Publications

2022

• Quadruplexes Are Everywhere…On the Other Strand Too: The i-Motif
  
  • Mergny Jean-Louis
  • Cheng Mingpan
  • Zhou Jun
  , 2022, pp.1-25. i-Motif (the name stems from “intercalated”), also known as i-DNA, is a pH-dependent four-stranded nucleic acid structure formed by cytosine-rich sequences via hemi-protonated and intercalated CC+ base pairs. Although this structure is favored at acidic pH, recent evidence has demonstrated its existence in vivo, stimulating the exploration of its biological roles. Before that, it was mostly regarded as a mere structural oddity, or a tool for bio- and nanotechnol- ogies: its unique pH-sensitive nature makes it a remarkable candidate as a nanodevice and pH sensor. In this chapter, we provide a general panorama of this structure. The history and basic knowledge of i-motif are provided first. Then, we present the main characterization methods of i-motif and factors affecting i-motif stability. Following that, we focus on the applications of i-motif in nanotechnology and analytical chemistry. Last, the interaction between i-motif and ligands and the physiological roles of i-motif are briefly introduced. We argue that the i-motif, similar to its complementary G-quadruplex, is an attractive structure for multidisciplinary approaches. It serves as a basic component for various applications and has been proposed to play biological roles in vivo. (10.1007/978-981-16-1313-5_5-1)
  DOI : 10.1007/978-981-16-1313-5_5-1
• Single-molecule-based imaging study of EGFR receptor nano-organization regulation : to pathophysiological mechanisms in kidney diseases
  
  • Hoang Thi Thuy
  , 2022. In the first part of the thesis, we revealed the distribution of EGF receptors and CD9 in the membrane of parietal epithelial cells (PEC) that are involved in inflammatory kidney diseases. First, we used the dSTORM technique to quantitatively map the localization of these proteins in the cell membrane and demonstrate their colocalization in parietal epithelial cells. These proteins are found to be localized in small domains with a radius of about 50 nm - 100 nm in the membrane of PEC cells. In the second part, we used a technique complementary to dSTORM, the single-particle tracking technique,to study the dynamics of the proteins in the cell membrane of different cell types. To analyze the trajectory obtained from singleparticle tracking, we introduced a new method to determine the free and confined portions of the protein motions. The confinement of EGFR was also analyzed by Bayesian inference to extract the confinement characteristics, the stiffness of the harmonic confining potential and the diffusion coefficient. We showed that the confinement characteristics depend on the cell type.
• Ultrafast photooxidation of protein-bound anionic flavin radicals
  
  • Zhuang Bo
  • Ramodiharilafy Rivo
  • Liebl Ursula
  • Aleksandrov Alexey
  • Vos Marten H.
  Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2022, 119 (8), pp.e2118924119. The photophysical properties of anionic semireduced flavin radicals are largely unknown despite their importance in numerous biochemical reactions. Here, we studied the photoproducts of these intrinsically unstable species in five different flavoprotein oxidases where they can be stabilized, including the well-characterized glucose oxidase. Using ultrafast absorption and fluorescence spectroscopy, we unexpectedly found that photoexcitation systematically results in the oxidation of protein-bound anionic flavin radicals on a time scale of less than ∼100 fs. The thus generated photoproducts decay back in the remarkably narrow 10- to 20-ps time range. Based on molecular dynamics and quantum mechanics computations, positively charged active-site histidine and arginine residues are proposed to be the electron acceptor candidates. Altogether, we established that, in addition to the commonly known and extensively studied photoreduction of oxidized flavins in flavoproteins, the reverse process (i.e., the photooxidation of anionic flavin radicals) can also occur. We propose that this process may constitute an excited-state deactivation pathway for protein-bound anionic flavin radicals in general. This hitherto undocumented photochemical reaction in flavoproteins further extends the family of flavin photocycles. (10.1073/pnas.2118924119)
  DOI : 10.1073/pnas.2118924119
• Photochemical and Molecular Dynamics Studies of Halide Binding in Flavoenzyme Glucose Oxidase
  
  • Zhuang Bo
  • Vos Marten
  • Aleksandrov Alexey
  ChemBioChem, Wiley-VCH Verlag, 2022, 23 (19), pp.e202200227. Glucose oxidase (GOX), a characteristic flavoprotein oxidase with widespread industrial applications, binds fluoride (F−) and chloride (Cl−). We investigated binding properties of halide inhibitors of GOX through time-resolved spectral characterization of flavin-related photochemical processes and molecular dynamic simulations. Cl− and F− bind differently to the protein active site and have substantial but opposite effects on the population and decay of the flavin excited state. Cl− binds closer to the flavin, whose excited-state decays in <100 fs due to anion-π interactions. Such interactions appear absent in F− binding, which, however, significantly increases the active-site rigidity leading to more homogeneous, picosecond fluorescence decay kinetics. These findings are discussed in relation to the mechanism of halide inhibition of GOX by occupying the accommodation site of catalytic intermediates and increasing the active-site rigidity (10.1002/cbic.202200227)
  DOI : 10.1002/cbic.202200227
• Guidance by followers ensures long-range coordination of cell migration through α-Catenin mechanoperception
  
