1
|
Kyrychenko A, Ladokhin AS. Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions. CHEM REC 2024; 24:e202300232. [PMID: 37695081 PMCID: PMC11113672 DOI: 10.1002/tcr.202300232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv, 61022, Ukraine
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, United States
| |
Collapse
|
2
|
Membrane Interactions of Apoptotic Inhibitor Bcl-xL: What Can Be Learned using Fluorescence Spectroscopy. BBA ADVANCES 2023; 3:100076. [PMID: 37082264 PMCID: PMC10074936 DOI: 10.1016/j.bbadva.2023.100076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
Permeabilization of the mitochondrial outer membrane-a point of no return in apoptotic regulation-is tightly controlled by proteins of the Bcl-2 family. Apoptotic inhibitor Bcl-xL is an important member of this family, responsible for blocking the permeabilization, and is also a promising target for anti-cancer drugs. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (i) a soluble folded conformation, (ii) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (iii) refolded membrane-inserted conformations, for which no structural data are available. In this review, we present the summary of the application of various methods of fluorescence spectroscopy for studying membrane interaction of Bcl-xL, and specifically the formation of the refolded inserted conformation. We discuss the application of environment-sensitive probes, Förster resonance energy transfer, fluorescence correlation spectroscopy, and fluorescent quenching for structural, thermodynamic, and functional characterization of protein-lipid interactions, which can benefit studies of other members of Bcl-2 (e.g., Bax, BAK, Bid). The conformational switching between various conformations of Bcl-xL depends on the presence of divalent cations, pH and lipid composition. This insertion-refolding transition also results in the release of the BH4 regulatory domain from the folded structure of Bcl-xL, which is relevant to the lipid-regulated conversion between canonical and non-canonical modes of apoptotic inhibition.
Collapse
|
3
|
Trusova V, Tarabara U, Zhytniakivska O, Vus K, Gorbenko G. Fӧrster resonance energy transfer analysis of amyloid state of proteins. BBA ADVANCES 2022; 2:100059. [PMID: 37082586 PMCID: PMC10074846 DOI: 10.1016/j.bbadva.2022.100059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/22/2022] [Indexed: 11/06/2022] Open
Abstract
The Förster resonance energy transfer (FRET) is a well-established and versatile spectroscopic technique extensively used for exploring a variety of biomolecular interactions and processes. The present review is intended to cover the main results of our FRET studies focused on amyloid fibrils, a particular type of disease-associated protein aggregates. Based on the examples of several fibril-forming proteins including insulin, lysozyme and amyloidogenic variants of N-terminal fragment of apolipoprotein A-I, it was demonstrated that: (i) the two- and three-step FRET with the classical amyloid marker Thioflavin T as an input donor has a high amyloid-sensing potential and can be used to refine the amyloid detection assays; (ii) the intermolecular time-resolved and single-molecule pulse interleaved excitation FRET can give quantitative information on the nucleation of amyloid fibrils; (iii) FRET between the membrane fluorescent probes and protein-associated intrinsic or extrinsic fluorophores is suitable for monitoring the membrane binding of fibrillar proteins, exploring their location relative to lipid-water interface and restructuring on a lipid matrix; (iv) the FRET-based distance estimation between fibril-bound donor and acceptor fluorophores can serve as one of the verification criteria upon structural modeling of amyloid fibrils.
Collapse
|
4
|
Bonardd S, Díaz Díaz D, Leiva A, Saldías C. Chromophoric Dendrimer-Based Materials: An Overview of Holistic-Integrated Molecular Systems for Fluorescence Resonance Energy Transfer (FRET) Phenomenon. Polymers (Basel) 2021; 13:4404. [PMID: 34960954 PMCID: PMC8705239 DOI: 10.3390/polym13244404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
Dendrimers (from the Greek dendros → tree; meros → part) are macromolecules with well-defined three-dimensional and tree-like structures. Remarkably, this hyperbranched architecture is one of the most ubiquitous, prolific, and recognizable natural patterns observed in nature. The rational design and the synthesis of highly functionalized architectures have been motivated by the need to mimic synthetic and natural-light-induced energy processes. Dendrimers offer an attractive material scaffold to generate innovative, technological, and functional materials because they provide a high amount of peripherally functional groups and void nanoreservoirs. Therefore, dendrimers emerge as excellent candidates since they can play a highly relevant role as unimolecular reactors at the nanoscale, acting as versatile and sophisticated entities. In particular, they can play a key role in the properties of light-energy harvesting and non-radiative energy transfer, allowing them to function as a whole unit. Remarkably, it is possible to promote the occurrence of the FRET phenomenon to concentrate the absorbed energy in photoactive centers. Finally, we think an in-depth understanding of this mechanism allows for diverse and prolific technological applications, such as imaging, biomedical therapy, and the conversion and storage of light energy, among others.
