Articles

Probing membrane protein interactions with their lipid raft environment using single-molecule tracking and Bayesian inference analysis.
- Türkcan Silvan
- Richly Maximilian U.
- Alexandrou Antigoni
- Masson Jean-Baptiste
PLoS ONE, Public Library of Science , 2013, 8 (1), pp.e53073 . The statistical properties of membrane protein random walks reveal information on the interactions between the proteins and their environments. These interactions can be included in an overdamped Langevin equation framework where they are injected in either or both the friction field and the potential field. Using a Bayesian inference scheme, both the friction and potential fields acting on the ε-toxin receptor in its lipid raft have been measured. Two types of events were used to probe these interactions. First, active events, the removal of cholesterol and sphingolipid molecules, were used to measure the time evolution of confining potentials and diffusion fields. Second, passive rare events, de-confinement of the receptors from one raft and transition to an adjacent one, were used to measure hopping energies. Lipid interactions with the ε-toxin receptor are found to be an essential source of confinement. ε-toxin receptor confinement is due to both the friction and potential field induced by cholesterol and sphingolipids. Finally, the statistics of hopping energies reveal sub-structures of potentials in the rafts, characterized by small hopping energies, and the difference of solubilization energy between the inner and outer raft area, characterized by higher hopping energies. (10.1371/journal.pone.0053073)
DOI : 10.1371/journal.pone.0053073
Arbitrary-detuning asynchronous optical sampling pump-probe spectroscopy of bacterial reaction centers
- Antonucci Laura
- Bonvalet Adeline
- Solinas Xavier
- Jones Mickael R.
- Vos Marten H.
- Joffre Manuel
Optics Letters, Optical Society of America - OSA Publishing , 2013, 38 (17), pp.3322-3324 . A recently reported variant of asynchronous optical sampling compatible with arbitrary unstabilized laser repetition rates is applied to pump-probe spectroscopy. This makes possible the use of a 5.1 MHz chirped pulse oscillator as the pump laser, thus extending the available time window to almost 200 ns with a time resolution as good as about 320 fs. The method is illustrated with the measurement in a single experiment of the complete charge transfer dynamics of the reaction center from Rhodobacter sphaeroides. © 2013 Optical Society of America (10.1364/OL.38.003322)
DOI : 10.1364/OL.38.003322
Achievement of cornea-like organizations in dense collagen I solutions: clues to the physico-chemistry of cornea morphogenesis
- de Sa Peixoto Paulo
- Deniset-Besseau Ariane
- Schmutz Marc
- Anglo Anny
- Illoul Corinne
- Schanne-Klein Marie-Claire
- Mosser Gervaise
Soft Matter, Royal Society of Chemistry , 2013, 9 (47), pp.11241-11248 . Multiphoton and electron microscopic analyses show that acido-soluble collagen I prepared in 5 mM acetic acid (pH 3.5) at concentration above 45 mg mL−1 spontaneously generates liquid crystal phases mimicking plywood organization found in cornea tissues. Those organizations extend for several hundred micrometers. Transmission electron microscopy reveals the presence of small nanofibrils organized in a complex phase, coupling overall smectic and cholesteric organizations together with local order. Those nanofibrils could be the mesogen elements giving rise to this plywood organization. These data provide clues to physico-chemical events that may take place in cornea morphogenesis in vivo. This result is invaluable for bioengineering fields, as this liquid crystal organization paves the way for the generation of collagen based bio-mimetic cornea matrices. (10.1039/c3sm52097h)
DOI : 10.1039/c3sm52097h
Picosecond binding of the his ligand to four-coordinate heme in cytochrome c ': A one-way gate for releasing proximal NO
- Yoo Byung-Kuk
- Lamarre Isabelle
- Martin Jean-Louis
- Andrew Colin R.