  • Boutillon Arthur
  • Escot Sophie
  • Elouin Amélie
  • Jahn Diego
  • González-Tirado Sebastián
  • Starruss Jörn
  • Brusch Lutz
  • David Nicolas B
  Developmental Cell, Elsevier, 2022. Morphogenesis, wound healing and some cancer metastases depend upon migration of cell collectives that need to be guided to their destination as well as coordinated with other cell movements. During zebrafish gastrulation, extension of the embryonic axis is led by the mesendodermal polster that migrates towards the animal pole, followed by axial mesoderm that is undergoing convergence and extension. We here investigate how polster cells are guided towards the animal pole. Using a combination of precise laser ablations, advanced transplantations and functional as well as silico approaches, we establish that the directional information guiding polster cells is mechanical, and is provided by the anteriorward migration of the following cells. This information is detected by cell-cell contact through E-Cadherin/α-Catenin mechanotransduction and propagates from cell to cell over the whole tissue. Such guidance of migrating cells by followers ensures long-range coordination of movements and developmental robustness. (10.1016/j.devcel.2022.05.001)
  DOI : 10.1016/j.devcel.2022.05.001
• Transient absorption in inorganic systems
  
  • Ha-Thi Minh-Huong
  • Burdzinski Gotard
  • Pino Thomas
  • Changenet Pascale
  , 2022. ransient absorption spectroscopy is one the most popular methods to study photochemistry and photophysics. This technique allows observation of the dynamics in the electronic excited states after photoexcitation over a wide range of timescales, from the femtosecond to the millisecond timescales. The probed relaxation dynamics involve multiple channels in competition, such as internal conversion, intersystem crossing, fluorescence, energy transfer, electron transfer, proton-coupled electron transfer, and chemical reactions. The aim of this chapter is to provide general background and discuss state-of-the-art experimental techniques for transient absorption measurements. This will be illustrated by recent applications to study photoinduced processes in inorganic systems including molecular and hybrid systems, in particular toward renewable energy applications. Desirable developments, by no means exhaustive, will then be discussed to sustain future research. (10.1007/978-3-030-63713-2_5)
  DOI : 10.1007/978-3-030-63713-2_5
• Flavoprotein Photochemistry: Fundamental Processes and Photocatalytic Perspectives
  
  • Zhuang Bo
  • Liebl Ursula
  • Vos Marten H.
  Journal of Physical Chemistry B, American Chemical Society, 2022, 126, pp.3199-3207. Flavins are highly versatile redox-active and colored cofactors in a large variety of proteins. These do include photoenzymes and photoreceptors, although the vast majority performs non-light-driven physiological functions. Nevertheless, electron transfer between flavins and specific nearby amino acid residues (in particular tyrosine, tryptophan, and presumably histidine and arginine) takes place upon excitation of flavin in many flavoproteins. For oxidized flavoproteins these reactions potentially have a photoprotective role. In this Perspective, we outline work on the characterization of early reaction intermediates not only in the relatively well-studied resting oxidized forms but also in the fully reduced and the intrinsically unstable semireduced forms, where ultrafast photooxidation of flavin was recently demonstrated. Along different lines, flavoprotein-based novel photocatalysts for biotechnological applications are presently emerging, employing both substrate photooxidation and photoreduction strategies. Deep insight into the fundamental flavin photochemical reactions may help in guiding and optimizing their development and in the exploration of novel photocatalytic approaches. (10.1021/acs.jpcb.2c00969)
  DOI : 10.1021/acs.jpcb.2c00969
• Enhanced intrapulse difference frequency generation in the mid-infrared by a spectrally dependent polarization state
  
  • Bournet Q.
  • Guichard F.
  • Natile M.
  • Zaouter Y.
  • Joffre M.
  • Bonvalet A.
  • Pupeza I.
  • Hofer C.
  • Druon F.
  • Hanna Marc
  • Georges Patrick
  Optics Letters, Optical Society of America - OSA Publishing, 2022, 47 (2), pp.261. We present a technique to optimize the intrapulse difference frequency generation efficiency for mid-IR generation. The approach employs a multi-order waveplate that is designed to selectively rotate the polarization state of the incoming spectral components on the relevant orthogonal axes for subsequent nonlinear interaction. We demonstrate a significant increase of the mid-IR average power generated by a factor ≥ 2.5 compared to the conventional scheme, due to an optimally distributed number of photons enrolled in the difference frequency generation process. (10.1364/OL.444908)
  DOI : 10.1364/OL.444908
• G-quadruplexes in helminth parasites
  
