TRAP-labeled Pma1 and Pma1-mEos3.2, pEMv2 sorts the tracks into two diffusive states: an essentially immobile state and a more mobile state. However, the mobile fraction of Pma1-mEos3.2 tracks is much smaller ([Formula: see text]) than the mobile fraction of TRAP-labeled Pma1 tracks ([Formula: see text]). In addition, the diffusivity of Pma1-mEos3.2's mobile state is several times smaller than the diffusivity of TRAP-labeled Pma1's mobile state. Thus, the two different labeling methods give rise to very different overall diffusive behaviors. To critically assess pEMv2's performance, we compare the diffusivity and covariance distributions of the experimental pEMv2-sorted populations to corresponding theoretical distributions, assuming that Pma1 displacements realize a Gaussian random process. The experiment-theory comparisons for both the TRAP-labeled Pma1 and Pma1-mEos3.2 reveal good agreement, bolstering the pEMv2 approach.
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Affiliation(s)
- Mary Lou P Bailey
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA
| | - Susan E Pratt
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA
- Department of Physics, Yale University, New Haven, CT, 06511, USA
| | | | - Yongdeng Zhang
- Department of Cell Biology, Yale University, New Haven, CT, 06511, USA
| | - Joerg Bewersdorf
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA
- Department of Physics, Yale University, New Haven, CT, 06511, USA
- Department of Cell Biology, Yale University, New Haven, CT, 06511, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
| | - Lynne J Regan
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Center for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, 06511, UK
| | - Simon G J Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA.
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA.
- Department of Physics, Yale University, New Haven, CT, 06511, USA.
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29
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Tacke E, Hoang MD, Tatoueix K, Keromnes B, Van Eslande E, Durand P, Pieters G, Chevalier A. Unprecedented perspectives on the application of CinNapht fluorophores provided by a "late-stage" functionalization strategy. Chem Sci 2023; 14:6000-6010. [PMID: 37293654 PMCID: PMC10246687 DOI: 10.1039/d3sc01365k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/02/2023] [Indexed: 06/10/2023] Open
Abstract
A simple and easy-to-implement process based on a nucleophilic aromatic substitution reaction with a wide variety of nucleophiles on a fluorinated CinNapht is described. This process has the key advantage of introducing multiple functionalities at a very late stage, thus providing access to new applications including the synthesis of photostable and bioconjugatable large Stokes shift red emitting dyes and selective organelle imaging agents, as well as AIEE-based wash-free lipid droplet imaging in live cells with high signal-to-noise ratio. The synthesis of bench-stable CinNapht-F has been optimized and can be reproduced on a large scale, making it an easy-to-store starting material that can be used at will to prepare new molecular imaging tools.
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Affiliation(s)
- Eléonore Tacke
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
| | - Minh-Duc Hoang
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
| | - Kevin Tatoueix
- Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris-Saclay, CEA, INRAE 91191 Gif-sur-Yvette France
| | - Benoît Keromnes
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
| | - Elsa Van Eslande
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
| | - Philippe Durand
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
| | - Gregory Pieters
- Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris-Saclay, CEA, INRAE 91191 Gif-sur-Yvette France
| | - Arnaud Chevalier
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
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30
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Todaro B, Ottalagana E, Luin S, Santi M. Targeting Peptides: The New Generation of Targeted Drug Delivery Systems. Pharmaceutics 2023; 15:1648. [PMID: 37376097 DOI: 10.3390/pharmaceutics15061648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Peptides can act as targeting molecules, analogously to oligonucleotide aptamers and antibodies. They are particularly efficient in terms of production and stability in physiological environments; in recent years, they have been increasingly studied as targeting agents for several diseases, from tumors to central nervous system disorders, also thanks to the ability of some of them to cross the blood-brain barrier. In this review, we will describe the techniques employed for their experimental and in silico design, as well as their possible applications. We will also discuss advancements in their formulation and chemical modifications that make them even more stable and effective. Finally, we will discuss how their use could effectively help to overcome various physiological problems and improve existing treatments.
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Affiliation(s)
- Biagio Todaro
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Elisa Ottalagana
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- Fondazione Pisana per la Scienza, Via Ferruccio Giovannini 13, San Giuliano Terme, 56017 Pisa, Italy
| | - Stefano Luin
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Melissa Santi
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
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31
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Molina M, Way LE, Ren Z, Liao Q, Wang X, Kim H. Using DNA flow-stretching assay as a tool to validate the tagging of DNA-binding proteins for single-molecule experiments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.19.533373. [PMID: 36993356 PMCID: PMC10055205 DOI: 10.1101/2023.03.19.533373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK-tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK-tag substantially altered ParB's DNA compaction rates, its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. While it is typically assumed that short peptide tags minimally perturb protein function, our results urge researchers to carefully validate the use of tags for protein labeling. Our comprehensive analysis can be expanded and used as a guide to assess the impacts of other tags on DNA-binding proteins in single-molecule assays.
