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Saudino G, Suraci D, Nasta V, Ciofi-Baffoni S, Banci L. Molecular Basis of Multiple Mitochondrial Dysfunctions Syndrome 2 Caused by CYS59TYR BOLA3 Mutation. Int J Mol Sci 2021; 22:4848. [PMID: 34063696 PMCID: PMC8125686 DOI: 10.3390/ijms22094848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022] Open
Abstract
Multiple mitochondrial dysfunctions syndrome (MMDS) is a rare neurodegenerative disorder associated with mutations in genes with a vital role in the biogenesis of mitochondrial [4Fe-4S] proteins. Mutations in one of these genes encoding for BOLA3 protein lead to MMDS type 2 (MMDS2). Recently, a novel phenotype for MMDS2 with complete clinical recovery was observed in a patient containing a novel variant (c.176G > A, p.Cys59Tyr) in compound heterozygosity. In this work, we aimed to rationalize this unique phenotype observed in MMDS2. To do so, we first investigated the structural impact of the Cys59Tyr mutation on BOLA3 by NMR, and then we analyzed how the mutation affects both the formation of a hetero-complex between BOLA3 and its protein partner GLRX5 and the iron-sulfur cluster-binding properties of the hetero-complex by various spectroscopic techniques and by experimentally driven molecular docking. We show that (1) the mutation structurally perturbed the iron-sulfur cluster-binding region of BOLA3, but without abolishing [2Fe-2S]2+ cluster-binding on the hetero-complex; (2) tyrosine 59 did not replace cysteine 59 as iron-sulfur cluster ligand; and (3) the mutation promoted the formation of an aberrant apo C59Y BOLA3-GLRX5 complex. All these aspects allowed us to rationalize the unique phenotype observed in MMDS2 caused by Cys59Tyr mutation.
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Affiliation(s)
- Giovanni Saudino
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (G.S.); (D.S.); (V.N.)
| | - Dafne Suraci
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (G.S.); (D.S.); (V.N.)
| | - Veronica Nasta
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (G.S.); (D.S.); (V.N.)
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (G.S.); (D.S.); (V.N.)
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (G.S.); (D.S.); (V.N.)
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), 50019 Sesto Fiorentino, Italy
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Fluorescence Anisotropy Sensor Comprising a Dual Hollow-Core Antiresonant Fiber Polarization Beam Splitter. SENSORS 2020; 20:s20113321. [PMID: 32545205 PMCID: PMC7308924 DOI: 10.3390/s20113321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 12/23/2022]
Abstract
Fluorescence anisotropy imaging and sensing is a widely recognized method for studying molecular orientation and mobility. However, introducing this technique to in vivo systems is a challenging task, especially when one considers multiphoton excitation methods. Past two decades have brought a possible solution to this issue in the form of hollow-core antiresonant fibers (HC-ARFs). The continuous development of their fabrication technology has resulted in the appearance of more and more sophisticated structures. One of the most promising concepts concerns dual hollow-core antiresonant fibers (DHC-ARFs), which can be used to split and combine optical signals, effectively working as optical fiber couplers. In this paper, the design of a fluorescence anisotropy sensor based on a DHC-ARF structure is presented. The main purpose of the proposed DHC-ARF is multiphoton-excited fluorescence spectroscopy; however, other applications are also possible.
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Prokopowicz M, Greń B, Cieśla J, Kierdaszuk B. Towards understanding the E. coli PNP binding mechanism and FRET absence between E. coli PNP and formycin A. Biophys Chem 2017; 230:99-108. [PMID: 28947300 DOI: 10.1016/j.bpc.2017.09.001] [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: 07/11/2017] [Revised: 08/25/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
The aim of this study is threefold: (1) augmentation of the knowledge of the E. coli PNP binding mechanism; (2) explanation of the previously observed 'lack of FRET' phenomenon and (3) an introduction of the correction (modified method) for FRET efficiency calculation in the PNP-FA complexes. We present fluorescence studies of the two E. coli PNP mutants (F159Y and F159A) with formycin A (FA), that indicate that the aromatic amino acid is indispensable in the nucleotide binding, additional hydroxyl group at position 159 probably enhances the strength of binding and that the amino acids pair 159-160 has a great impact on the spectroscopic properties of the enzyme. The experiments were carried out in hepes and phosphate buffers, at pH7 and 8.3. Two methods, a conventional and a modified one, that utilizes the dissociation constant, for calculations of the energy transfer efficiency (E) and the acceptor-to-donor distance (r) between FA and the Tyr (energy donor) were employed. Total difference spectra were calculated for emission spectra (λex 280nm, 295nm, 305nm and 313nm) for all studied systems. Time-resolved techniques allowed to conclude the existence of a specific structure formed by amino acids at positions 159 and 160. The results showed an unexpected pattern change of FRET in the mutants, when compared to the wild type enzyme and a probable presence of a structure created between 159 and 160 residue, that might influence the binding efficiency. Additionally, we confirmed the indispensable role of the modification of the FRET efficiency (E) calculation on the fraction of enzyme saturation in PNP-FA systems.