  • Cantara Alessio
  • Luo Yu
  • Dobrovolná Michaela
  • Bohalova Natalia
  • Fojta Miroslav
  • Verga Daniela
  • Guittat Lionel
  • Cucchiarini Anne
  • Savrimoutou Solène
  • Häberli Cécile
  • Guillon Jean
  • Keiser Jennifer
  • Brázda Václav
  • Mergny Jean
  Nucleic Acids Research, Oxford University Press, 2022, 50 (5), pp.2719–2735. Parasitic helminths infecting humans are highly prevalent infecting ∼2 billion people worldwide, causing inflammatory responses, malnutrition and anemia that are the primary cause of morbidity. In addition, helminth infections of cattle have a significant economic impact on livestock production, milk yield and fertility. The etiological agents of helminth infections are mainly Nematodes (roundworms) and Platyhelminths (flatworms). G-quadruplexes (G4) are unusual nucleic acid structures formed by G-rich sequences that can be recognized by specific G4 ligands. Here we used the G4Hunter Web Tool to identify and compare potential G4 sequences (PQS) in the nuclear and mitochondrial genomes of various helminths to identify G4 ligand targets. PQS are nonrandomly distributed in these genomes and often located in the proximity of genes. Unexpectedly, a Nematode, Ascaris lumbricoides, was found to be highly enriched in stable PQS. This species can tolerate high-stability G4 structures, which are not counter selected at all, in stark contrast to most other species. We experimentally confirmed G4 formation for sequences found in four different parasitic helminths. Small molecules able to selectively recognize G4 were found to bind to Schistosoma mansoni G4 motifs. Two of these ligands demonstrated potent activity both against larval and adult stages of this parasite. (10.1093/nar/gkac129)
  DOI : 10.1093/nar/gkac129
• An Optimized Buffer for Repeatable Multicolor STORM
  
  • Abdelsayed Vaky
  • Boukhatem Hadjer
  • Olivier Nicolas
  ACS photonics, American Chemical Society, 2022. (10.1021/acsphotonics.2c01249)
  DOI : 10.1021/acsphotonics.2c01249
• Inline amplification of mid-infrared intrapulse difference frequency generation
  
  • Bournet Q.
  • Jonusas M.
  • Zheng A.
  • Guichard F.
  • Natile M.
  • Zaouter Y.
  • Joffre M.
  • Bonvalet A.
  • Druon F.
  • Hanna Marc
  • Georges P.
  Optics Letters, Optical Society of America - OSA Publishing, 2022, 47 (19), pp.4885. We demonstrate an ultrafast mid-infrared source architecture that implements both intrapulse difference frequency generation (iDFG) and further optical parametric amplification (OPA), in an all-inline configuration. The source is driven by a nonlinearly compressed high-energy Yb-doped-fiber amplifier delivering 7.4 fs pulses at a central wavelength of 1030 nm, at a repetition rate of 250 kHz. It delivers 1 µJ, 73 fs pulses at a central wavelength of 8 µm, tunable over more than one octave. By enrolling all the pump photons in the iDFG process and recycling the long wavelength pump photons amplified in the iDFG in the subsequent OPA, we obtain an unprecedented overall optical efficiency of 2%. These performances, combining high energy and repetition rate in a very simple all-inline setup, make this technique ideally suited for a growing number of applications, such as high harmonic generation in solids or two-dimensional infrared spectroscopy experiments. (10.1364/OL.467792)
  DOI : 10.1364/OL.467792
• Early processes in heme-based CO-sensing proteins
  
  • Vos Marten H
  • Salman Mayla
  • Liebl Ursula
  Frontiers in Molecular Biosciences, Frontiers Media, 2022, 9, pp.1046412. Carbon monoxide has been recognized relatively recently as signaling molecule, and only very few dedicated natural CO sensor proteins have been identified so far. These include in particular heme-based transcription factors: the bacterial sensor proteins CooA and RcoM. In these 6-coordinated systems, exchange between an internal protein residue and CO as a heme ligand in the sensor domain affects the properties of the DNA-binding domain. Using light to dissociate heme-ligand bonds can in principle initiate this switching process. We review the efforts to use this method to investigate early processes in ligand switching and signaling, with an emphasis on the CO-"trapping" properties of the heme cavity. These features are unusual for most heme proteins, but common for heme-based CO sensors. (10.3389/fmolb.2022.1046412)
  DOI : 10.3389/fmolb.2022.1046412