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Affiliation(s)
- Miranda Molina
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, Texas, United States of America
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, Texas, United States of America
- These authors contributed equally
| | - Lindsey E. Way
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, Indiana, United States of America
- These authors contributed equally
| | - Zhongqing Ren
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, Indiana, United States of America
| | - Qin Liao
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, Indiana, United States of America
| | - Xindan Wang
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, Indiana, United States of America
| | - HyeongJun Kim
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, Texas, United States of America
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, Texas, United States of America
- Lead contact
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32
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Xu R, Ouyang L, Chen H, Zhang G, Zhe J. Recent Advances in Biomolecular Detection Based on Aptamers and Nanoparticles. BIOSENSORS 2023; 13:bios13040474. [PMID: 37185549 PMCID: PMC10136534 DOI: 10.3390/bios13040474] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023]
Abstract
The fast, accurate detection of biomolecules, ranging from nucleic acids and small molecules to proteins and cellular secretions, plays an essential role in various biomedical applications. These include disease diagnostics and prognostics, environmental monitoring, public health, and food safety. Aptamer recognition (DNA or RNA) has gained extensive attention for biomolecular detection due to its high selectivity, affinity, reproducibility, and robustness. Concurrently, biosensing with nanoparticles has been widely used for its high carrier capacity, stability and feasibility of incorporating optical and catalytic activity, and enhanced diffusivity. Biosensors based on aptamers and nanoparticles utilize the combination of their advantages and have become a promising technology for detecting of a wide variety of biomolecules with high sensitivity, reliability, specificity, and detection speed. Via various sensing mechanisms, target biomolecules have been quantified in terms of optical (e.g., colorimetric and fluorometric), magnetic, and electrical signals. In this review, we summarize the recent advances in and compare different aptamer-nanoparticle-based biosensors by nanoparticle types and detection mechanisms. We also share our views on the highlights and challenges of the different nanoparticle-aptamer-based biosensors.
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Affiliation(s)
- Ruiting Xu
- Department of Mechanical Engineering, University of Akron, Akron, OH 44325, USA
| | - Leixin Ouyang
- Department of Mechanical Engineering, University of Akron, Akron, OH 44325, USA
| | - Heyi Chen
- Department of Mechanical Engineering, University of Akron, Akron, OH 44325, USA
| | - Ge Zhang
- Department of Biomedical Engineering, University of Akron, Akron, OH 44325, USA
| | - Jiang Zhe
- Department of Mechanical Engineering, University of Akron, Akron, OH 44325, USA
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33
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Karaca SA, Temel T, Uğur DY. Development of a sensitive HPLC method with fluorescence detection for determination of motilin in human plasma. Bioanalysis 2023; 15:219-229. [PMID: 37015034 DOI: 10.4155/bio-2023-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Background: Motilin is a peptide-structured gastrointestinal system hormone. In this study, a sensitive HPLC-fluorescence detection method was developed and validated for the quantification of motilin in human plasma. Materials & methods: Optimization processes were carried out with the experimental design methodology. Analyses were performed on a C8 column (4.6 × 150 mm, 3.5 μm particles) using water and acetonitrile containing trifluoroacetic acid as the mobile phase. Results & conclusion: The method was linear from 2 to 200 ng/ml of motilin. The assay variability was less than 5%. The limit of quantification was found to be 1.84 ng/ml. The applicability of the developed method was successfully demonstrated by quantifying the levels of motilin in human plasma samples.
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Affiliation(s)
- Sakine Atila Karaca
- Department of Analytical Chemistry, Faculty of Pharmacy, Anadolu University, Eskisehir, 26470, Turkey
| | - Tuncer Temel
- Department of Internal Medicine, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Duygu Yeniceli Uğur
- Department of Analytical Chemistry, Faculty of Pharmacy, Anadolu University, Eskisehir, 26470, Turkey
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34
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Liu K, Xu Z, Zhao Z, Chen Y, Chai Y, Ma L, Li S. A Dual Fluorescence Assay Enables High-Throughput Screening for Poly(ethylene terephthalate) Hydrolases. CHEMSUSCHEM 2023; 16:e202202019. [PMID: 36511949 DOI: 10.1002/cssc.202202019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/03/2022] [Indexed: 06/17/2023]
Abstract
The drastically increasing consumption of petroleum-derived plastics hasserious environmental impacts and raises public concerns. Poly(ethylene terephthalate) (PET) is amongst the most extensively produced synthetic polymers. Enzymatic hydrolysis of PET recently emerged as an enticing path for plastic degradation and recycling. In-lab directed evolution has revealed the great potential of PET hydrolases (PETases). However, the time-consuming and laborious PETase assays hinder the identification of effective variants in large mutant libraries. Herein, we devise and validate a dual fluorescence-based high-throughput screening (HTS) assay for a representative IsPETase. The two-round HTS of a pilot library consisting of 2850 IsPETase variants yields six mutant IsPETases with 1.3-4.9 folds improved activities. Compared to the currently used structure- or computational redesign-based PETase engineering, this HTS approach provides a new strategy for discovery of new beneficial mutation patterns of PETases.