- Negrerie Michel
Journal of the American Chemical Society, American Chemical Society , 2013, 135 (8), pp.3248-3254 . We provide a direct demonstration of a "kinetic trap" mechanism in the proximal 5-coordinate heme-nitrosyl complex (5c-NO) of cytochrome c' from Alcaligenes xylosoxidans (AXCP) in which picosecond rebinding of the endogenous His ligand following heme-NO dissociation acts as a one-way gate for the release of proximal NO into solution. This demonstration is based upon picosecond transient absorption changes following NO photodissociation of the proximal 5c-NO AXCP complex. We have determined the absolute transient absorption spectrum of 4-coordinate ferrous heme to which NO rebinds with a time constant tNO = 7 ps (kNO = 1.4 × 1011 s-1) and shown that rebinding of the proximal histidine to the 4-coordinate heme takes place with a time constant tHis = 100 ± 10 ps (kHis = 1010 s-1) after the release of NO from the proximal heme pocket. This rapid His reattachment acts as a one-way gate for releasing proximal NO by precluding direct proximal NO rebinding once it has left the proximal heme pocket and requiring NO rebinding from solution to proceed via the distal heme face. Cop. 2013 American Chemical Society. (10.1021/ja312140f)
DOI : 10.1021/ja312140f
Crystal structure of Cex1p reveals the mechanism of tRNA trafficking between nucleus and cytoplasm
- Nozawa Kayo
- Ishitani Ryuichiro
- Yoshihisa Tohru
- Sato Mamoru
- Arisaka Fumio
- Kanamaru Shuji
- Dohmae Naoshi
- Mangroo Dev
- Senger Bruno
- Becker Hubert F.
- Nureki Osamu
Nucleic Acids Research, Oxford University Press , 2013, 41 (6), pp.3901-3914 . In all eukaryotes, transcribed precursor tRNAs are maturated by processing and modification processes in nucleus and are transported to the cytoplasm. The cytoplasmic export protein (Cex1p) captures mature tRNAs from the nuclear export receptor (Los1p) on the cytoplasmic side of the nuclear pore complex, and it delivers them to eukaryotic elongation factor 1alpha. This conserved Cex1p function is essential for the quality control of mature tRNAs to ensure accurate translation. However, the structural basis of how Cex1p recognizes tRNAs and shuttles them to the translational apparatus remains unclear. Here, we solved the 2.2 A resolution crystal structure of Saccharomyces cerevisiae Cex1p with C-terminal 197 disordered residues truncated. Cex1p adopts an elongated architecture, consisting of N-terminal kinase-like and a C-terminal alpha-helical HEAT repeat domains. Structure-based biochemical analyses suggested that Cex1p binds tRNAs on its inner side, using the positively charged HEAT repeat surface and the C-terminal disordered region. The N-terminal kinase-like domain acts as a scaffold to interact with the Ran-exportin (Los1p.Gsp1p) machinery. These results provide the structural basis of Los1p.Gsp1p.Cex1p.tRNA complex formation, thus clarifying the dynamic mechanism of tRNA shuttling from exportin to the translational apparatus. (10.1093/nar/gkt010)
DOI : 10.1093/nar/gkt010
Attenuated internal reflection terahertz imaging
- Wojdyla Antoine
- Gallot Guilhem
Optics Letters, Optical Society of America - OSA Publishing , 2013, 38 (2), pp.112-114 . We present a terahertz (THz) imaging technique based on attenuated internal reflection, which is ideally suited for the analysis of liquid and biological samples. Inserted in a THz time-domain system, and using a high-resistivity low loss silicon prism to couple the THz wave into the sample, the detection scheme is based on the relative differential spectral phase of two orthogonal polarizations. Biological sample imaging as well as subwavelength (?/16) longitudinal resolution are demonstrated. Cop. 2013 Optical Society of America.
Upregulation of Adhesion Molecules on Leukemia Targets Improves the Efficacy of Cytotoxic T Cells Transduced With Chimeric Anti-CD19 Receptor
- Laurin David
- Marin Virna
- Biagi Ettore
- Pizzitola Irene
- Agostoni Valentina
- Gallot Géraldine
- Vié Henri
- Christine Jacob Marie
- Chaperot Laurence
- Aspord Caroline
- Plumas Joël
Journal of Immunotherapy, Lippincott, Williams & Wilkins , 2013, 36 (3), pp.181-189 . (10.1097/CJI.0b013e318288f8c1)
DOI : 10.1097/CJI.0b013e318288f8c1
Parallel measurements of reaction kinetics using ultralow-volumes
- Fradet Etienne
- Abbyad Paul
- Vos Marten H.