Collapse
Affiliation(s)
- Sebastián Bonardd
- Departamento de Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez S/N, La Laguna, 38206 Tenerife, Spain; (S.B.); (D.D.D.)
- Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, La Laguna, 38206 Tenerife, Spain
| | - David Díaz Díaz
- Departamento de Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez S/N, La Laguna, 38206 Tenerife, Spain; (S.B.); (D.D.D.)
- Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, La Laguna, 38206 Tenerife, Spain
- Institutfür Organische Chemie, Universität Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
| | - Angel Leiva
- Departamento de Química Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Macul, Santiago, CL 7820436, USA;
| | - César Saldías
- Departamento de Química Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Macul, Santiago, CL 7820436, USA;
| |
Collapse
|
5
|
Delgadillo RF, Carnes KA, Zaleta-Rivera K, Olmos O, Parkhurst LJ. A FLIM Microscopy Based on Acceptor-Detected Förster Resonance Energy Transfer. Anal Chem 2021; 93:4841-4849. [PMID: 33691398 PMCID: PMC7992049 DOI: 10.1021/acs.analchem.0c04492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Time-resolved donor-detected
Förster resonance energy transfer
(trDDFRET) allows the observation of molecular interactions of dye-labeled
biomolecules in the ∼10–100 Å region. However,
we can observe longer-range interactions when using time-resolved
acceptor-detected FRET (trADFRET), since the signal/noise ratio can
be improved when observing the acceptor emission. Therefore, we propose
a new methodology based on trADFRET to construct a new fluorescence
lifetime microscopy (FLIM-trADFRET) technique to observe biological
machinery in the range of 100–300 Å in vivo, the last
frontier in biomolecular medicine. The integrated trADFRET signal
is extracted in such a way that noise is canceled, and more photons
are collected, even though trADFRET and trDDFRET have the same rate
of transfer. To assess our new methodology, proof of concept was demonstrated
with a set of well-defined DNA scaffolds.
Collapse
Affiliation(s)
- Roberto F Delgadillo
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, Nebraska 68588-0304, United States.,Tecnologico de Monterrey, School of Engineering and Sciences, Av. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo Leon 64849, Monterrey, Mexico.,BASF Enzymes LLC, 3550 John Hopkins Ct, San Diego, California 92121, United States
| | - Katie A Carnes
- GlaxoSmithKline, Medicinal Science and Technology, CMC Analytical - Drug Substance and Product Analysis, King of Prussia, Pennsylvania, 19406, United States
| | - Kathia Zaleta-Rivera
- Department of Bioengineering, University of California San Diego, San Diego, California, 92093-0412, United States
| | - Omar Olmos
- Tecnologico de Monterrey, School of Engineering and Sciences, Av. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo Leon 64849, Monterrey, Mexico
| | - Lawrence J Parkhurst
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, Nebraska 68588-0304, United States
| |
Collapse
|
6
|
Basak S, Sakia N, Dougherty L, Guo Z, Wu F, Mindlin F, Lary JW, Cole JL, Ding F, Bowen ME. Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer. J Mol Biol 2021; 433:166793. [PMID: 33388290 DOI: 10.1016/j.jmb.2020.166793] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 12/03/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022]
Abstract
Many proteins are composed of independently-folded domains connected by flexible linkers. The primary sequence and length of such linkers can set the effective concentration for the tethered domains, which impacts rates of association and enzyme activity. The length of such linkers can be sensitive to environmental conditions, which raises questions as to how studies in dilute buffer relate to the highly-crowded cellular environment. To examine the role of linkers in domain separation, we measured Fluorescent Protein-Fluorescence Resonance Energy Transfer (FP-FRET) for a series of tandem FPs that varied in the length of their interdomain linkers. We used discrete molecular dynamics to map the underlying conformational distribution, which revealed intramolecular contact states that we confirmed with single molecule FRET. Simulations found that attached FPs increased linker length and slowed conformational dynamics relative to the bare linkers. This makes the CLYs poor sensors of inherent linker properties. However, we also showed that FP-FRET in CLYs was sensitive to solvent quality and macromolecular crowding making them potent environmental sensors. Finally, we targeted the same proteins to the plasma membrane of living mammalian cells to measure FP-FRET in cellulo. The measured FP-FRET when tethered to the plasma membrane was the same as that in dilute buffer. While caveats remain regarding photophysics, this suggests that the supertertiary conformational ensemble of these CLY proteins may not be affected by this specific cellular environment.