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Affiliation(s)
- Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Ziping Xu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Zhiyi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Yuexing Chen
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Yating Chai
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Li Ma
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No. 168 Wenhai Middle Rd, Qingdao, Shandong, 266237, P. R. China
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35
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Woodhouse N, Majer J, Marshall P, Hood S, Notingher I. Quantification of Drugs in Brain and Liver Mimetic Tissue Models Using Raman Spectroscopy. APPLIED SPECTROSCOPY 2023; 77:246-260. [PMID: 36320126 PMCID: PMC10034474 DOI: 10.1177/00037028221139494] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Quantitative analysis of drug delivery with in biological systems is an integral challenge in drug development. Analytical techniques are important for assessing both drug target delivery, target action, and drug toxicology. Using mimetic tissue models, we have investigated the efficacy of Raman spectroscopy in quantitative detection of alkyne group and deuterated drugs in rat brain and rat liver tissue models. Lasers with 671 nm and 785 nm wavelengths were assessed for their feasibility in this application due to opposing relative benefits and disadvantages. Thin tissue sections have been tested as a practical means of reducing autofluorescent background by minimizing out-of-focus tissue and therefore maximizing photobleaching rates. Alkyne-tagged drugs were quantitatively measured at 18 ± 5 μg/g drug/tissue mass ratio in rat brain and at 34 ± 6 μg/g in rat liver. Quantification calibration curves were generated for a range of concentrations from 0-500 μg/g. These results show the potential of Raman spectroscopy as a diffraction-limited spatially resolved imaging technique for assessing drug delivery in tissue applications.
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Affiliation(s)
- Nathan Woodhouse
- School of Physics and Astronomy,
University
of Nottingham, Nottingham, UK
| | | | | | | | - Ioan Notingher
- School of Physics and Astronomy,
University
of Nottingham, Nottingham, UK
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36
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Hajba L, Jeong S, Chung DS, Guttman A. Capillary Gel Electrophoresis of Proteins: Historical overview and recent advances. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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37
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Del Real Mata C, Jeanne O, Jalali M, Lu Y, Mahshid S. Nanostructured-Based Optical Readouts Interfaced with Machine Learning for Identification of Extracellular Vesicles. Adv Healthc Mater 2023; 12:e2202123. [PMID: 36443009 DOI: 10.1002/adhm.202202123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/14/2022] [Indexed: 11/30/2022]
Abstract
Extracellular vesicles (EVs) are shed from cancer cells into body fluids, enclosing molecular information about the underlying disease with the potential for being the target cancer biomarker in emerging diagnosis approaches such as liquid biopsy. Still, the study of EVs presents major challenges due to their heterogeneity, complexity, and scarcity. Recently, liquid biopsy platforms have allowed the study of tumor-derived materials, holding great promise for early-stage diagnosis and monitoring of cancer when interfaced with novel adaptations of optical readouts and advanced machine learning analysis. Here, recent advances in labeled and label-free optical techniques such as fluorescence, plasmonic, and chromogenic-based systems interfaced with nanostructured sensors like nanoparticles, nanoholes, and nanowires, and diverse machine learning analyses are reviewed. The adaptability of the different optical methods discussed is compared and insights are provided into prospective avenues for the translation of the technological approaches for cancer diagnosis. It is discussed that the inherent augmented properties of nanostructures enhance the sensitivity of the detection of EVs. It is concluded by reviewing recent integrations of nanostructured-based optical readouts with diverse machine learning models as novel analysis ventures that can potentially increase the capability of the methods to the point of translation into diagnostic applications.