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Affiliation(s)
- Małgorzata Prokopowicz
- Inter-Faculty Interdisciplinary Doctoral Studies in Natural Sciences and Mathematics, University of Warsaw, Stefana Banacha 2C, Warsaw 02-097, Poland; Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, Warsaw 02-089, Poland.
| | - Bartosz Greń
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, Warsaw 02-089, Poland
| | - Joanna Cieśla
- Department of Drug Technology and Biotechnology, Institute of Biotechnology Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, Warsaw 00-664, Poland
| | - Borys Kierdaszuk
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, Warsaw 02-089, Poland
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Liebau J, Pettersson P, Szpryngiel S, Mäler L. Membrane Interaction of the Glycosyltransferase WaaG. Biophys J 2016; 109:552-63. [PMID: 26244737 DOI: 10.1016/j.bpj.2015.06.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 11/30/2022] Open
Abstract
The glycosyltransferase WaaG is involved in the synthesis of lipopolysaccharides that constitute the outer leaflet of the outer membrane in Gram-negative bacteria such as Escherichia coli. WaaG has been identified as a potential antibiotic target, and inhibitor scaffolds have previously been investigated. WaaG is located at the cytosolic side of the inner membrane, where the enzyme catalyzes the transfer of the first outer-core glucose to the inner core of nascent lipopolysaccharides. Here, we characterized the binding of WaaG to membrane models designed to mimic the inner membrane of E. coli. Based on the crystal structure, we identified an exposed and largely α-helical 30-residue sequence, with a net positive charge and several aromatic amino acids, as a putative membrane-interacting region of WaaG (MIR-WaaG). We studied the peptide corresponding to this sequence, along with its bilayer interactions, using circular dichroism, fluorescence quenching, fluorescence anisotropy, and NMR. In the presence of dodecylphosphocholine, MIR-WaaG was observed to adopt a three-dimensional structure remarkably similar to the segment in the crystal structure. We found that the membrane interaction of WaaG is conferred at least in part by MIR-WaaG and that electrostatic interactions play a key role in binding. Moreover, we propose a mechanism of anchoring WaaG to the inner membrane of E. coli, where the central part of MIR-WaaG inserts into one leaflet of the bilayer. In this model, electrostatic interactions as well as surface-exposed Tyr residues bind WaaG to the membrane.
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Affiliation(s)
- Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Scarlett Szpryngiel
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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Siraj N, El-Zahab B, Hamdan S, Karam TE, Haber LH, Li M, Fakayode SO, Das S, Valle B, Strongin RM, Patonay G, Sintim HO, Baker GA, Powe A, Lowry M, Karolin JO, Geddes CD, Warner IM. Fluorescence, Phosphorescence, and Chemiluminescence. Anal Chem 2015; 88:170-202. [PMID: 26575092 DOI: 10.1021/acs.analchem.5b04109] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Noureen Siraj
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Bilal El-Zahab
- Department of Mechanical and Materials Engineering, Florida International University , Miami, Florida 33174, United States
| | - Suzana Hamdan
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Tony E Karam
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Louis H Haber
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Min Li
- Process Development Center, Albemarle Corporation , Baton Rouge, Louisiana 70805, United States
| | - Sayo O Fakayode
- Department of Chemistry, Winston-Salem State University , Winston-Salem, North Carolina 27110, United States
| | - Susmita Das
- Department of Civil Engineering, Adamas Institute of Technology , Barasat, Kolkata 700126, West Bengal India
| | - Bertha Valle
- Department of Chemistry, Texas Southern University , Houston, Texas 77004, United States
| | - Robert M Strongin
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Gabor Patonay
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-4098, United States
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Gary A Baker
- Department of Chemistry, University of Missouri Columbia , Columbia, Missouri 65211-7600, United States
| | - Aleeta Powe
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40208, United States
| | - Mark Lowry
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Jan O Karolin
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Chris D Geddes
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Isiah M Warner
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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Sobieraj M, Krzyśko KA, Jarmuła A, Kalinowski MW, Lesyng B, Prokopowicz M, Cieśla J, Gojdź A, Kierdaszuk B. A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A. J Mol Model 2015; 21:75. [PMID: 25754135 PMCID: PMC4353879 DOI: 10.1007/s00894-015-2602-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/01/2015] [Indexed: 11/25/2022]