Collapse
Affiliation(s)
- Sujit Basak
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Nabanita Sakia
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634-0978, USA
| | - Laura Dougherty
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Zhuojun Guo
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Fang Wu
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Frank Mindlin
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Jeffrey W Lary
- National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, CT 06269, USA
| | - James L Cole
- National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, CT 06269, USA; Department of Molecular and Cell Biology, and Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634-0978, USA
| | - Mark E Bowen
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA.
| |
Collapse
|
7
|
Abstract
FRET is both a phenomenon and a spectroscopic technique, capable of measuring one geometric quantity: kappa-squared divided by the sixth power of the donor-acceptor distance. Kappa-squared is often replaced by a constant even though such a replacement may lead to serious errors. Kappaphobia, the fear of kappa or the reluctance to deal with kappa-squared adequately, is a looming presence in the FRET community. Unfortunately, this reluctance, or fear, is often tolerated, and sometimes encouraged. A decrease in kappaphobia will lead to an increase in the impact and success of FRET.
Collapse
Affiliation(s)
- B Wieb VanDerMeer
- Professor Emeritus of Physics and Biophysics, Western Kentucky University, Bowling Green, KY 42101, United States of America
| |
Collapse
|
8
|
Khoshbin Z, Housaindokht MR, Verdian A. A low-cost paper-based aptasensor for simultaneous trace-level monitoring of mercury (II) and silver (I) ions. Anal Biochem 2020; 597:113689. [PMID: 32199832 DOI: 10.1016/j.ab.2020.113689] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/22/2020] [Accepted: 03/12/2020] [Indexed: 01/30/2023]
Abstract
Mercury (Hg2+) and silver (Ag+) ions possess the harmful effects on public health and environment that makes it essential to develop the sensing techniques with great sensitivity for the ions. Metal ions commonly coexist in the different biological and environmental systems. Hence, it is an urgent demand to design a simple method for the simultaneous detection of metal ions, peculiarly in the case of coexisting Hg2+ and Ag+. This study introduces a low-cost paper-based aptasensor to monitor Hg2+ and Ag+, simultaneously. The strategy of the sensing array is according to the conformational changes of Hg2+- and Ag+-specific aptamers and their release from the GO surface after the injection of the target sample on the sensing platform. Through monitoring the fluorescence recovery changes against the concentrations of the ions, Hg2+ and Ag+ can be determined as low as 1.33 and 1.01 pM. The paper-based aptasensor can simultaneously detect the ions within about 10 min. The aptasensor is applied prosperously to monitor Hg2+ and Ag+ in human serum, water, and milk. The designed aptasensor with the main advantages of simplicity and feasibility holds the supreme potential to develop a cost-effective sensing method for environmental monitoring, food control, and human diagnostics.
Collapse
Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
| |
Collapse
|
9
|
Conformational Switching in Bcl-xL: Enabling Non-Canonic Inhibition of Apoptosis Involves Multiple Intermediates and Lipid Interactions. Cells 2020; 9:cells9030539. [PMID: 32111007 PMCID: PMC7140517 DOI: 10.3390/cells9030539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 12/21/2022] Open
Abstract
The inhibition of mitochondrial permeabilization by the anti-apoptotic protein Bcl-xL is crucial for cell survival and homeostasis. Its inhibitory role requires the partitioning of Bcl-xL to the mitochondrial outer membrane from an inactive state in the cytosol, leading to its extensive refolding. The molecular mechanisms behind these events and the resulting conformations in the bilayer are unclear, and different models have been proposed to explain them. In the most recently proposed non-canonical model, the active form of Bcl-xL employs its N-terminal BH4 helix to bind and block its pro-apoptotic target. Here, we used a combination of various spectroscopic techniques to study the release of the BH4 helix (α1) during the membrane insertion of Bcl-xL. This refolding was characterized by a gradual increase in helicity due to the lipid-dependent partitioning-coupled folding and formation of new helix αX (presumably in the originally disordered loop between helices α1 and α2). Notably, a comparison of various fluorescence and circular dichroism measurements suggested the presence of multiple Bcl-xL conformations in the bilayer. This conclusion was explicitly confirmed by single-molecule measurements of Förster Resonance Energy Transfer from Alexa-Fluor-488-labeled Bcl-xL D189C to a mCherry fluorescent protein attached at the N-terminus. These measurements clearly indicated that the refolding of Bcl-xL in the bilayer is not a two-state transition and involves multiple membranous intermediates of variable compactness.