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Affiliation(s)
| | - Olivia Jeanne
- McGill University, Department of Bioengineering, Montreal, QC, H3A 0E9, Canada
| | - Mahsa Jalali
- McGill University, Department of Bioengineering, Montreal, QC, H3A 0E9, Canada
| | - Yao Lu
- McGill University, Department of Bioengineering, Montreal, QC, H3A 0E9, Canada
| | - Sara Mahshid
- McGill University, Department of Bioengineering, Montreal, QC, H3A 0E9, Canada
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38
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Montiel L, Spada F, Crisp A, Serdjukow S, Carell T, Frischmuth T. Divergent Synthesis of Ultrabright and Dendritic Xanthenes for Enhanced Click-Chemistry-Based Bioimaging. Chemistry 2023; 29:e202202633. [PMID: 36317813 PMCID: PMC10107433 DOI: 10.1002/chem.202202633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 12/13/2022]
Abstract
Biorthogonal labelling with fluorescent small molecules is an indispensable tool for diagnostic and biomedical applications. In dye-based 5-ethynyl-2'-deoxyuridine (EdU) cell proliferation assays, augmentation of the fluorescent signal entails an overall enhancement in the sensitivity and quality of the method. To this end, a rapid, divergent synthetic procedure that provides ready-to-click pH-insensitive rhodamine dyes exhibiting outstanding brightness was established. Compared to the shortest available synthesis of related high quantum-yielding rhodamines, two fewer synthetic steps are required. In a head-to-head imaging comparison involving copper(I)-catalyzed azide alkyne cycloaddition reactions with in vitro administered EdU, our new 3,3-difluoroazetidine rhodamine azide outperformed the popular 5-TAMRA-azide, making it among the best available choices when it comes to fluorescent imaging of DNA. In a further exploration of the fluorescence properties of these dyes, a set of bis-MPA dendrons carrying multiple fluorescein or rhodamine units was prepared by branching click chemistry. Fluorescence self-quenching of fluorescein- and rhodamine-functionalized dendrons limited the suitability of the dyes as labels in EdU-based experiments but provided new insights into these effects.
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Affiliation(s)
- Luis Montiel
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany.,Department of Chemistry, Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universität München (LMU), Butenandtstr. 5-13, 81377, Munich, Germany
| | - Fabio Spada
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Antony Crisp
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Sascha Serdjukow
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Thomas Carell
- Department of Chemistry, Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universität München (LMU), Butenandtstr. 5-13, 81377, Munich, Germany
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39
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Alshareedah I, Banerjee PR. Measurement of Protein and Nucleic Acid Diffusion Coefficients Within Biomolecular Condensates Using In-Droplet Fluorescence Correlation Spectroscopy. Methods Mol Biol 2023; 2563:199-213. [PMID: 36227474 PMCID: PMC9884114 DOI: 10.1007/978-1-0716-2663-4_9] [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] [Indexed: 11/06/2022]
Abstract
Liquid-liquid phase separation of protein and RNA complexes into biomolecular condensates has emerged as a ubiquitous phenomenon in living systems. These protein-RNA condensates are thought to be involved in many biological functions in all forms of life. One of the most sought-after properties of these condensates is their dynamical properties, as they are a major determinant of condensate physiological function and disease processes. Measurement of the diffusion dynamics of individual components in a multicomponent biomolecular condensate is therefore routinely performed. Here, we outline the experimental procedure for performing in-droplet fluorescence correlation spectroscopy (FCS) measurements to extract the diffusion coefficient of individual molecules within a biomolecular condensate in vitro. Unlike more common experiments such as fluorescence recovery after photobleaching (FRAP), where data interpretation is not straightforward and strictly model dependent, FCS offers a robust and more accurate way to quantify biomolecular diffusion rates in the dense phase. The small observation volume allows FCS experiments to report on the local diffusion coefficient within a spatial resolution of <1 μm, making it ideal for probing spatial inhomogeneities within condensates as well as variable dynamics within subcompartments of multiphasic condensates.
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Affiliation(s)
| | - Priya R Banerjee
- Department of Physics, University at Buffalo SUNY, Buffalo, NY, USA.
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40
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dos Santos Rodrigues FH, Delgado GG, Santana da Costa T, Tasic L. Applications of fluorescence spectroscopy in protein conformational changes and intermolecular contacts. BBA ADVANCES 2023; 3:100091. [PMID: 37207090 PMCID: PMC10189374 DOI: 10.1016/j.bbadva.2023.100091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
Emission fluorescence is one of the most versatile and powerful biophysical techniques used in several scientific subjects. It is extensively applied in the studies of proteins, their conformations, and intermolecular contacts, such as in protein-ligand and protein-protein interactions, allowing qualitative, quantitative, and structural data elucidation. This review, aimed to outline some of the most widely used fluorescence techniques in this area, illustrate their applications and display a few examples. At first, the data on the intrinsic fluorescence of proteins is disclosed, mainly on the tryptophan side chain. Predominantly, research to study protein conformational changes, protein interactions, and changes in intensities and shifts of the fluorescence emission maximums were discussed. Fluorescence anisotropy or fluorescence polarization is a measurement of the changing orientation of a molecule in space, concerning the time between the absorption and emission events. Absorption and emission indicate the spatial alignment of the molecule's dipoles relative to the electric vector of the electromagnetic wave of excitation and emitted light, respectively. In other words, if the fluorophore population is excited with vertically polarized light, the emitted light will retain some polarization based on how fast it rotates in solution. Therefore, fluorescence anisotropy can be successfully used in protein-protein interaction investigations. Then, green fluorescent proteins (GFPs), photo-transformable fluorescent proteins (FPs) such as photoswitchable and photoconvertible FPs, and those with Large Stokes Shift (LSS) are disclosed in more detail. FPs are potent tools for the study of biological systems. Their versatility and wide range of colours and properties allow many applications. Finally, the application of fluorescence in life sciences is exposed, especially the application of FPs in fluorescence microscopy techniques with super-resolution that enables precise in vivo photolabeling to monitor the movement and interactions of target proteins.
