Alexandros Koutsioubas

Influence of ibuprofen on phospholipid membranes

A basic understanding of biological membranes is of paramount importance as these membranes comprise the very building blocks of life itself. Cells depend in their function on a range of properties of the membrane, which are important for the stability and function of the cell, information and nutrient transport, waste disposal, and finally the admission of drugs into the cell and also the deflection of bacteria and viruses. We have investigated the influence of ibuprofen on the structure and dynamics of L-α-phosphatidylcholine (SoyPC) membranes by means of grazing incidence small-angle neutron scattering, neutron reflectometry, and grazing incidence neutron spin echo spectroscopy. From the results of these experiments, we were able to determine that ibuprofen induces a two-step structuring behavior in the SoyPC films, where the structure evolves from the purely lamellar phase for pure SoyPC over a superposition of two hexagonal phases to a purely hexagonal phase at high concentrations. A relaxation, which is visible when no ibuprofen is present in the membrane, vanishes upon addition of ibuprofen. This we attribute to a stiffening of the membrane. This behavior may be instrumental in explaining the toxic behavior of ibuprofen in long-term application.

Ab Initio and All-Atom Modeling of Detergent Organization around Aquaporin-0 Based on SAXS Data

A necessary initial step for the application of small angle X-ray scattering (SAXS) as an analytical probe for structural investigations of membrane proteins in solution is the precise knowledge of the structure of spontaneously formed detergent assemblies around the protein. Following our recent article (Berthaud et al. J. Am. Chem. Soc. 2012, 134, 10080-10088) on the study of the n-dodecyl β-D-maltopyranoside (dDM) corona surrounding Aquaporin-0 tetramers in solution, we aimed at the development of more elaborate models, exploiting the information content of the scattering data. Two additional approaches are developed here for the fit of SAXS experimental data, one based on a generalized ab initio algorithm for the construction of a coarse-grained representation of the detergent assemblies, and a second based on atomistic molecular dynamics. Accordingly, we are able to fit the SAXS experimental data and obtain a better insight concerning the structure of the detergent corona around the hydrophobic part of the Aquaporin-0 surface. The present analysis scheme represents an additional step toward future conformational studies of transmembrane proteins in solution.

Memprot: a program to model the detergent corona around a membrane protein based on SEC–SAXS data

Systematic SAXS simulations have been analysed over a wide range of parameters in order to better understand the detergent corona around a membrane protein.

Self-Diffusion in Amorphous Silicon.

The present Letter reports on self-diffusion in amorphous silicon. Experiments were done on ^{29}Si/^{nat}Si heterostructures using neutron reflectometry and secondary ion mass spectrometry. The diffusivities follow the Arrhenius law in the temperature range between 550 and 700 °C with an activation energy of (4.4±0.3)  eV. In comparison with single crystalline silicon the diffusivities are tremendously higher by 5 orders of magnitude at about 700 °C, which can be interpreted as the consequence of a high diffusion entropy.

Structural basis of the signalling through a bacterial membrane receptor HasR deciphered by an integrative approach

In bacteria, some scarce nutrients are sensed, bound and internalized by their specific transporter. In the present study, using an integrative structural approach, we study HasR, a bacterial haem transporter in both its free and its loaded forms.

The high-intensity reflectometer of the Jülich Centre for Neutron Science: MARIA

MARIA is a world class vertical sample reflectometer dedicated to the investigation of thin films in the fields of magnetism, soft matter and biology. With the elliptical vertically focusing guide and a wavelength resolution of Δλ/λ = 10%, the non-polarized flux at the sample position amounts to 1.2 × 108 n (s cm2)−1. Besides the polarized and non-polarized reflectivity mode for specular and off-specular reflectivity measurements, MARIA can also be used to carry out grazing-incidence small-angle neutron scattering investigations.

Low-Resolution Structure of Detergent-Solubilized Membrane Proteins from Small-Angle Scattering Data

Despite the ever-increasing usage of small-angle scattering as a valuable complementary method in the field of structural biology, applications concerning membrane proteins remain elusive mainly due to experimental challenges and the relative lack of theoretical tools for the treatment of scattering data. This fact adds up to general difficulties encountered also by other established methods (crystallography, NMR) for the study of membrane proteins. Following the general paradigm of ab initio methods for low-resolution restoration of soluble protein structure from small-angle scattering data, we construct a general multiphase model with a set of physical constraints, which, together with an appropriate minimization procedure, gives direct structural information concerning the different components (protein, detergent molecules) of detergent-solubilized membrane protein complexes. Assessment of the methods precision and robustness is evaluated by performing shape restorations from simulated data of a tetrameric α-helical membrane channel (Aquaporin-0) solubilized by n-Dodecyl β-D-Maltoside and from previously published small-angle neutron scattering experimental data of the filamentous hemagglutinin adhesin β-barrel protein transporter solubilized by n-Octyl β-D-glucopyranoside. It is shown that the acquisition of small-angle neutron scattering data at two different solvent contrasts, together with an estimation of detergent aggregation number around the protein, permits the reliable reconstruction of the shape of membrane proteins without the need for any prior structural information.

Time-Resolved Neutron Reflectivity during Supported Membrane Formation by Vesicle Fusion

The formation of supported lipid bilayers (SLB) on hydrophilic substrates through the method of unilamelar vesicle fusion is used routinely in a wide range of biophysical studies. In an effort to control and better understand the fusion process on the substrate, many experimental studies employing different techniques have been devoted to the elucidation of the fusion mechanism. In the present work, we follow the kinetics of membrane formation using time-resolved (TR) neutron reflectivity, focusing on the structural changes near the solid/liquid interface. A clear indication of stacked bilayer structure is observed during the intermediate phase of SLB formation. Adsorbed lipid mass decrease is also measured in the final stage of the process. We have found that it is essential for the analysis of the experimental results to treat the shape of adsorbed lipid vesicles on an attractive substrate theoretically. The overall findings are discussed in relation to proposed fusion mechanisms from the literature, and we argue that our observations favor a model involving enhanced adhesion of incoming vesicles on the edges of already-formed bilayer patches.

Erratum: Self-Diffusion in Amorphous Silicon [Phys. Rev. Lett. 116, 025901 (2016)].

This corrects the article DOI: 10.1103/PhysRevLett.116.025901.