Collapse
|
10
|
Pope JR, Johnson RL, Jamieson WD, Worthy HL, Kailasam S, Ahmed RD, Taban I, Auhim HS, Watkins DW, Rizkallah PJ, Castell OK, Jones DD. Association of Fluorescent Protein Pairs and Its Significant Impact on Fluorescence and Energy Transfer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 8:2003167. [PMID: 33437587 PMCID: PMC7788595 DOI: 10.1002/advs.202003167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Indexed: 06/01/2023]
Abstract
Fluorescent proteins (FPs) are commonly used in pairs to monitor dynamic biomolecular events through changes in proximity via distance dependent processes such as Förster resonance energy transfer (FRET). The impact of FP association is assessed by predicting dimerization sites in silico and stabilizing the dimers by bio-orthogonal covalent linkages. In each tested case dimerization changes inherent fluorescence, including FRET. GFP homodimers demonstrate synergistic behavior with the dimer being brighter than the sum of the monomers. The homodimer structure reveals the chromophores are close with favorable transition dipole alignments and a highly solvated interface. Heterodimerization (GFP with Venus) results in a complex with ≈87% FRET efficiency, significantly below the 99.7% efficiency predicted. A similar efficiency is observed when the wild-type FPs are fused to a naturally occurring protein-protein interface system. GFP complexation with mCherry results in loss of mCherry fluorescence. Thus, simple assumptions used when monitoring interactions between proteins via FP FRET may not always hold true, especially under conditions whereby the protein-protein interactions promote FP interaction.
Collapse
Affiliation(s)
- Jacob R. Pope
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
| | - Rachel L. Johnson
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
| | | | - Harley L. Worthy
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
- Present address:
Henry Wellcome Building for BiocatalysisBiosciencesUniversity of ExeterExeterEX4 4QDUK
| | - Senthilkumar Kailasam
- McGill University and Genome Quebec Innovation CentreMontrealQuebecH3A 0G1Canada
- Department of Human GeneticsMcGill UniversityMontrealQuebecCanada
| | - Rochelle D. Ahmed
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
| | - Ismail Taban
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
| | - Husam Sabah Auhim
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
- Department of BiologyCollege of ScienceUniversity of BaghdadBaghdadIraq
| | - Daniel W. Watkins
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
- Present address:
School of BiochemistryUniversity of BristolBristolBS8 1QUUK
| | | | | | - D. Dafydd Jones
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
| |
Collapse
|
11
|
Daskalakis V, Maity S, Hart CL, Stergiannakos T, Duffy CDP, Kleinekathöfer U. Structural Basis for Allosteric Regulation in the Major Antenna Trimer of Photosystem II. J Phys Chem B 2019; 123:9609-9615. [DOI: 10.1021/acs.jpcb.9b09767] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Vangelis Daskalakis
- Department of Environmental Science and Technology, Cyprus University of Technology, 30 Archbishop Kyprianou Street, 3603, Limassol, Cyprus
| | - Sayan Maity
- Department of Physics & Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Cameron Lewis Hart
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Taxiarchis Stergiannakos
- Department of Environmental Science and Technology, Cyprus University of Technology, 30 Archbishop Kyprianou Street, 3603, Limassol, Cyprus
| | - Christopher D. P. Duffy
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Ulrich Kleinekathöfer
- Department of Physics & Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| |
Collapse
|
12
|
|
13
|
Location of TEMPO-PC in Lipid Bilayers: Implications for Fluorescence Quenching. J Membr Biol 2019; 253:73-77. [PMID: 31541260 DOI: 10.1007/s00232-019-00094-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022]
Abstract
The characterization of the behavior of lipid-attached spin probes in a bilayer is of fundamental importance for correct interpretation of the results of both EPR and fluorescence studies of protein-membrane interactions. The knowledge of the immersion depth of TEMPO spin probe attached to lipid headgroup in TEMPO-PC is critical for the determination of the transverse location of fluorescence probes attached to proteins and peptides. The question of bilayer penetration of TEMPO moiety in TEMPO-PC has recently came into prominence in two studies of interfacial solvation (Cheng et al. in Biophys J 109:330-339, 2015; Lee et al. in Biophys J 111:2481-2491, 2016). Here, we re-examine the arguments on TEMPO penetration using the cross-validation of MD simulations and depth-dependent fluorescence-quenching experiments, which confirms that TEMPO in TEMPO-PC penetrates below the level of phosphate groups. The proper analysis of fluorescence quenching requires the use of Tempo position below the level of phosphate groups; and failure to do so will result in substantial systematic errors in determining the penetration of the labeled site on a membrane protein.