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Affiliation(s)
| | - Gonzalo Garcia Delgado
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, University of Campinas, P. O. Box 6154, Campinas 13083-970, SP, Brazil
| | - Thyerre Santana da Costa
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, University of Campinas, P. O. Box 6154, Campinas 13083-970, SP, Brazil
| | - Ljubica Tasic
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, University of Campinas, P. O. Box 6154, Campinas 13083-970, SP, Brazil
- Corresponding author: Ljubica Tasic: IQ, UNICAMP, Rua Josué de Castro sn, 13083-970 Campinas, SP, Brazil
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41
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Martin MI, Pati AK, Abeywickrama CS, Bar S, Kilic Z, Altman RB, Blanchard SC. Leveraging Baird aromaticity for advancement of bioimaging applications. J PHYS ORG CHEM 2023; 36:e4449. [PMID: 36590885 PMCID: PMC9799245 DOI: 10.1002/poc.4449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 02/01/2023]
Abstract
In this perspective, we highlight the recent progress in utilizing Baird aromatic species to improve fluorophore performance in microscopy and imaging applications. We specifically focus on the origins of the use of Baird aromaticity in fluorescence applications, the development of “self‐healing” fluorophores leveraging cyclooctatetraene’ Baird aromaticity, and where developments need to occur to optimize this technology.
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Affiliation(s)
- Maxwell I. Martin
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTNUSA
| | - Avik K. Pati
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
| | - Chathura S. Abeywickrama
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTNUSA
| | - Sukanta Bar
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTNUSA
| | - Zeliha Kilic
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
| | - Roger B. Altman
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTNUSA
| | - Scott C. Blanchard
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTNUSA
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42
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Ganser LR, Ge Y, Myong S. Single-Molecule Fluorescence Methods to Study Protein-RNA Interactions Underlying Biomolecular Condensates. Methods Mol Biol 2023; 2563:149-160. [PMID: 36227472 DOI: 10.1007/978-1-0716-2663-4_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Many biomolecular condensates, including nucleoli and stress granules, form via dynamic multivalent protein-protein and protein-RNA interactions. These molecular interactions nucleate liquid-liquid phase separation (LLPS) and determine condensate properties, such as size and fluidity. Here, we outline the experimental procedures for single-molecule fluorescence experiments to probe protein-RNA interactions underlying LLPS. The experiments include single-molecule Förster (Fluorescence) resonance energy transfer (smFRET) to monitor protein-induced conformational changes in the RNA, protein-induced fluorescence enhancement (PIFE) to measure protein-RNA encounters, and single-molecule nucleation experiments to quantify the association and buildup of proteins on a nucleating RNA. Together, these experiments provide complementary approaches to elucidate a molecular view of the protein-RNA interactions that drive ribonucleoprotein condensate formation.
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Affiliation(s)
- Laura R Ganser
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Yingda Ge
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
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43
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Kumarswamyreddy N, Nakagawa A, Endo H, Shimotohno A, Torii KU, Bode JW, Oishi S. Chemical synthesis of the EPF-family of plant cysteine-rich proteins and late-stage dye attachment by chemoselective amide-forming ligations. RSC Chem Biol 2022; 3:1422-1431. [PMID: 36544577 PMCID: PMC9709926 DOI: 10.1039/d2cb00155a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Chemical protein synthesis can provide well-defined modified proteins. Herein, we report the chemical synthesis of plant-derived cysteine-rich secretory proteins and late-stage derivatization of the synthetic proteins. The syntheses were achieved with distinct chemoselective amide bond forming reactions - EPF2 by native chemical ligation (NCL), epidermal patterning factor (EPF) 1 by the α-ketoacid-hydroxylamine (KAHA) ligation, and fluorescent functionalization of their folded variants by potassium acyltrifluoroborate (KAT) ligation. The chemically synthesized EPFs exhibit bioactivity on stomatal development in Arabidopsis thaliana. Comprehensive synthesis of EPF derivatives allowed us to identify suitable fluorescent variants for bioimaging of the subcellar localization of EPFs.
