Molecular model for the self-assembly of the cyclic lipodepsipeptide pseudodesmin A

Self-assembly of peptides into supramolecular structures represents an active field of research with potential applications ranging from material science to medicine. Their study typically involves the application of a large toolbox of spectroscopic and imaging techniques. However, quite often, the structural aspects remain underexposed. Besides, molecular modeling of the self-assembly process is usually difficult to handle, since a vast conformational space has to be sampled. Here, we have used an approach that combines short molecular dynamics simulations for peptide dimerization and NMR restraints to build a model of the supramolecular structure from the dimeric units. Experimental NMR data notably provide crucial information about the conformation of the monomeric units, the supramolecular assembly dimensions, and the orientation of the individual peptides within the assembly. This in silico/in vitro mixed approach enables us to define accurate atomistic models of supramolecular structures of the bacterial cyclic lipodepsipeptide pseudodesmin A

Use of molecular dynamics simulations to study the interactions between barley allelochemicals and plant plasma membrane

Gramine and hordenine, two alkaloids produced by barley, were shown to inhibit the growth of a common weed (Matricaria recutita L.). This feature could be useful in order to reach a more sustainable weeds management. In vitro experiments have proven that both molecules do interact with lipid bilayers (made of a phosphatidylglycerol (PG) lipid) mimicking plant plasma membranes and are able to modify some of their properties. Moreover, gramine was shown to be more effective than hordenine in both inhibiting weeds growth and altering lipid bilayers properties, suggesting that interactions with membranes could be linked to their mode of action. Molecular dynamics (MD) simulations are carried out in order to get an insight into the molecular mechanisms that underlie these interactions with model membranes and to discriminate between gramine behavior and hordenine behavior

Anisotropic rate-dependent mechanical behavior of Poly(Lactic Acid) processed by Material Extrusion Additive Manufacturing

The strain-rate dependence of the yield stress for Material Extrusion Additive Manufacturing (ME-AM) polylactide samples was investigated. Apparent densities of the ME-AM processed tensile test specimens were measured and taken into account in order to study the effects of the ME-AM processing step on the material behavior. Three different printing parameters were changed to investigate their influence on mechanical properties, i.e. infill velocity, infill orientation angle, and bed temperature. Additionally, compression molded test samples were manufactured in order to determine bulk properties, which have been compared to the ME-AM sample sets. Anisotropy was detected in the strain-rate dependence of the yield stresses. ME-AM samples with an infill angle of 0° have a higher strain-rate dependence than specimens with αor = 90°. Remarkably, the strain-rate dependence manifested by the ME-AM samples is considerably lower than that displayed by compression molded test specimens. The Ree-Eyring modification of the Eyring flow rule is able to accurately describe the strain-rate dependence of the yield stresses, taking two molecular deformation processes into account to describe the yield kinetics. The results from this paper further show a change from a brittle behavior in case of compression molded samples to a semi-ductile behavior for some of the ME-AM sample sets. This change is attributed to the processing phase and stresses the importance that the temperature profile (initial fast cooling combined with successive heating cycles) and the strain profile during ME-AM processing have on the resulting mechanical properties. Both these profiles are significantly different from the thermo-mechanical history that material elements experience during conventional processing methods, e.g. injection or compression molding. This paper can be seen as initial work that can help to further develop predictive numerical tools for Material Extrusion Additive Manufacturing, as well as for the design of structural components

Controlling molecular mobility and ductile–brittle transitions of polycarbonate copolymers

To control molecular mobility and study its effects on mechanical properties, we synthesized two series of poly(ester carbonate) and polycarbonate copolymers with different linkages: (B x t) n ( x = 3, 5, 7, 9) and (B x T) n ( x = 1, 3, 5, 7, 9), where t represents the terephthalate, T represents the tetramethyl bisphenol A carbonate linkages, and B is the conventional bisphenol-A (BPA) carbonate. These two series of materials have distinct differences in their relaxation behaviors and chain mobility, as indicated by the Π-flip motion of the phenylene rings in the B x blocks. Uniaxial tensile tests of the copolymers indicate that the brittle–ductile transition (BDT) temperatures of the copolymers are correlated to whether the Γ-relaxation peaks due to the B x sequence is fully established. The materials possessing more fully established low-temperature Γ peaks give rise to a lower BDT. Also, the locations of the Γ peaks are correlated to the ring flips of the B x blocks of polymer chains. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1730–1740, 2001Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/35007/1/1146_ftp.pd

Yield stress distribution in injection-mouldedglassy polymers

A methodology for structural analysis simulations is presented that incorporates the distribution of mechanical propertiesalong the geometrical dimensions of injection-moulded amorphous polymer products. It is based on a previously developedmodelling approach, where the thermomechanical history experienced during processing was used to determine the yield stressat the end of an injection-moulding cycle. Comparison between experimental data and simulation results showed an excellentquantitative agreement, both for short-term tensile tests as well as long-term creep experiments over a range of strain rates,applied stresses, and testing temperatures. Changes in mould temperature and component wall thickness, which directly affectthe cooling profiles and, hence, the mechanical properties, were well captured by the methodology presented. Furthermore, itturns out that the distribution of the yield stress along a tensile bar is one of the triggers for the onset of the (strong) localizationgenerally observed in experiments.Spanish Government (Ministry of Sci-ence and Innovation, Ministry of Economy and Competitiveness)through grant numbers RYC-2010-07171 and DPI2011-25470This is the peer reviewed version of the following article: Verbeeten, W. M., Kanters, M. J., Engels, T. A. and Govaert, L. E. (2015), Yield stress distribution in injection-moulded glassy polymers. Polym. Int., 64(11): 1527–1536, which has been published in final form at http://dx.doi.org/10.1002/pi.4898. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archivin

