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Socas LB, Ambroggio EE. Introducing the multi-dimensional spectral phasors: a tool for the analysis of fluorescence excitation-emission matrices. Methods Appl Fluoresc 2022; 10. [PMID: 35139496 DOI: 10.1088/2050-6120/ac5389] [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: 09/20/2021] [Accepted: 02/09/2022] [Indexed: 11/12/2022]
Abstract
The use of phasors to analyze fluorescence data was first introduced for time-resolved studies for a simpler mathematical analysis of the fluorescence-decay curves. Recently, this approach was extended to steady-state experiments with the introduction of the spectral phasors (SP), derived from the Fourier transform of the fluorescence emission spectrum. In this work, we revise key mathematical aspects that lead to an interpretation of SP as the characteristic function of a probability distribution. This formalism allows us to introduce a new tool, called multi-dimensional spectral phasor (MdSP) that seize, not only the information from the emission spectrum, but from the full excitation-emission matrix (EEM). In addition, we developed a homemade open-source Java software to facilitate the MdSP data processing. Due to this mathematical conceptualization, we settled a mechanism for the use of MdSP as a tool to tackle spectral signal unmixing problems in a more accurate way than SP. As a proof of principle, with the use of MdSP we approach two important biophysical questions: protein conformational changes and protein-ligand interactions. Specifically, we experimentally measure the EEM changes upon denaturation of human serum albumin (HSA) or during its association with the fluorescence dye 1,8-anilinonaphtalene sulphate (ANS) detected via tryptophan-ANS Förster Resonance Energy Transfer (FRET). In this sense, MdSP allows us to obtain information of the system in a simpler and finer way than the traditional SP. Specifically, understanding a protein's EEM as a molecular fingerprint opens new doors for the use of MdSP as a tool to analyze and comprehend protein conformational changes and interactions.
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Affiliation(s)
- Luis Bp Socas
- Química Biológica, Centro de Investigaciones en Química Biológica de Córdoba, Haya de la Torre y Medina Allende s/n, Cordoba, Córdoba, X5000HUA, ARGENTINA
| | - Ernesto Esteban Ambroggio
- Química Biológica, CIQUIBIC Química Biológica, Haya de la Torre y Medina Allende s/n, Cordoba, X5000HUA, ARGENTINA
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Pérez Socas LB, Ambroggio EE. The influence of myristoylation, liposome surface charge and nucleic acid interaction in the partition properties of HIV-1 Gag-N-terminal peptides to membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183421. [PMID: 32710855 DOI: 10.1016/j.bbamem.2020.183421] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 01/10/2023]
Abstract
The group-specific antigen (GAG) polyprotein of HIV-1 is the main coordinator of the virus assembly process at the plasma membrane (PM) and is directed by its N-terminal matrix domain (MA). MA is myristoylated and possess a highly basic region (HBR) responsible for the interaction with the negative lipids of the PM, especially with PIP2. In addition, MA binds RNA molecules proposed as a regulatory step of the assembly process. Here we study the interaction of a synthetic peptide (N-terminal 21 amino acids of MA) and liposomes of different compositions using a variety of biophysical techniques. Particularly, we use the fluorescence properties of the single tryptophan of the peptide to analyze its partition to membranes, where we harness for first time the analytical ability of spectral phasors method to study this interaction. We found that electrostatic interactions play an important role for peptide partition to membranes and myristoylation reduces the free energy of the process. Interestingly, we observe that while the presence of PIP2 does not cause measurable changes on the peptide-membrane interaction, the interaction is favored by cholesterol. Additionally, we found that the partition process goes through a transition state involving peptide disaggregation and changes in the peptide secondary structure. On the other hand, we found that the presence of oligonucleotides competes with the interaction with lipids by increasing peptide solubility. In summary, we think that our results, in context of the current knowledge of the role of HIV-1 MA, contribute to a better molecular understanding of the membrane association process.
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Affiliation(s)
- Luis Benito Pérez Socas
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica-Ranwel Caputto, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina; CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina
| | - Ernesto Esteban Ambroggio
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica-Ranwel Caputto, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina; CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina.
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Vergeldt FJ, Prusova A, Fereidouni F, Amerongen HV, Van As H, Scheenen TWJ, Bader AN. Multi-component quantitative magnetic resonance imaging by phasor representation. Sci Rep 2017; 7:861. [PMID: 28408740 PMCID: PMC5429833 DOI: 10.1038/s41598-017-00864-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/20/2017] [Indexed: 12/02/2022] Open
Abstract
Quantitative magnetic resonance imaging (qMRI) is a versatile, non-destructive and non-invasive tool in life, material, and medical sciences. When multiple components contribute to the signal in a single pixel, however, it is difficult to quantify their individual contributions and characteristic parameters. Here we introduce the concept of phasor representation to qMRI to disentangle the signals from multiple components in imaging data. Plotting the phasors allowed for decomposition, unmixing, segmentation and quantification of our in vivo data from a plant stem, a human and mouse brain and a human prostate. In human brain images, we could identify 3 main T2 components and 3 apparent diffusion coefficients; in human prostate 5 main contributing spectral shapes were distinguished. The presented phasor analysis is model-free, fast and accurate. Moreover, we also show that it works for undersampled data.
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Affiliation(s)
- Frank J Vergeldt
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands.,Wageningen NMR Centre, Wageningen University & Research, Wageningen, The Netherlands
| | - Alena Prusova
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA, USA
| | - Herbert van Amerongen
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands.,MicroSpectroscopy Centre, Wageningen University and Research, Wageningen, The Netherlands
| | - Henk Van As
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands. .,Wageningen NMR Centre, Wageningen University & Research, Wageningen, The Netherlands.
| | - Tom W J Scheenen
- Department of Radiology and Nuclear Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Arjen N Bader
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands. .,MicroSpectroscopy Centre, Wageningen University and Research, Wageningen, The Netherlands.
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Malacrida L, Gratton E, Jameson DM. Model-free methods to study membrane environmental probes: a comparison of the spectral phasor and generalized polarization approaches. Methods Appl Fluoresc 2015; 3:047001. [PMID: 27182438 PMCID: PMC4862737 DOI: 10.1088/2050-6120/3/4/047001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this note, we present a discussion of the advantages and scope of model-free analysis methods applied to the popular solvatochromic probe LAURDAN, which is widely used as an environmental probe to study dynamics and structure in membranes. In particular, we compare and contrast the generalized polarization approach with the spectral phasor approach. To illustrate our points we utilize several model membrane systems containing pure lipid phases and, in some cases, cholesterol or surfactants. We demonstrate that the spectral phasor method offers definitive advantages in the case of complex systems.
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Affiliation(s)
- Leonel Malacrida
- Área de Investigación Respiratoria, Departamento de Fisiopatología, Hospital de Medicina-Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Biochemistry and Proteomic Analytical Unit, Institut Pasteur of Montevideo, Montevideo, Uruguay
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Biomedical Engineering Department, University of California at Irvine, Irvine, CA 92697, USA
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, 651 Halo St., BSB222, Honolulu, HI 96813, USA
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