- Baroud Charles N.
Lab on a Chip, Royal Society of Chemistry , 2013, 13 (22), pp.4326-4330 . We present a new platform for the production and manipulation of microfluidic droplets in view of measuring the evolution of a chemical reaction. Contrary to existing approaches, our device uses gradients of confinement to produce a single drop on demand and guide it to a pre-determined location. In this way, two nanoliter drops containing different reagents can be placed in contact and merged together, in order to trigger a chemical reaction. The reaction rate is extracted from an analysis of the observed reaction-diffusion front. We show that the results obtained using this platform are in excellent agreement with stopped-flow measurements, while decreasing the sample consumption 5000 fold. We also show how the device operation can be parallelized in order to react an initial sample with a range of compounds or concentrations, on a single integrated chip. This integrated chip thus further reduces sample consumption while reducing the time required for the experimental runs from hours to minutes. (10.1039/c3lc50768h)
DOI : 10.1039/c3lc50768h
Primary processes in heme-based sensor proteins
- Liebl Ursula
- Lambry Jean-Christophe
- Vos Marten H.
Biochimica et Biophysica Acta Proteins and Proteomics, Elsevier , 2013, 1834 (9), pp.1684-1692 . A wide and still rapidly increasing range of heme-based sensor proteins has been discovered over the last two decades. At the molecular level, these proteins function as bistable switches in which the catalytic activity of an enzymatic domain is altered mostly by binding or dissociation of small gaseous ligands (O2, NO or CO) to the heme in a sensor domain. The initial "signal" at the heme level is subsequently transmitted within the protein to the catalytic site, ultimately leading to adapted expression levels of specific proteins. Making use of the photolability of the heme-ligand bond that mimics thermal dissociation, early processes in this intra-protein signaling pathway can be followed using ultrafast optical spectroscopic techniques; they also occur on timescales accessible to molecular dynamics simulations. Experimental studies performed over the last decade on proteins including the sensors FixL (O2), CooA (CO) and soluble guanylate cyclase (NO) are reviewed with an emphasis on emerging general mechanisms. After heme-ligand bond breaking, the ligand can escape from the heme pocket and eventually from the protein, or rebind directly to the heme. Remarkably, in all sensor proteins the rebinding, specifically of the sensed ligand, is highly efficient. This "ligand trap" property possibly provides means to smoothen the effects of fast environmental fluctuations on the switching frequency. For 6-coordinate proteins, where exchange between an internal heme-bound residue and external gaseous ligands occurs, the study of early processes starting from the unliganded form indicates that mobility of the internal ligand may facilitate signal transfer. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. Cop. 2013 Elsevier B.V. All rights reserved. (10.1016/j.bbapap.2013.02.025)
DOI : 10.1016/j.bbapap.2013.02.025
Configurational fluctuations and flavin-substrate interactions in the flavoenzyme ThyX studied by time- and spectrally resolved fluorescence
- Laptenok Sergey P.
- Bouzhir-Sima Latifa
- Myllykallio Hannu
- Liebl Ursula
- Vos Marten H.