Abstract
Predicting FRET pathways in proteins using computer simulation techniques is very important for reliable interpretation of experimental data. A novel and relatively simple methodology has been developed and applied to purine nucleoside phosphorylase (PNP) complexed with a fluorescent ligand - formycin A (FA). FRET occurs between an excited Tyr residue (D*) and FA (A). This study aims to interpret experimental data that, among others, suggests the absence of FRET for the PNPF159A mutant in complex with FA, based on novel theoretical methodology. MD simulations for the protein molecule containing D*, and complexed with A, are carried out. Interactions of D* with its molecular environment are accounted by including changes of the ESP charges in S1, compared to S0, and computed at the SCF-CI level. FRET probability W F depends on the inverse six-power of the D*-A distance, R da . The orientational factor 0 < k(2) < 4 between D* and A is computed and included in the analysis. Finally W F is time-averaged over the MD trajectories resulting in its mean value. The red-shift of the tyrosinate anion emission and thus lack of spectral overlap integral and thermal energy dissipation are the reasons for the FRET absence in the studied mutants at pH 7 and above. The presence of the tyrosinate anion results in a competitive energy dissipation channel and red-shifted emission, thus in consequence in the absence of FRET. These studies also indicate an important role of the phenyl ring of Phe159 for FRET in the wild-type PNP, which does not exist in the Ala159 mutant, and for the effective association of PNP with FA. In a more general context, our observations point out very interesting and biologically important properties of the tyrosine residue in its excited state, which may undergo spontaneous deprotonation in the biomolecular systems, resulting further in unexpected physical and/or biological phenomena. Until now, this observation has not been widely discussed in the literature.
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Affiliation(s)
- M. Sobieraj
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - K. A. Krzyśko
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
- Bioinformatics Laboratory, Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - A. Jarmuła
- Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - M. W. Kalinowski
- Bioinformatics Laboratory, Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - B. Lesyng
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
- Bioinformatics Laboratory, Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - M. Prokopowicz
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - J. Cieśla
- Department of Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | - A. Gojdź
- Department of Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | - B. Kierdaszuk
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
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Ghisaidoobe ABT, Chung SJ. Intrinsic tryptophan fluorescence in the detection and analysis of proteins: a focus on Förster resonance energy transfer techniques. Int J Mol Sci 2014; 15:22518-38. [PMID: 25490136 PMCID: PMC4284722 DOI: 10.3390/ijms151222518] [Citation(s) in RCA: 517] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/08/2014] [Accepted: 11/18/2014] [Indexed: 12/18/2022] Open
Abstract
Förster resonance energy transfer (FRET) occurs when the distance between a donor fluorophore and an acceptor is within 10 nm, and its application often necessitates fluorescent labeling of biological targets. However, covalent modification of biomolecules can inadvertently give rise to conformational and/or functional changes. This review describes the application of intrinsic protein fluorescence, predominantly derived from tryptophan (λ EX ≈ 280 nm, λ EM ≈ 350 nm), in protein-related research and mainly focuses on label-free FRET techniques. In terms of wavelength and intensity, tryptophan fluorescence is strongly influenced by its (or the proteinlocal environment, which, in addition to fluorescence quenching, has been applied to study protein conformational changes. Intrinsic Förster resonance energy transfer (iFRET), a recently developed technique, utilizes the intrinsic fluorescence of tryptophan in conjunction with target-specific fluorescent probes as FRET donors and acceptors, respectively, for real time detection of native proteins.
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Affiliation(s)
| | - Sang J Chung
- Department of Chemistry, Dongguk University, Seoul 100-715, Korea.
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N-terminal region of human chemokine receptor CXCR3: Structural analysis of CXCR3(1–48) by experimental and computational studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1868-80. [DOI: 10.1016/j.bbapap.2014.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 11/20/2022]
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