Collapse
|
14
|
Hochreiter B, Kunze M, Moser B, Schmid JA. Advanced FRET normalization allows quantitative analysis of protein interactions including stoichiometries and relative affinities in living cells. Sci Rep 2019; 9:8233. [PMID: 31160659 PMCID: PMC6547726 DOI: 10.1038/s41598-019-44650-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/20/2019] [Indexed: 12/31/2022] Open
Abstract
FRET (Fluorescence Resonance Energy Transfer) measurements are commonly applied to proof protein-protein interactions. However, standard methods of live cell FRET microscopy and signal normalization only allow a principle assessment of mutual binding and are unable to deduce quantitative information of the interaction. We present an evaluation and normalization procedure for 3-filter FRET measurements, which reflects the process of complex formation by plotting FRET-saturation curves. The advantage of this approach relative to traditional signal normalizations is demonstrated by mathematical simulations. Thereby, we also identify the contribution of critical parameters such as the total amount of donor and acceptor molecules and their molar ratio. When combined with a fitting procedure, this normalization facilitates the extraction of key properties of protein complexes such as the interaction stoichiometry or the apparent affinity of the binding partners. Finally, the feasibility of our method is verified by investigating three exemplary protein complexes. Altogether, our approach offers a novel method for a quantitative analysis of protein interactions by 3-filter FRET microscopy, as well as flow cytometry. To facilitate the application of this method, we created macros and routines for the programs ImageJ, R and MS-Excel, which we make publicly available.
Collapse
Affiliation(s)
- Bernhard Hochreiter
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria
| | - Markus Kunze
- Medical University Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, Vienna, Austria
| | - Bernhard Moser
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria
| | - Johannes A Schmid
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria.
| |
Collapse
|
15
|
Höfig H, Otten J, Steffen V, Pohl M, Boersma AJ, Fitter J. Genetically Encoded Förster Resonance Energy Transfer-Based Biosensors Studied on the Single-Molecule Level. ACS Sens 2018; 3:1462-1470. [PMID: 29979038 DOI: 10.1021/acssensors.8b00143] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetically encoded Förster resonance energy transfer (FRET)-based biosensors for the quantification of ligand molecules change the magnitude of FRET between two fluorescent proteins upon binding a target metabolite. When highly sensitive sensors are being designed, extensive sensor optimization is essential. However, it is often difficult to verify the ideas of modifications made to a sensor during the sensor optimization process because of the limited information content of ensemble FRET measurements. In contrast, single-molecule detection provides detailed information and higher accuracy. Here, we investigated a set of glucose and crowding sensors on the single-molecule level. We report the first comprehensive single-molecule study of FRET-based biosensors with reasonable counting statistics and identify characteristics in the single-molecule FRET histograms that constitute fingerprints of sensor performance. Hence, our single-molecule approach extends the toolbox of methods aiming to understand and optimize the design of FRET-based biosensors.