EPJ Web of Conferences, EDP Sciences , 2013, 41, pp.07011 . Femtosecond-resolved fluorescence of bacterial thymidilate synthase using a Kerr-gate based setup identifies a close-by tyrosine involved in flavin fluorescence quenching, shows that the substrate dUMP acts as a strong quencher itself and highlights functional configurational flexibility. © Owned by the authors, published by EDP Sciences, 2013 (10.1051/epjconf/20134107011)
DOI : 10.1051/epjconf/20134107011
Numerical simulation of polarization-resolved second harmonic microscopy in birefringent media
- Gusachenko Ivan
- Schanne-Klein Marie-Claire
Physical Review A : Atomic, molecular, and optical physics [1990-2015], American Physical Society , 2013, 88 (5), pp.053811 . Polarization-resolved second-harmonic microscopy has recently emerged as a valuable technique for in situ imaging of collagen structure in tissues. Nevertheless, collagen-rich tissues such as tendon, ligament, skin dermis, bone, cornea, or artery exhibit a heterogeneous and anisotropic architecture that results in complex optical properties. While experimental evidence of polarization distortions has been reported in various tissues, the physics of second-harmonic imaging within such tissues is not fully understood yet. In this work, we performed numerical simulations of polarization-resolved second-harmonic generation in a strongly focused regime within a birefringent tissue. We show that vectorial components due to strong focusing have a rather small effect on the measurement of the second-harmonic tensorial response, while birefringence and optical dispersion may affect these measurements dramatically. We show indeed that a difference in the focal field distribution for ordinary and extraordinary waves results in different phase-matching conditions, which strongly affects the relative efficacy of second-harmonic generation for different polarizations. These results are of great interest for extracting reliable quantitative parameters from second-harmonic images. ©2013 American Physical Society (10.1103/PhysRevA.88.053811)
DOI : 10.1103/PhysRevA.88.053811
Microscopie multiphoton illuminée par nappe : imagerie de fluorescence rapide et en profondeur dans les tissus vivants
- Supatto Willy
Photoniques, EDP Sciences , 2012 (62), pp.33-37 . (10.1051/photon/20126233)
DOI : 10.1051/photon/20126233
Third-harmonic generation microscopy with Bessel beams: a numerical study
- Olivier Nicolas
- Débarre Delphine
- Mahou Pierre
- Beaurepaire Emmanuel
Optics Express, Optical Society of America - OSA Publishing , 2012, 20 (22), pp.24886-24902 . We study theoretically and numerically third-harmonic generation (THG) from model geometries (interfaces, slabs, periodic media) illuminated by Bessel beams produced by focusing an annular intensity profile. Bessel beams exhibit a phase and intensity distribution near focus different from Gaussian beams, resulting in distinct THG phase matching properties and coherent scattering directions. Excitation wave vectors are controlled by adjusting the bounding aperture angles of the Bessel beam. In addition to extended depth-of-field imaging, this opens interesting perspectives for coherent nonlinear microscopy, such as extracting sample spatial frequencies in the λ/8 - λ range in the case of organized media. © 2012 OSA (10.1364/OE.20.024886)
DOI : 10.1364/OE.20.024886
In situ 3D characterization of historical coatings and wood using multimodal nonlinear optical microscopy
- Latour Gaël
- Echard Jean-Philippe
- Didier Marie
- Schanne-Klein Marie-Claire
Optics Express, Optical Society of America - OSA Publishing , 2012, 20 (22), pp.24623-24635 . We demonstrate multimodal nonlinear optical imaging of historical artifacts by combining Second Harmonic Generation (SHG) and Two-Photon Excited Fluorescence (2PEF) microscopies. We first identify the nonlinear optical response of materials commonly encountered in coatings of cultural heritage artifacts by analyzing one- and multi-layered model samples. We observe 2PEF signals from cochineal lake and sandarac and show that pigments and varnish films can be discriminated by exploiting their different emission spectral ranges as in luminescence linear spectroscopy. We then demonstrate SHG imaging of a filler, plaster, composed of bassanite particles which exhibit a non centrosymmetric crystal structure. We also show that SHG/2PEF imaging enables the visualization of wood microstructure through typically 60 µm-thick coatings by revealing crystalline cellulose (SHG signal) and lignin (2PEF signal) in the wood cell walls. Finally, in situ multimodal nonlinear imaging is demonstrated in a historical violin. SHG/2PEF imaging thus appears as a promising non-destructive and contactless tool for in situ 3D investigation of historical coatings and more generally for wood characterization and coating analysis at micrometer scale. © 2012 OSA (10.1364/OE.20.024623)
DOI : 10.1364/OE.20.024623
In situ three-dimensional monitoring of collagen fibrillogenesis using SHG microscopy.
- Bancelin Stéphane
- Aimé Carole
- Coradin Thibaud
- Schanne-Klein Marie-Claire
Biomedical optics express, Optical Society of America - OSA Publishing , 2012, 3 (6), pp.1446-54 . We implemented in situ time-lapse Second Harmonic Generation (SHG) microscopy to monitor the three-dimensional (3D) self-assembly of collagen in solution. As a proof of concept, we tuned the kinetics of fibril formation by varying the pH and measured the subsequent exponential increase of fibril volume density in SHG images. We obtained significantly different time constants at pH = 6.5 ± 0.3 and at pH = 7.5 ± 0.3. Moreover, we showed that we could focus on the growth of a single isolated collagen fibril because SHG microscopy is sensitive to well-organized fibrils with diameter below the optical resolution. This work illustrates the potential of SHG microscopy for the rational design and characterization of collagen-based biomaterials. (10.1364/BOE.3.001446)
DOI : 10.1364/BOE.3.001446
Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels.