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Affiliation(s)
- Nandarapu Kumarswamyreddy
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya UniversityChikusa Nagoya 464-8602Japan,Department of Chemistry, Indian Institute of Technology TirupatiTirupati517619Andhra PradeshIndia
| | - Ayami Nakagawa
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya UniversityChikusa Nagoya 464-8602Japan
| | - Hitoshi Endo
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya UniversityChikusa Nagoya 464-8602Japan
| | - Akie Shimotohno
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya UniversityChikusa Nagoya 464-8602Japan
| | - Keiko U. Torii
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya UniversityChikusa Nagoya 464-8602Japan,Howard Hughes Medical Institute and Department of Molecular Biosciences, The University of Texas at AustinAustinTX 78712USA
| | - Jeffrey W. Bode
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya UniversityChikusa Nagoya 464-8602Japan,Department of Chemistry and Applied Biosciences, ETH ZürichZürich 8093Switzerland
| | - Shunsuke Oishi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya UniversityChikusa Nagoya 464-8602Japan
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44
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Gueta O, Amiram M. Expanding the chemical repertoire of protein-based polymers for drug-delivery applications. Adv Drug Deliv Rev 2022; 190:114460. [PMID: 36030987 DOI: 10.1016/j.addr.2022.114460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 01/24/2023]
Abstract
Expanding the chemical repertoire of natural and artificial protein-based polymers (PBPs) can enable the production of sequence-defined, yet chemically diverse, biopolymers with customized or new properties that cannot be accessed in PBPs composed of only natural amino acids. Various approaches can enable the expansion of the chemical repertoire of PBPs, including chemical and enzymatic treatments or the incorporation of unnatural amino acids. These techniques are employed to install a wide variety of chemical groups-such as bio-orthogonally reactive, cross-linkable, post-translation modifications, and environmentally responsive groups-which, in turn, can facilitate the design of customized PBP-based drug-delivery systems with modified, fine-tuned, or entirely new properties and functions. Here, we detail the existing and emerging technologies for expanding the chemical repertoire of PBPs and review several chemical groups that either demonstrate or are anticipated to show potential in the design of PBP-based drug delivery systems. Finally, we provide our perspective on the remaining challenges and future directions in this field.
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Affiliation(s)
- Osher Gueta
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel
| | - Miriam Amiram
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
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45
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Tanaka S, Narumi T, Mase N, Sato K. Hydrazide-Mediated Solubilizing Strategy for Poorly Soluble Peptides Using a Dialkoxybenzaldehyde Linker. Chem Pharm Bull (Tokyo) 2022; 70:707-715. [PMID: 36184453 DOI: 10.1248/cpb.c22-00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proteins modified in a controlled manner with artificial moieties such as fluorophores or affinity tags have been shown to be a powerful tool for functional or structural analysis of proteins. A reliable way to prepare proteins with a well-defined modification is protein synthesis. Although many successful syntheses have been reported, the poor aqueous solubility of synthetic intermediates causes difficulty in the chemical synthesis of proteins. Here we describe a solubilizing strategy for poorly soluble peptides which uses chemoselective incorporation of a hydrophilic tag onto a hydrazide in a peptide. We found that a hydrophilic tag possessing a dialkoxybenzaldehyde moiety can react with peptide hydrazides through reductive N-alkylation. No protecting groups are required for this reaction, and peptides modified in this way show enhanced solubility and consequently good peak separation during HPLC purification. The tag can be removed subsequently by treatment with trifluoroacetic acid to generate a free hydrazide, which can be converted in a one-pot reaction to a thioester for further modification. This method was validated by synthesis of a Lys63-linked ubiquitin dimer derivative. This late-stage solubilization can be applied in principal to any peptide and opens the possibility of the synthesis of proteins that have previously been considered inaccessible due to their poor solubility.