Collapse
Affiliation(s)
- Henning Höfig
- I. Physikalisches Institut (IA), RWTH Aachen, 52074 Aachen, Germany
- ICS-5: Molecular Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Julia Otten
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Victoria Steffen
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Arnold J. Boersma
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700 AB Groningen, Netherlands
| | - Jörg Fitter
- I. Physikalisches Institut (IA), RWTH Aachen, 52074 Aachen, Germany
- ICS-5: Molecular Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
| |
Collapse
|
16
|
van Rosmalen M, Krom M, Merkx M. Tuning the Flexibility of Glycine-Serine Linkers To Allow Rational Design of Multidomain Proteins. Biochemistry 2017; 56:6565-6574. [PMID: 29168376 PMCID: PMC6150656 DOI: 10.1021/acs.biochem.7b00902] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Flexible
polypeptide linkers composed of glycine and serine are
important components of engineered multidomain proteins. We have previously
shown that the conformational properties of Gly-Gly-Ser repeat linkers
can be quantitatively understood by comparing experimentally determined
Förster resonance energy transfer (FRET) efficiencies of ECFP-linker-EYFP
proteins to theoretical FRET efficiencies calculated using wormlike
chain and Gaussian chain models. Here we extend this analysis to include
linkers with different glycine contents. We determined the FRET efficiencies
of ECFP-linker-EYFP proteins with linkers ranging in length from 25
to 73 amino acids and with glycine contents of 33.3% (GSSGSS), 16.7%
(GSSSSSS), and 0% (SSSSSSS). The FRET efficiency decreased with an
increasing linker length and was overall lower for linkers with less
glycine. Modeling the linkers using the WLC model revealed that the
experimentally observed FRET efficiencies were consistent with persistence
lengths of 4.5, 4.8, and 6.2 Å for the GSSGSS, GSSSSS, and SSSSSS
linkers, respectively. The observed increase in linker stiffness with
reduced glycine content is much less pronounced than that predicted
by a classical model developed by Flory and co-workers. We discuss
possible reasons for this discrepancy as well as implications for
using the stiffer linkers to control the effective concentrations
of connected domains in engineered multidomain proteins.
Collapse
Affiliation(s)
- Martijn van Rosmalen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Mike Krom
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| |
Collapse
|
17
|
Yao J, Li L, Li P, Yang M. Quantum dots: from fluorescence to chemiluminescence, bioluminescence, electrochemiluminescence, and electrochemistry. NANOSCALE 2017; 9:13364-13383. [PMID: 28880034 DOI: 10.1039/c7nr05233b] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, nanotechnology has become one of the major forces driving basic and applied research. As a novel class of inorganic fluorochromes, research into quantum dots (QDs) has become one of the fastest growing fields of nanotechnology today. QDs are made of a semiconductor material with tunable physical dimensions as well as unique optoelectronic properties, and have attracted multidisciplinary research efforts to further their potential bioanalytical applications. Recently, numerous optical properties of QDs, such as narrow emission band peaks, broad absorption spectra, intense signals, and remarkable resistance to photobleaching, have made them biocompatible and sensitive for biological assays. In this review, we give an overview of these exciting materials and describe their potential, especially in biomolecules analysis, including fluorescence detection, chemiluminescence detection, bioluminescence detection, electrochemiluminescence detection, and electrochemical detection. Finally, conclusions are made, including highlighting some critical challenges remaining and a perspective of how this field can be expected to develop in the future.
Collapse
Affiliation(s)
- Jun Yao
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, Sichuan 610500, People's Republic of China.
| | | | | | | |
Collapse
|
18
|
Kyrychenko A, Rodnin MV, Ghatak C, Ladokhin AS. Computational refinement of spectroscopic FRET measurements. Data Brief 2017; 12:213-221. [PMID: 28459092 PMCID: PMC5397103 DOI: 10.1016/j.dib.2017.03.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/23/2017] [Accepted: 03/28/2017] [Indexed: 01/02/2023] Open
Abstract
This article supplies raw data related to a research article entitled “Joint refinement of FRET measurements using spectroscopic and computational tools” (Kyrychenko et al., 2017) [1], in which we demonstrate the use of molecular dynamics simulations to estimate FRET orientational factors in a benchmark donor-linker-acceptor system of enhanced cyan (ECFP) and enhanced yellow (EYFP) fluorescent proteins. This can improve the recalculation of donor-acceptor distance information from single-molecule FRET measurements.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine.,Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center Kansas City, KS66160-7421, USA
| | - Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center Kansas City, KS66160-7421, USA
| | - Chiranjib Ghatak
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center Kansas City, KS66160-7421, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center Kansas City, KS66160-7421, USA
| |
Collapse
|