Juan Elezgaray

Evidence for Cardiolipin Binding Sites on the Membrane-Exposed Surface of the Cytochrome bc(1)

The respiratory chain is located in the inner membrane of mitochondria and produces the major part of the ATP used by a cell. Cardiolipin (CL), a double charged phospholipid composing ~10-20% of the mitochondrial membrane, plays an important role in the function and supramolecular organization of the respiratory chain complexes. We present an extensive set of coarse-grain molecular dynamics (CGMD) simulations aiming at the determination of the preferential interfaces of CLs on the respiratory chain complex III (cytochrome bc(1), CIII). Six CL binding sites are identified, including the CL binding sites known from earlier structural studies and buried into protein cavities. The simulations revealed the importance of two subunits of CIII (G and K in bovine heart) for the structural integrity of these internal CL binding sites. In addition, new binding sites are found on the membrane-exposed protein surface. The reproducibility of these binding sites over two species (bovine heart and yeast mitochondria) points to an important role for the function of the respiratory chain. Interestingly the membrane-exposed CL binding sites are located on the matrix side of CIII in the inner membrane and thus may provide localized sources of proton ready for uptake by CIII. Furthermore, we found that CLs bound to those membrane-exposed sites bridge the proteins during their assembly into supercomplexes by sharing the binding sites.

Pore Formation Induced by an Antimicrobial Peptide: Electrostatic Effects ☆

We investigate the mode of action of Cateslytin, an antimicrobial peptide, on zwitterionic biomembranes by performing numerical simulations and electrophysiological measurements on membrane vesicles. Using this natural beta-sheet antimicrobial peptide secreted during stress as a model we show that a single peptide is able to form a stable membrane pore of 1 nm diameter of 0.25 nS conductance found both from calculation and electrical measurements. The resulting structure does not resemble the barrel-stave or carpet models earlier predicted, but is very close to that found in the simulation of alpha-helical peptides. Based on the simulation of a mutated peptide and the effects of small external electric fields, we conclude that electrostatic forces play a crucial role in the process of pore formation.

Direct visualization of transient thermal response of a DNA origami.

The DNA origami approach enables the construction of complex objects from DNA strands. A fundamental understanding of the kinetics and thermodynamics of DNA origami assembly is extremely important for building large DNA structures with multifunctionality. Here both experimental and theoretical studies of DNA origami melting were carried out in order to reveal the reversible association/disassociation process. Furthermore, by careful control of the temperature cycling via in situ thermally controlled atomic force microscopy, the self-assembly process of a rectangular DNA origami tile was directly visualized, unveiling key mechanisms underlying their structural and thermodynamic features.

High-resolution surface-plasmon imaging in air and in water: V(z) curve and operating conditions

We present what are believed to be the first images obtained with a far-field high-resolution scanning surface-plasmon microscope in an aqueous medium. Measurements of V(z), the output response of the microscope, versus defocus z give a signature of the surface-plasmon propagation. V(z) is strongly conditioned by the laser beam diameter and the objectives numerical aperture, and we show how the operating mode (in air and in water) must be chosen to maximize the surface-plasmon field and to minimize diffraction (edge) effects.

A systematic method to derive force fields for coarse-grained simulations of phospholipids

A general method to derive effective force fields for the simulation of coarse-grained versions of phospholipids is presented. The specific case of the dimyristoylphosphatidylcholine (DMPC) bilayers is considered in detail. It is shown that key structural properties are fairly well reproduced, improving the results obtained with other methods. In particular, we obtain rather accurate descriptions of the water–lipid interactions that mimic important hydration properties.

Amplitude and phase images of cellular structures with a scanning surface plasmon microscope

Imaging cellular internal structure at nanometer scale axial resolution with non invasive microscopy techniques has been a major technical challenge since the nineties. We propose here a complement to fluorescence based microscopies with no need of staining the biological samples, based on a Scanning Surface Plasmon Microscope (SSPM). We describe the advantages of this microscope, namely the possibility of both amplitude and phase imaging and, due to evanescent field enhancement by the surface plasmon resonance, a very high resolution in Z scanning (Z being the axis normal to the sample). We show for fibroblast cells (IMR90) that SSPM offers an enhanced detection of index gradient regions, and we conclude it is very well suited to discriminate regions of variable density in biological media such as cell compartments, nucleus, nucleoli and membranes.

Instabilities of front patterns in reaction-diffusion systems

Abstract Recent experiments in chemical reaction-diffusion systems with externally imposed concentration gradients may provide access to a host of spatio-temporal pattern formation phenomena. These systems tend to form steep reaction fronts in response to the external gradient. We use singular perturbation techniques, normal form calculations and numerical simulations to investigate the existence and the stability of such sustained fronts. In one-dimensional systems, the theoretical predictions are found in quantitative agreement with direct simulations of the Hopf bifurcation from steady to periodically oscillating front structures observed in the Couette flow reactor. Also conditions are found under which oscillations of the spatial structure become chaotic. In two-dimensional systems, we address the issue of realizing an experimental situation hitherto unattained: a one-dimensional chain of coupled oscillators at the onset of the Hopf destabilization of the front structure. We point out the intimate relationship between the frequency of oscillation, ω, of the homogeneous front pattern and the characteristic wavelength, λ, of the Turing pattern that can develop along the front; λ ≈ 2 π( D ω ) 1 2 . We comment on subsequent bifurcations that may result from the nonlinear interaction between Hopf and Turing instabilities as the precursors to spatio-temporal chaos. In conclusion, we emphasize the possibility of probing the transition to “mediated defect turbulence” in thin film gel reactors.

Coherent structures in random media and wavelets

Abstract We construct low-dimensional dynamical models for the motion of coherent structures such as those frequently observed in extended turbulent flows. These models are derived from the wavelet based Galerkin projection of the PDE describing the flow and account for the (local) interaction of a small number of coherent structures. We show that, under rather general assumptions, the wavelet projection is close to the proper orthogonal decomposition, in the average energy sense. In the specific case of the 1D Kuramoto-Sivashinsky equation, we show (numerically) that the dynamics of our model agrees qualitatively with that of the original KS equation.

Diffraction phase microscopy: retrieving phase contours on living cells with a wavelet-based space-scale analysis

Abstract. We propose a two-dimensional (2-D) space-scale analysis of fringe patterns collected from a diffraction phase microscope based on the 2-D Morlet wavelet transform. We show that the adaptation of a ridge detection method with anisotropic 2-D Morlet mother wavelets is more efficient for analyzing cellular and high refractive index contrast objects than Fourier filtering methods since it can separate phase from intensity modulations. We compare the performance of this ridge detection method on theoretical and experimental images of polymer microbeads and experimental images collected from living myoblasts.

Cooperativity in the annealing of DNA origamis

DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by the presence of short, single stranded DNA sequences (staples), that hold together separate regions of the scaffold. In this paper, we modelize the annealing-melting properties of these DNA constructions. The model captures important features such as the hysteresis between melting and annealing, as well as the dependence upon the topology of the scaffold. We show that cooperativity between staples is critical to quantitatively explain the folding process of DNA origamis.