Stability of Nanopeptides: Structure and Molecular Exchange of Self-assembled Peptide Fibers.

Often nanostructures formed by self-assembly of small molecules based on hydrophobic interactions are rather unstable, causing morphological changes or even dissolution when exposed to changes in aqueous media. In contrast, peptides offer precise control of the nanostructure through a range of molecular interactions where physical stability can be engineered in and, to a certain extent, decoupled from size via rational design. Here, we investigate a family of peptides that form beta-sheet nanofibers and demonstrate a remarkable physical stability even after attachment of poly(ethylene glycol). We employed small-angle neutron/X-ray scattering, circular dichroism spectroscopy, and molecular dynamics simulation techniques to investigate the detailed nanostructure, stability, and molecular exchange. The results for the most stable sequence did not reveal any structural alterations or unimer exchange for temperatures up to 85 °C in the biologically relevant pH range. Only under severe mechanical perturbation (i.e., tip sonication) would the fibers break up, which is reflected in a very high activation barrier for unimer exchange of ∼320 kJ/mol extracted from simulations. The results give important insight into the relation between molecular structure and stability of peptide nanostructure that is important for, e.g., biomedical applications.

The buckling-condensation mechanism driving gas vesicle collapse.

Gas vesicles (GVs) are proteinaceous cylindrical shells found within bacteria or archea growing in aqueous environments and are composed primarily of two proteins, gas vesicle protein A and C (GvpA and GvpC). GVs exhibit strong performance as next-generation ultrasound contrast agents due to their gas-filled interior, tunable collapse pressure, stability in vivo and functionalizable exterior. However, the exact mechanism leading to GV collapse remains inconclusive, which leads to difficulty in predicting collapse pressures for different species of GVs and in extending favorable nonlinear response regimes. Here, we propose a two stage mechanism leading to GV loss of echogenicity and rupture under hydrostatic pressure: elastic buckling of the cylindrical shell coupled with condensation driven weakening of the GV membrane. Our goal is to therefore test whether the final fracture of the GV membrane occurs by the interplay of both mechanisms or purely through buckling failure as previously believed. To do so, we (1) compare the theoretical condensation and buckling pressures with that for experimental GV collapse and (2) describe how condensation can lead to plastic buckling failure. GV shell properties that are necessary input to this theoretical description, such as the elastic moduli and wettability of GvpA, are determined using molecular dynamics simulations of a novel structural model of GvpA that better represents the hydrophobic core. For GVs that are not reinforced by GvpC, this analytical framework shows that the experimentally observed pressures resulting in loss of echogenicity coincide with both the elastic buckling and condensation pressure regimes. We also found that the stress strain curve for GvpA wetted on both the interior and exterior exhibits a loss of mechanical stability compared to GvpA only wetted on the exterior by the bulk solution. We identify a pressure vs. vesicle size regime where condensation can occur prior to buckling, which may preclude nonlinear shell buckling responses in contrast imaging.

Atomistic Modeling of Peptide Aggregation and ß-Sheet Structuring in Corn Zein for Viscoelasticity.

The structure-function relationships of plant-based proteins that give rise to desirable texture attributes in order to mimic meat products are generally unknown. In particular, it is not clear how to engineer viscoelasticity to impart cohesiveness and proper mouthfeel; however, it is known that intermolecular ß-sheet structures have the potential to enhance the viscoelastic property. Here, we investigated the propensity of selected peptide segments within common corn α-zein variants to maintain stable aggregates and ß-sheet structures. Simulations on dimer systems showed that stability was influenced by the initial orientation and the presence of contiguous small hydrophobic residues. Simulations using eight-peptide ß-sheet oligomers revealed that peptide sequences without proline had higher levels of ß-sheet structuring. Additionally, we identified that sequences with a dimer hydrogen-bonding density of >22% tended to have a larger percent ß-sheet conformation. These results contribute to understanding how the viscoelasticity of zein can be increased for use in plant-based meat analogues.

Organic Nanotube with Subnanometer, pH-Responsive Lumen.

While many synthetic nanotubes with a hydrophobic lumen and fast molecular transport have been developed, decorating the interior of these channels with polar and/or responsive functional groups remains challenging. In transmembrane proteins like the aquaporin and M2 channels, the presence of histidine residues in a mostly hydrophobic channel has led to enhanced selectivity and pH-based activation. Herein, we report the synthesis of Bzim-CP, a cyclic octapeptide that contains a benzimidazole functionality as a chemical and structural mimic of histidine. Bzim-CP undergoes different protonation states, forms subnanometer nanotubes, and projects two different ionizable functionalities into the lumen. Present studies open up synthetic possibilities to functionalize subnanometer porous channels as a basis toward understanding new transport phenomena.

Perilimbal sclera mechanical properties: Impact on intraocular pressure in porcine eyes.