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Affiliation(s)
- Shoko Tanaka
- Graduate School of Science and Technology, Shizuoka University
| | - Tetsuo Narumi
- Graduate School of Science and Technology, Shizuoka University.,Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University.,Research Institute of Green Science and Technology, Shizuoka University
| | - Nobuyuki Mase
- Graduate School of Science and Technology, Shizuoka University.,Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University.,Research Institute of Green Science and Technology, Shizuoka University
| | - Kohei Sato
- Graduate School of Science and Technology, Shizuoka University.,Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University.,Research Institute of Green Science and Technology, Shizuoka University
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46
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Kern W, Müller M, Bandl C, Krempl N, Kratzer M. Anti-Adhesive Organosilane Coating Comprising Visibility on Demand. Polymers (Basel) 2022; 14:polym14194006. [PMID: 36235954 PMCID: PMC9573108 DOI: 10.3390/polym14194006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 12/03/2022] Open
Abstract
There is a wide application field for anti-adhesive and hydrophobic coatings, stretching from self-cleaning surfaces over anti-graffiti and release coatings to demolding aids in the production of polymers. The typical materials for the latter are hard coatings, including TiN, CrN, diamond-like carbon, etc. Alternatively, organosilane coatings based on perfluorinated compounds or molecules with long alkyl side chains can be employed. Although these functional layers are generally required to be invisible, there is a demand for a straightforward approach, which enables the temporary control of successful and homogeneous application as well as abrasion and wear of the coatings during use. For this purpose, a visibility-on-demand property was introduced to an already established anti-adhesive organosilane coating by incorporation of 1,8-naphthalimide-N-propyltriethoxysilane (NIPTES) as a fluorescent marker molecule. While the naphthalimide unit provides blue fluorescence under UV irradiation, the ethoxy groups of NIPTES enable the covalent coupling to the coating as a result of the hydrolysis and condensation reactions. As a consequence, the fluorescent marker molecule NIPTES can simply be added to the coating solution as an additional organosilane component, without the need for changes in the approved deposition procedure. The generated fluorescent anti-adhesive coatings were characterized by contact angle measurements, atomic force microscopy (AFM), as well as by different spectroscopic techniques, including FTIR, UV-Vis, fluorescence and X-ray photoelectron spectroscopy (XPS). In addition, the on-demand control function provided by the introduced fluorescence properties was evaluated along an injection molding process.
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Affiliation(s)
- Wolfgang Kern
- Montanuniversität Leoben, Chair in Chemistry of Polymeric Materials, Otto-Glöckel-Straße 2, A-8700 Leoben, Austria
| | - Matthias Müller
- Montanuniversität Leoben, Chair in Chemistry of Polymeric Materials, Otto-Glöckel-Straße 2, A-8700 Leoben, Austria
| | - Christine Bandl
- Montanuniversität Leoben, Chair in Chemistry of Polymeric Materials, Otto-Glöckel-Straße 2, A-8700 Leoben, Austria
- Correspondence: ; Tel.: +43-3842-402-2306
| | - Nina Krempl
- Montanuniversität Leoben, Chair in Polymer Processing, Otto-Glöckel-Straße 2, A-8700 Leoben, Austria
| | - Markus Kratzer
- Montanuniversität Leoben, Chair in Physics, Franz-Josef-Straße 18, 8700 Leoben, Austria
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47
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Patterson K, Romero-Reyes MA, Heemstra JM. Fluorescence Quenching of Xanthene Dyes during Amide Bond Formation Using DMTMM. ACS OMEGA 2022; 7:33046-33053. [PMID: 36157719 PMCID: PMC9494652 DOI: 10.1021/acsomega.2c03085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Fluorophore bioconjugation to proteins, nucleic acids, and other important molecules can provide a powerful approach to sensing, imaging, and quantifying chemical and biological processes. One of the most prevalent methods for fluorophore attachment is through the formation of amide bonds, which are often facilitated by coupling agents to activate carboxylic acid moieties for subsequent nucleophilic attack by amines. 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methyl-morpholinium chloride (DMTMM) is among the most popular of these coupling agents for bioconjugation due to its ability to facilitate amide bond formation in water. After observing quenching of 5-fluoresceinamine (5-FAM)-conjugated oligonucleotides in the presence of DMTMM, we sought to evaluate the magnitude and scope of this challenge by surveying the effect of DMTMM on a range of fluorescent dyes. A higher quenching effect was consistently observed for xanthene dyes compared to that for cyanine dyes. Further analysis of the impact of DMTMM on FAM shows that quenching occurs independently of whether the dye is free in solution or attached to an oligonucleotide or antibody. Furthermore, we found that FAM-conjugated DNA was unable to recover its fluorescence after the removal of DMTMM, and UV-vis and NMR analyses suggest the formation of new products, such as an adduct formed between FAM and the dimethoxytriazine of DMTMM. As such, DMTMM at high concentrations is not recommended for coupling reactions where targets are fluorescently labeled. This research serves as a word of caution to those utilizing xanthene-containing fluorophores in bioconjugation reactions involving DMTMM.
