Computational study of ligand binding in lipid transfer proteins: Structures,interfaces, and free energies of protein‐lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein‐ligand interactions. We present here a computational study of protein‐ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries in molecular dynamics calculations, we computed Poisson‐Boltzmann electrostatic potentials, solvation energies, properties of the protein‐ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein‐lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity. © 2012 Wiley Periodicals, Inc.     

Onset of oscillatory binary fluid convection in three-dimensional cells

The purpose of this work is to investigate the influence of the transverse walls on the onset of convection in a horizontal rectangular cavity of infinite length filled with a binary mixture when heated from below. For the first time we take into account the effect of the third dimension without making any approximation and considering realistic boundary conditions. In previous numerical works the width of the cell was either taken to be infinity (bulk mixtures) or different approximations usually valid in the narrow cell limit were assumed (i.e., Hele–Shaw and non-ideal Hele–Shaw approximations). The results we find show that the presence of the walls has a considerable effect on the onset of convection even for intermediate transverse aspect ratio cells. They also show that the approximations generally assumed fail to reproduce the correct behaviour of the critical parameters in an important range of aspect ratio values when the primary bifurcation is oscillatory. We have compared the critical values of the Rayleigh number and the frequency with those reported in the literature (Ohlsen et al. [1]) and we find a quantitative agreement within the experimental error. PACS 47.20.Bp, 47.27.Te, 47.54.+r     

Poly(urea)urethanes based on amorphous quaternizable hard segments and a crystalline polyol derived from castor oil

A set of poly(urea)urethanes (PUU), with different contents of amorphous hard segment and castor oil-derived crystalline polyol as soft segment, was prepared combining bulk and solution polymerizations. It is shown that both the soft segment crystallinity and hard segment glassy nature control the stiffness of the materials and that phase mixing at intermediate hard segment compositions produces softer materials. Upon yielding, PUU developed large plasticity associated to the nature of soft segments. At longer strains, PUU presented strain-induced crystallization related both to soft segments alignment and crystallization, leading to strong and tough materials, especially with high hard segment content compositions. Despite the hydrophobicity of the soft segments, the PUU with 65 wt% hard segment content was dispersable in water after quaternization with acetic acid. The high amount of urea groups in this quaternized PUU makes one think of these types of polymers as promising water soluble environmentally friendly strong adhesives, coatings, or water soluble polymeric electrolites.     

Design and Preparation of Single‐Chain Nanocarriers Mimicking Disordered Proteins for Combined Delivery of Dermal Bioactive Cargos

Inspired by the multifunctionality of vitamin D‐binding protein and the multiple transient‐binding behavior of some intrinsically disordered proteins (IDPs), a polymeric platform is designed, prepared, and characterized for combined delivery of dermal protective and anticancer bioactive cargos on the basis of artificial single‐chain nano‐objects mimicking IDPs. For the first time ever, simultaneous delivery of folic acid or vitamin B₉, and hinokitiol, a relevant natural bioactive compound that exhibits anticancer activity against human malignant melanoma cells, from these multidirectionally self‐assembled unimolecular nanocarriers is illustrated.

     

Studying nanomagnets and magnetic heterostructures with X-ray PEEM at the Swiss Light Source

Polarization dependent X-ray absorption spectroscopy and microscopy enables the element selective investigation of magnetic systems at the nanoscale. At the Swiss Light Source a photoemission electron microscope is used for the study of a broad variety of systems. Here, a review of recent activities is presented with a focus on instrumental and analytical developments. A new procedure for the 3 dimensional determination of the magnetization vector has been developed, and is demonstrated for GdFeCo microstructures displaying in-plane and out-of-plane domains, and sub-20 nm Fe nanoparticles. The recent progress for measurements in applied magnetic fields is presented and a new set-up for time-resolved measurements employing femtosecond laser pulses is described.     