- Creze Christophe
- Ligabue Alessio
- Laurent Sébastien
- Lestini Roxane
- Laptenok Sergey P.
- Khun Joelle
- Vos Marten H.
- Czjzek Mirjam
- Myllykallio Hannu
- Flament Didier
Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology , 2012, 287 (19), pp.15648-60 . Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5' and 3' flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction. (10.1074/jbc.M112.346361)
DOI : 10.1074/jbc.M112.346361
Polarization-resolved second-harmonic generation in tendon upon mechanical stretching
- Gusachenko Ivan
- Tran Viet
- Goulam Houssen Yannick
- Allain Jean-Marc
- Schanne-Klein Marie-Claire
Biophysical Journal, Biophysical Society , 2012, 102 (9), pp.2220-2229 . Collagen is a triple-helical protein that forms various macromolecular organizations in tissues and is responsible for the biomechanical and physical properties of most organs. Second-harmonic generation (SHG) microscopy is a valuable imaging technique to probe collagen fibrillar organization. In this article, we use a multiscale nonlinear optical formalism to bring theoretical evidence that anisotropy of polarization-resolved SHG mostly reflects the micrometer-scale disorder in the collagen fibril distribution. Our theoretical expectations are confirmed by experimental results in rat-tail tendon. To that end, we report what to our knowledge is the first experimental implementation of polarization-resolved SHG microscopy combined with mechanical assays, to simultaneously monitor the biomechanical response of rat-tail tendon at macroscopic scale and the rearrangement of collagen fibrils in this tissue at microscopic scale. These experiments bring direct evidence that tendon stretching corresponds to straightening and aligning of collagen fibrils within the fascicle. We observe a decrease in the SHG anisotropy parameter when the tendon is stretched in a physiological range, in agreement with our numerical simulations. Moreover, these experiments provide a unique measurement of the nonlinear optical response of aligned fibrils. Our data show an excellent agreement with recently published theoretical calculations of the collagen triple helix hyperpolarizability. Copyright © 2012 Biophysical Society (10.1016/j.bpj.2012.03.068)
DOI : 10.1016/j.bpj.2012.03.068
Methodology for reconstructing early zebrafish development from in vivo multiphoton microscopy.
- Luengo-Oroz Miguel Angel
- Rubio-Guivernau José L.
- Faure Emmanuel
- Savy Thierry
- Duloquin Louise
- Olivier Nicolas
- Pastor-Escuredo David
- Ledesma-Carbayo María Jesús
- Debarre Delphine
- Bourgine Paul
- Beaurepaire Emmanuel
- Peyriéras Nadine
- Santos Andrés
IEEE Transactions on Image Processing, Institute of Electrical and Electronics Engineers , 2012, 21 (4), pp.2335-40 . Investigating cell dynamics during early zebrafish embryogenesis requires specific image acquisition and analysis strategies. Multiharmonic microscopy, i.e., second- and third-harmonic generations, allows imaging cell divisions and cell membranes in unstained zebrafish embryos from 1- to 1000-cell stage. This paper presents the design and implementation of a dedicated image processing pipeline (tracking and segmentation) for the reconstruction of cell dynamics during these developmental stages. This methodology allows the reconstruction of the cell lineage tree including division timings, spatial coordinates, and cell shape until the 1000-cell stage with minute temporal accuracy and micrometer spatial resolution. Data analysis of the digital embryos provides an extensive quantitative description of early zebrafish embryogenesis. (10.1109/TIP.2011.2177911)
DOI : 10.1109/TIP.2011.2177911
Ultrafast heme-ligand recombination in truncated hemoglobin HbO from Mycobacterium tuberculosis: A ligand cage
- Jasaitis Audrius
- Ouellet Hugues
- Lambry Jean-Christophe
- Martin Jean-Louis
- Friedman Joel M.