Low-diluted Phenacetinum disrupted the melanoma cancer cell migration

Dynamic and reciprocal interactions generated by the communication between tumor cells and their matrix microenvironment, play a major role in the progression of a tumor. Indeed, the adhesion of specific sites to matrix components, associated with the repeated and coordinated formation of membrane protrusions, allow tumor cells to move along a determined pathway. Our study analyzed the mechanism of action of low-diluted Phenacetinum on murine cutaneous melanoma process in a fibronectin matrix environment. We demonstrated a reduction of dispersed cell migration, early and for as long as 24 h, by altering the formation of cell protrusions. Moreover, low-diluted Phenacetinum decreased cell stiffness highly on peripheral areas, due to a disruption of actin filaments located just under the plasma membrane. Finally, it modified the structure of the plasma membrane by accumulating large ordered lipid domains and disrupted B16 cell migration by a likely shift in the balance between ordered and disordered lipid phases. Whereas the correlation between the excess of lipid raft and cytoskeleton disrupting is not as yet established, it is clear that low-diluted Phenacetinum acts on the actin cytoskeleton organization, as confirmed by a decrease of cell stiffness affecting ultimately the establishment of an effective migration process

Homology modeling and in vivo functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase

The P1B ATPase Heavy Metal ATPase 4 (HMA4) is responsible for zinc and cadmium translocation from roots to shoots in the plant Arabidopsis thaliana. It couples ATP hydrolysis to cytosolic domain movements enabling metal transport across the membrane. Thanks to high conservation level within the P-type ATPase family, the role of the HMA4 cytoplasmic catalytic domains can be inferred from well characterized pumps. In contrast, the function of its terminal cytosolic extensions as well as the metal permeation mechanism through the membrane remains elusive. Here, homology modeling of the HMA4 transmembrane region was conducted based on the crystal structure of a ZntA bacterial homolog. The analysis highlighted amino acids forming a metal permeation pathway, whose importance was subsequently investigated functionally through mutagenesis and complementation experiments in plants. Although the zinc pathway displayed overall conservation among the two proteins, significant differences were observed, especially in the entrance area with altered electronegativity and the presence of a salt bridge/H-bond network. The analysis also newly identified amino acids whose mutation results in total or partial loss of the protein function. In addition, comparison of zinc and cadmium accumulation in shoots of A. thaliana complemented lines revealed a number of HMA4 mutants exhibiting different abilities in zinc and cadmium translocation. These observations could be instrumental to design low cadmium accumulating crops, hence decreasing human cadmium exposure

Linoleic and linolenic acid hydroperoxides interact differentially with biomimetic plant membranes in a lipid specific manner

Linoleic and linolenic acid hydroperoxides (HPOs) constitute key intermediate oxylipins playing an important role as signaling molecules during plant defense processes in response to biotic or abiotic stress. They have also been demonstrated in vitro as antimicrobial agents against plant fungi and bacteria. To reach the phytopathogens in vivo, the HPOs biosynthesized in the plant cells must cross the plant plasma membrane (PPM) where they can also interact with plasma membrane lipids and have an effect on their organization.In the present study, we have investigated the interaction properties of HPOs with PPM at a molecular level using biophysical tools combining in vitro and in silico approaches and using plant biomimetic lipid systems. Our results have shown that HPOs are able to interact with PPM lipids and perturb their lateral organization. Glucosylceramide (GluCer) is a privileged partner, sitosterol lessens their binding and the presence of both GluCer and sitosterol further reduces their interaction. Hydrophobic effect and polar interactions are involved in the binding. The chemical structure of HPOs influences their affinity for PPM lipids. The presence of three double bonds in the HPO molecule gives rise to a higher affinity comparatively to two double bonds, which can be explained by their differential interaction with the lipid polar headgroups.ARC-FIELD project 13/17-1

Determination of the mechanical properties of amorphous materials through instrumented nanoindentation

A novel methodology based on instrumented indentation is developed to determine the mechanical properties of amorphous materials which present cohesive-frictional behaviour. The approach is based on the concept of a universal hardness equation, which results from the assumption of a characteristic indentation pressure proportional to the hardness. The actual universal hardness equation is obtained from a detailed finite element analysis of the process of sharp indentation for a very wide range of material properties, and the inverse problem (i.e. how to extract the elastic modulus, the compressive yield strength and the friction angle) from instrumented indentation is solved. The applicability and limitations of the novel approach are highlighted. Finally, the model is validated against experimental data in metallic and ceramic glasses as well as polymers, covering a wide range of amorphous materials in terms of elastic modulus, yield strength and friction angle