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FRET theoretical predictions concerning freely diffusive dyes inside spherical container: how to choose the best pair? Photochem Photobiol Sci 2021; 20:275-283. [PMID: 33721256 DOI: 10.1007/s43630-021-00016-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/27/2021] [Indexed: 10/22/2022]
Abstract
FRET has been massively used to see if biomolecules were bounded or not by labelling both biomolecules by one dye of a FRET pair. This should give a digital answer to the question (fluorescence of the acceptor: high FRET efficency: molecules associated, fluorescence of the donor: low FRET efficency: molecules dissociated). This has been used, inter alia, at the single-molecule scale in containers, such as liposomes. One perspective of the field is to reduce the container's size to study the effect of confinement on binding. The problem is that if the two dyes are encapsulated inside a small liposome, they could have a significant probability to be close one from the other one (and thus to undergo a high FRET efficiency event without binding). This is why we suggest here a theoretical model which gives mean FRET efficiency as a function of liposome radius (the model applies to any spherical container) and Förster radius to help the experimentalist to choose their experimental set-up. Besides, the influence of side effect on mean FRET efficiency has been studied as well. We show here that if this "background FRET" is most of the time non-quantitative, it can remain significant and which makes data analysis trickier. We could show as well that if this background FRET obviously increases when liposome radius decreases, this variation was lower than the one which could be expected because of side effect. We show as well the FRET efficiency function distribution which let the experimentalist know the probability to get one FRET efficiency value.
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Burger M, Rein S, Weber S, Gräber P, Kacprzak S. Distance measurements in the F 0F 1-ATP synthase from E. coli using smFRET and PELDOR spectroscopy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 49:1-10. [PMID: 31705179 DOI: 10.1007/s00249-019-01408-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/09/2019] [Accepted: 10/29/2019] [Indexed: 12/12/2022]
Abstract
Fluorescence resonance energy transfer in single enzyme molecules (smFRET, single-molecule measurement) allows the measurement of multicomponent distance distributions in complex biomolecules similar to pulsed electron-electron double resonance (PELDOR, ensemble measurement). Both methods use reporter groups: FRET exploits the distance dependence of the electric interaction between electronic transition dipole moments of the attached fluorophores, whereas PELDOR spectroscopy uses the distance dependence of the interaction between the magnetic dipole moments of attached spin labels. Such labels can be incorporated easily to cysteine residues in the protein. Comparison of distance distributions obtained with both methods was carried out with the H+-ATPase from Escherichia coli (EF0F1). The crystal structure of this enzyme is known. It contains endogenous cysteines, and as an internal reference two additional cysteines were introduced (EF0F1-γT106C-εH56C). These positions were chosen to allow application of both methods under optimal conditions. Both methods yield very similar multicomponent distance distributions. The dominating distance distribution (> 50%) is due to the two cysteines introduced by site-directed mutagenesis and the distance is in agreement with the crystal structure. Two additional distance distributions are detected with smFRET and with PELDOR. These can be assigned by comparison with the structure to labels at endogenous cysteines. One additional distribution is detected only with PELDOR. The comparison indicates that under optimal conditions smFRET and PELDOR result in the same distance distributions. PELDOR has the advantage that different distributions can be obtained with ensemble measurements, whereas FRET requires single-molecule techniques.
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Affiliation(s)
- Markus Burger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Stephan Rein
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Peter Gräber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany.
| | - Sylwia Kacprzak
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
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Gráczer É, Szimler T, Garamszegi A, Konarev PV, Lábas A, Oláh J, Palló A, Svergun DI, Merli A, Závodszky P, Weiss MS, Vas M. Dual Role of the Active Site Residues of Thermus thermophilus 3-Isopropylmalate Dehydrogenase: Chemical Catalysis and Domain Closure. Biochemistry 2016; 55:560-74. [PMID: 26731489 DOI: 10.1021/acs.biochem.5b00839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The key active site residues K185, Y139, D217, D241, D245, and N102 of Thermus thermophilus 3-isopropylmalate dehydrogenase (Tt-IPMDH) have been replaced, one by one, with Ala. A drastic decrease in the kcat value (0.06% compared to that of the wild-type enzyme) has been observed for the K185A and D241A mutants. Similarly, the catalytic interactions (Km values) of these two mutants with the substrate IPM are weakened by more than 1 order of magnitude. The other mutants retained some (1-13%) of the catalytic activity of the wild-type enzyme and do not exhibit appreciable changes in the substrate Km values. The pH dependence of the wild-type enzyme activity (pK = 7.4) is shifted toward higher values for mutants K185A and D241A (pK values of 8.4 and 8.5, respectively). For the other mutants, smaller changes have been observed. Consequently, K185 and D241 may constitute a proton relay system that can assist in the abstraction of a proton from the OH group of IPM during catalysis. Molecular dynamics simulations provide strong support for the neutral character of K185 in the resting state of the enzyme, which implies that K185 abstracts the proton from the substrate and D241 assists the process via electrostatic interactions with K185. Quantum mechanics/molecular mechanics calculations revealed a significant increase in the activation energy of the hydride transfer of the redox step for both D217A and D241A mutants. Crystal structure analysis of the molecular contacts of the investigated residues in the enzyme-substrate complex revealed their additional importance (in particular that of K185, D217, and D241) in stabilizing the domain-closed active conformation. In accordance with this, small-angle X-ray scattering measurements indicated the complete absence of domain closure in the cases of D217A and D241A mutants, while only partial domain closure could be detected for the other mutants. This suggests that the same residues that are important for catalysis are also essential for inducing domain closure.
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Affiliation(s)
- Éva Gráczer
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| | - Tamás Szimler
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| | - Anita Garamszegi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| | - Petr V Konarev
- European Molecular Biology Laboratory , Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Anikó Lábas
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics , Gellért tér 4., H-1111 Budapest, Hungary
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics , Gellért tér 4., H-1111 Budapest, Hungary
| | - Anna Palló
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| | - Dmitri I Svergun
- European Molecular Biology Laboratory , Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Angelo Merli
- Dipartimento di Bioscienze, Universitá degli Studi di Parma , Viale G.P. Usberti 23/A, I-43100 Parma, Italy
| | - Péter Závodszky
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin für Materialien und Energie , Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Mária Vas
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
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Resetca D, Wilson DJ. Characterizing rapid, activity-linked conformational transitions in proteins via sub-second hydrogen deuterium exchange mass spectrometry. FEBS J 2013; 280:5616-25. [DOI: 10.1111/febs.12332] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/26/2013] [Accepted: 05/01/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Diana Resetca
- Department of Chemistry; York University; Toronto Ontario Canada
| | - Derek J. Wilson
- Department of Chemistry; York University; Toronto Ontario Canada
- Center for Research in Mass Spectrometry; Department of Chemistry; York University; Toronto Ontario Canada
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