Raman spectra and structure of a 25mer HCV RNA

We have employed Raman spectroscopy to investigate the conformation of an (Hepatitis C virus) HCV RNA 25mer (1–25 nucleotides) in solution. The principal findings of this study are (1) the A‐form secondary structure involving C3′‐ endo/anti ribofuranose pucker is predominant; (2) some uridine and guanosine nucleoside residues adopt the C2′‐ endo/anti and C3′‐ endo/syn conformations, respectively, which appear in looped nucleotide sequences; and (3) six out of nine guanine residues are base‐paired probably forming a stem. These results are interpreted as formation of a hairpin whose secondary structure is consistent with that proposed on the basis of phylogenetic comparisons with other viral RNAs. Copyright © 2009 John Wiley & Sons, Ltd.     

Furan synthesis through AuCl3-catalysed cycloisomerisation of β-alkynyl β-ketoesters

AuCl₃ efficiently catalyses the cycloisomerisation of readily available β-alkynyl β-ketoesters to generate trisubstituted furans. The substrate scope is wide and the reaction is high yielding and operationally simple.     

Electrostatic force microscopy measurements of CdSe-PS nanoparticles and CdSe-PS/poly(styrene-b-butadiene-b-styrene) nanocomposites

Electrostatic force microscopy (EFM) measurements were performed to analyze the conductive properties of CdSe nanoparticles functionalized with polystyrene (PS) brushes and embedded in a poly(styrene-b-butadiene-b-styrene) triblock copolymer. CdSe nanoparticles were synthesized aqueously and functionalized with polystyrene chains by the grafting through technique. CdSe-PS nanoparticles obtained after 5 and 8 h of polymerization were analyzed, in order to study the effect of the molecular weight of PS chains on conductive properties. EFM results showed the maintenance of the conductive properties of CdSe nanoparticles through functionalization reactions and even when they were confined in the block copolymer. Due to the low differences between the values obtained in the response of the samples to the charged tip, no effect of the molecular weight of brushes was confirmed.     

Generation of nanocomposites based on polystyrene-grafted CdSe nanoparticles by grafting through and block copolymer

Continuing with our previous work, in which CdSe nanoparticles were functionalized with polystyrene (PS) brushes (CdSe-PS) by the grafting through method, nanocomposites were prepared by adding them to a poly(styrene-b-butadiene-b-styrene) (SBS) triblock copolymer. After characterizing CdSe-PS nanoparticles obtained at different polymerization times of 3, 5, and 8 h by means of thermogravimetric analysis and gel permeation chromatography, CdSe-PS nanoparticles obtained after 5 h of polymerization (CdSe-PS(5h)) were chosen as the most adequate for the generation of nanocomposites. Atomic force microscopy (AFM) was used for morphological characterization of SBS/CdSe-PS(5h) nanocomposites. AFM images showed a good dispersion of the nanoparticles in the block copolymer, with the placement of the nanoparticles in the PS domains due to the improved affinity obtained by their functionalization with PS brushes.     

The short time regime of segmental dynamics of glass-forming polymers

The short time regime (10⁻¹³ s ≤ t ≤ 10⁻¹¹ s) of the segmental dynamics of several glass-forming polymers with different chemical microstructure and glass-transition temperature has been investigated by means of time of flight (TOF) neutron scattering techniques. In this paper we present a summary of the main results obtained as well as the theoretical framework proposed by us to interpret these results. The main conclusion is that the segmental dynamics of glass-forming polymers display in the very short time range (t = 2 ps) a crossover from a simple exponential behaviour towards a non-exponential regime. The first exponential decay, which is controlled by C-C rotational barriers, can be understood as a trace of the behaviour of the system in absence of the effects (correlations, cooperativity, memory effects…) which characterise the dense supercooled liquid like state against the normal liquid state. The non-exponential regime at t > 2 ps corresponds to what is usually understood as α and β relaxations. Some implications of these results are also discussed.