- Guertin Michel
- Vos Marten H.
Chemical Physics, Elsevier , 2012, 396, pp.10-16 . Truncated hemoglobin HbO from Mycobacterium tuberculosis displays very slow exchange of diatomic ligands with its environment. Using femtosecond spectroscopy, we show that upon photoexcitation, ligands rebind with unusual speed and efficiency. Only ∼1% O2 can escape from the heme pocket and less than 1% NO. Most remarkably, CO rebinding occurs for 95%, predominantly in 1.2 ns. The general CO rebinding properties are unexpectedly robust against changes in the interactions with close by aromatic residues Trp88 (G8) and Tyr36 (CD1). Molecular dynamics simulations of the CO complex suggest that interactions of the ligand with structural water molecules as well as its rotational freedom play a role in the high reactivity of the ligand and the heme. The slow exchange of ligands between heme and environment may result from a combination of hindered ligand access to the heme pocket by the network of distal aromatic residues, and low escape probability from the pocket. (10.1016/j.chemphys.2011.04.003)
DOI : 10.1016/j.chemphys.2011.04.003
Accuracy of correction in modal sensorless adaptive optics.
- Facomprez Aurélie
- Beaurepaire Emmanuel
- Débarre Delphine
Optics Express, Optical Society of America - OSA Publishing , 2012, 20 (3), pp.2598-612 . We investigate theoretically and experimentally the parameters governing the accuracy of correction in modal sensorless adaptive optics for microscopy. On the example of two-photon fluorescence imaging, we show that using a suitable number of measurements, precise correction can be obtained for up to 2 radians rms aberrations without optimising the aberration modes used for correction. We also investigate the number of photons required for accurate correction when signal acquisition is shot-noise limited. We show that only 10(4) to 10(5) photons are required for complete correction so that the correction process can be implemented with limited extra-illumination and associated photoperturbation. Finally, we provide guidelines for implementing an optimal correction algorithm depending on the experimental conditions.
Quaternary Structure Controls Ligand Dynamics in Soluble Guanylate Cyclase
- Yoo Byung-Kuk
- Lamarre Isabelle
- Martin Jean-Louis
- Negrerie Michel
Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology , 2012, 287, pp.6851-6859 . Soluble guanylate cyclase (sGC) is the mammalian endogenous nitric oxide (NO) receptor. The mechanisms of activation and deactivation of this heterodimeric enzyme are unknown. For deciphering them, functional domains can be overexpressed. We have probed the dynamics of the diatomic ligands NO and CO within the isolated heme domain β1(190) of human sGC by piconanosecond absorption spectroscopy. After photo-excitation of nitrosylated sGC, only NO geminate rebinding occurs in 7.5 ps. In β1(190), both photo-dissociation of 5c-NO and photo-oxidation occur, contrary to sGC, followed by NO rebinding (7 ps) and back-reduction (230 ps and 2 ns). In full-length sGC, CO geminate rebinding to the heme does not occur. In contrast, CO geminately rebinds to β1(190) with fast multiphasic process (35, 171, and 18 ns). We measured the bimolecular association rates kon = 0.075 ± 0.01 × 106 M−1*s−1 for sGC and 0.83 ± 0.1 × 106 M−1*s−1 for β1(190). These different dynamics reflect conformational changes and less proximal constraints in the isolated heme domain with respect to the dimeric native sGC. We concluded that the α-subunit and the β1(191-619) domain exert structural strains on the heme domain. These strains are likely involved in the transmission of the energy and relaxation toward the activated state after Fe2+-His bond breaking. This also reveals the heme domain plasticity modulated by the associated domains and subunit. (10.1074/jbc.M111.299297)
DOI : 10.1074/jbc.M111.299297
A Bayesian Inference Scheme to Extract Diffusivity and Potential Fields from Confined Single-Molecule Trajectories
- Tuerkcan Silvan
- Alexandrou Antigoni
- Masson Jean-Baptiste