There is extensive knowledge on the relationship of posterior scleral biomechanics and intraocular pressure (IOP) load on glaucomatous optic neuropathy; however, the role for biomechanical influence of the perilimbal scleral tissue on the aqueous humor drainage pathway, including the distal venous outflow system, and IOP regulation is not fully understood. The purpose of this work is to study the outflow characteristics of perfused porcine eyes relative to the biomechanical properties of the perilimbal sclera, the posterior sclera and the cornea. Enucleated porcine eyes from eleven different animals were perfused with surrogate aqueous at two fixed flow rates while monitoring their IOP. After perfusion, mechanical stress-strain and relaxation tests were conducted on specimens of perilimbal sclera, posterior sclera, and cornea from the same perfused eyes. Statistical analysis of the data demonstrated a strong correlation between increased tangent modulus of the perilimbal sclera tissues and increased perfusion IOP (R2 = 0.74, p = 0.0006 at lower flow rate and R2 = 0.71, p = 0.0011 at higher flow rate). In contrast, there were no significant correlations between IOP and the tangent modulus of the other tissues (Posterior sclera: R2 = 0.17 at lower flow rate and R2 = 0.30 at higher flow rate; cornea: R2 = 0.02 at lower flow rate and R2<0.01 at higher flow rate) nor the viscoelastic properties of any tissue (R2 ≤ 0.08 in all cases). Additionally, the correlation occurred for IOP and not net outflow facility (R2 ≤ 0.12 in all cases). These results provide new evidence that IOP in perfused porcine eyes is strongly influenced by the tangent modulus, sometimes called the tissue stiffness, of the most anterior portion of the sclera, i.e. the limbus.

A knowledge-based approach to estimating the magnitude and spatial patterns of potential threats to soil biodiversity.

Because of the increasing pressures exerted on soil, below-ground life is under threat. Knowledge-based rankings of potential threats to different components of soil biodiversity were developed in order to assess the spatial distribution of threats on a European scale. A list of 13 potential threats to soil biodiversity was proposed to experts with different backgrounds in order to assess the potential for three major components of soil biodiversity: soil microorganisms, fauna, and biological functions. This approach allowed us to obtain knowledge-based rankings of threats. These classifications formed the basis for the development of indices through an additive aggregation model that, along with ad-hoc proxies for each pressure, allowed us to preliminarily assess the spatial patterns of potential threats. Intensive exploitation was identified as the highest pressure. In contrast, the use of genetically modified organisms in agriculture was considered as the threat with least potential. The potential impact of climate change showed the highest uncertainty. Fourteen out of the 27 considered countries have more than 40% of their soils with moderate-high to high potential risk for all three components of soil biodiversity. Arable soils are the most exposed to pressures. Soils within the boreal biogeographic region showed the lowest risk potential. The majority of soils at risk are outside the boundaries of protected areas. First maps of risks to three components of soil biodiversity based on the current scientific knowledge were developed. Despite the intrinsic limits of knowledge-based assessments, a remarkable potential risk to soil biodiversity was observed. Guidelines to preliminarily identify and circumscribe soils potentially at risk are provided. This approach may be used in future research to assess threat at both local and global scale and identify areas of possible risk and, subsequently, design appropriate strategies for monitoring and protection of soil biota.

European perspective of ecosystem services and related policies.

In this article, we focus on the importance of terrestrial ecosystems and the services they provide. European Union policies, contributing to the conservation and maintenance of ecosystem services in Europe are discussed and their current impacts briefly reviewed in the light of the main challenges that European ecosystems might face in the near future.

Estimating the soil organic carbon content for European NUTS2 regions based on LUCAS data collection.

Under the European Union Thematic Strategy for Soil Protection, the European Commission Directorate-General for the Environment and the European Environmental Agency (EEA) identified a decline in soil organic carbon and soil losses by erosion as priorities for the collection of policy relevant soil data at European scale. Moreover, the estimation of soil organic carbon content is of crucial importance for soil protection and for climate change mitigation strategies. Soil organic carbon is one of the attributes of the recently developed LUCAS soil database. The request for data on soil organic carbon and other soil attributes arose from an on-going debate about efforts to establish harmonized datasets for all EU countries with data on soil threats in order to support modeling activities and display variations in these soil conditions across Europe. In 2009, the European Commission's Joint Research Centre conducted the LUCAS soil survey, sampling ca. 20,000 points across 23 EU member states. This article describes the results obtained from analyzing the soil organic carbon data in the LUCAS soil database. The collected data were compared with the modeled European topsoil organic carbon content data developed at the JRC. The best fitted comparison was performed at NUTS2 level and showed underestimation of modeled data in southern Europe and overestimation in the new central eastern member states. There is a good correlation in certain regions for countries such as the United Kingdom, Slovenia, Italy, Ireland, and France. Here we assess the feasibility of producing comparable estimates of the soil organic carbon content at NUTS2 regional level for the European Union (EU27) and draw a comparison with existing modeled data. In addition to the data analysis, we suggest how the modeled data can be improved in future updates with better calibration of the model.