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Affiliation(s)
- Kristen
N. Patterson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Misael A. Romero-Reyes
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Chemistry, Hanover College, Hanover, Indiana 47243, United States
| | - Jennifer M. Heemstra
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
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48
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Heck JR, Miele E, Mouthaan RP, Frosz MH, Knowles TPJ, Euser TG. Label-free monitoring of proteins in optofluidic hollow-core photonic crystal fibres. Methods Appl Fluoresc 2022; 10. [PMID: 36084629 DOI: 10.1088/2050-6120/ac9113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/09/2022] [Indexed: 11/11/2022]
Abstract
The fluorescent detection of proteins without labels or stains, which affect their behaviour and require additional genetic or chemical preparation, has broad applications to biological research. However, standard approaches require large sample volumes or analyse only a small fraction of the sample. Here we use optofluidic hollow-core photonic crystal fibres to detect and quantify sub-microlitre volumes of unmodified bovine serum albumin (BSA) protein down to 100 nM concentrations. The optofluidic fibre's waveguiding properties are optimised for guidance at the (auto)fluorescence emission wavelength, enabling fluorescence collection from a 10 cm long excitation region, increasing sensitivity. The observed spectra agree with spectra taken from a conventional cuvette-based fluorimeter, corrected for the guidance properties of the fibre. The BSA fluorescence depended linearly on BSA concentration, while only a small hysteresis effect was observed, suggesting limited biofouling of the fibre sensor. Finally, we briefly discuss how this method could be used to study aggregation kinetics. With small sample volumes, the ability to use unlabelled proteins, and continuous flow, the method will be of interest to a broad range of protein-related research.
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Affiliation(s)
- Jan Robert Heck
- Department of Physics, Cambridge University, JJ Thomson Ave, Cambridge, CB3 071, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Ermanno Miele
- Department of Physics, Cambridge University, JJ Thomson Ave, Cambridge, Cambridgeshire, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Ralf P Mouthaan
- Department of Physics, Cambridge University, JJ Thomson Ave, Cambridge, Cambridgeshire, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Michael H Frosz
- Max Planck Institute for the Science of Light, Max-Planck-Institut fuer die Physik des Lichts, Staudtstr. 2, Erlangen, 91058, GERMANY
| | - Tuomas P J Knowles
- Department of Physics, Cambridge University, JJ Thomson Ave, Cambridge, Cambridgeshire, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Tijmen G Euser
- Department of Physics, Cambridge University, JJ Thomson Ave, Cambridge, Cambridgeshire, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
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49
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Synthesis, crystal structure and metal ion sensing ability of novel 4-amino-3-nitroso-2H-chromen-2-one: Interaction studies with calf thymus-DNA. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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50
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Pastore AJ, Ficaretta E, Chatterjee A, Davidson VL. Substitution of the sole tryptophan of the cupredoxin, amicyanin, with 5-hydroxytryptophan alters fluorescence properties and energy transfer to the type 1 copper site. J Inorg Biochem 2022; 234:111895. [PMID: 35696758 PMCID: PMC9753554 DOI: 10.1016/j.jinorgbio.2022.111895] [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: 03/14/2022] [Revised: 05/17/2022] [Accepted: 06/02/2022] [Indexed: 12/01/2022]
Abstract
Amicyanin is a type 1 copper protein with a single tryptophan residue. Using genetic code expansion, the tryptophan was selectively replaced with the unnatural amino acid, 5-hydroxytryptophan (5-HTP). The 5-HTP substituted amicyanin exhibited absorbance at 300-320 nm, characteristic of 5-HTP and not seen in native amicyanin. The fluorescence emission maximum in 5-HTP substituted amicyanin is redshifted from 318 nm in native amicyanin to 331 nm and to 348 nm in the unfolded protein. The fluorescence quantum yield of 5-HTP substituted amicyanin mutant was much less than that of native amicyanin. Differences in intrinsic fluorescence are explained by differences in the excited states of tryptophan versus 5-HTP and the intraprotein environment. The substitution of tryptophan with 5-HTP did not affect the visible absorbance and redox potential of the copper, which is 10 Å away. In amicyanin and other cupredoxins, an unexplained quenching of the intrinsic fluorescence by the bound copper is observed. However, the fluorescence of 5-HTP substituted amicyanin is not quenched by the copper. It is shown that the mechanism of quenching in native amicyanin is Förster, or fluorescence, resonance energy transfer (FRET). This does not occur in 5-HTP substituted amicyanin because the fluorescence quantum yield is significantly lower and the red-shift of fluorescence emission maximum decreases overlap with the near UV absorbance of copper. Characterization of the distinct fluorescence properties of 5-HTP relative to tryptophan in amicyanin provides a basis for spectroscopic interrogation of the protein microenvironment using 5-HTP, and long-distance interactions with transition metals.
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Affiliation(s)
- Anthony J Pastore
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Elise Ficaretta
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA.
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