Biophysical Journal, Biophysical Society , 2012, 102 (10), pp.2288-2298 . Currently used techniques for the analysis of single-molecule trajectories only exploit a small part of the available information stored in the data. Here, we apply a Bayesian inference scheme to trajectories of confined receptors that are targeted by pore-forming toxins to extract the two-dimensional confining potential that restricts the motion of the receptor. The receptor motion is modeled by the overdamped Langevin equation of motion. The method uses most of the information stored in the trajectory and converges quickly onto inferred values, while providing the uncertainty on the determined values. The inference is performed on the polynomial development of the potential and on the diffusivities that have been discretized on a mesh. Numerical simulations are used to test the scheme and quantify the convergence toward the input values for forces, potential, and diffusivity. Furthermore, we show that the technique outperforms the classical mean-square-displacement technique when forces act on confined molecules because the typical mean-square-displacement analysis does not account for them. We also show that the inferred potential better represents input potentials than the potential extracted from the position distribution based on Boltzmann statistics that assumes statistical equilibrium. (10.1016/j.bpj.2012.01.063)
DOI : 10.1016/j.bpj.2012.01.063
Asynchronous optical sampling with arbitrary detuning between laser repetition rates
- Antonucci Laura
- Solinas Xavier
- Bonvalet Adeline
- Joffre Manuel
Optics Express, Optical Society of America - OSA Publishing , 2012, 20 (16), pp.17928-17937 . A method of asynchronous optical sampling based on free-running lasers with no requirement on the repetition rates is presented. The method is based on the a posteriori determination of the delay between each pair of pulses. A resolution better than 400 fs over 13 ns total delay scan is demonstrated. In addition to the advantages of conventional asynchronous sampling techniques, this method allows a straightforward implementation on already-existing laser systems using a fiber-based setup and an appropriate acquisition procedure. (C) 2012 Optical Society of America (10.1364/OE.20.017928)
DOI : 10.1364/OE.20.017928
Nitric oxide binding to the cardiolipin complex of ferric cytochrome
- Silkstone G.
- Kapetanaki Sofia M.
- Husu I.
- Vos Marten H.
- Wilson M.T.
Biochemistry, American Chemical Society , 2012, 51 (34), pp.6760-6766 . Cardiolipin, a phospholipid specific to the mitochondrion, interacts with the small electron transfer heme protein cytochrome c through both electrostatic and hydrophobic interactions. Once in a complex with cardiolipin, cytochrome c has been shown to undergo a conformational change that leads to the rupture of the bond between the heme iron and the intrinsic sulfur ligand of a methionine residue and to enhance the peroxidatic properties of the protein considered important to its apoptotic activity. Here we report that the ferric cytochrome c/cardiolipin complex binds nitric oxide tightly through a multistep process in which the first step is the relatively slow displacement (5 s-1) from heme coordination of an intrinsic ligand that replaces methionine in the complex. Nanosecond photolysis of the nitrosyl adduct demonstrated that a fraction of the nitric oxide escapes from the heme pocket and subsequently recombines to the heme in second-order processes (k = 1.8 × 106 and 5.5 × 105 M-1 s-1) that, under these conditions, were much faster than recombination of the intrinsic ligand with which they compete. Ultrafast (femtosecond) laser photolysis showed that the geminate recombination of nitric oxide to the heme occurred with time constants (? = 22 and 72 ps) and that ~23% of the photolyzed nitric oxide escaped into the bulk phase. This high value for the escape fraction relative to other heme proteins indicates the open nature of the heme pocket in this complex. These results are summarized in a scheme and are discussed in terms of the possible modulation of the apoptotic activity of cytochrome c by nitric oxide. Cop. 2012 American Chemical Society. (10.1021/bi300596)
DOI : 10.1021/bi300596
Diffraction from a subwavelength elliptic aperture: Analytic approximate aperture fields
- Masson Jean-Baptiste
- Gallot Guilhem
Journal of the Optical Society of America. A Optics, Image Science, and Vision, Optical Society of America , 2012, 29 (9), pp.2005-2014 . An analytical approximate solution of the electromagnetic field on a subwavelength elliptical hole in a thin perfectly conducting screen is presented. Illumination is a linear polarized, normally incident plane wave. A polynomial development method is used and allows one to obtain an easy-to-use analytical solution of the fields, which can be used to build analytical expressions of aperture fields for apertures in anisotropic structures. © 2012 Optical Society of America. (10.1364/josaa.29.002005)
DOI : 10.1364/josaa.29.002005