Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages.

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation. © 2013 Elsevier Ltd.

The impact of sand slugs against beams and plates: Coupled discrete particle/finite element simulations

The impact of a slug of dry sand particles against a metallic sandwich beam or circular sandwich plate is analysed in order to aid the design of sandwich panels for shock mitigation. The sand particles interact via a combined linear-spring-and-dashpot law whereas the face sheets and compressible core of the sandwich beam and plate are treated as rate-sensitive, elastic-plastic solids. The majority of the calculations are performed in two dimensions and entail the transverse impact of end-clamped monolithic and sandwich beams, with plane strain conditions imposed. The sand slug is of rectangular shape and comprises a random loose packing of identical, circular cylindrical particles. These calculations reveal that loading due to the sand is primarily inertial in nature with negligible fluid-structure interaction: the momentum transmitted to the beam is approximately equal to that of the incoming sand slug. For a slug of given incoming momentum, the dynamic deflection of the beam increases with decreasing duration of sand-loading until the impulsive limit is attained. Sandwich beams with thick, strong cores significantly outperform monolithic beams of equal areal mass. This performance enhancement is traced to the "sandwich effect" whereby the sandwich beams have a higher bending strength than that of the monolithic beams. Three-dimensional (3D) calculations are also performed such that the sand slug has the shape of a circular cylindrical column of finite height, and contains spherical sand particles. The 3D slug impacts a circular monolithic plate or sandwich plate and we show that sandwich plates with thick strong cores again outperform monolithic plates of equal areal mass. Finally, we demonstrate that impact by sand particles is equivalent to impact by a crushable foam projectile. The calculations on the equivalent projectile are significantly less intensive computationally, yet give predictions to within 5% of the full discrete particle calculations for the monolithic and sandwich beams and plates. These foam projectile calculations suggest that metallic foam projectiles can be used to simulate the loading by sand particles within a laboratory setting. © 2013 Elsevier Ltd.

Controlled amine functionality in self-assembled monolayers via the hidden amine route: chemical and electronic tunability.

A synthetic strategy for fabricating a dense amine functionalized self-assembled monolayer (SAM) on hydroxylated surfaces is presented. The assembly steps are monitored by X-ray photoelectron spectroscopy, Fourier transform infrared- attenuated total reflection, atomic force microscopy, variable angle spectroscopic ellipsometry, UV-vis surface spectroscopy, contact angle wettability, and contact potential difference measurements. The method applies alkylbromide-trichlorosilane for the fabrication of the SAM followed by surface transformation of the bromine moiety to amine by a two-step procedure: S(N)2 reaction that introduces the hidden amine, phthalimide, followed by the removal of the protecting group and exposing the free amine. The use of phthalimide moiety in the process enabled monitoring the substitution reaction rate on the surface (by absorption spectroscopy) and showed first-order kinetics. The simplicity of the process, nonharsh reagents, and short reaction time allow the use of such SAMs in molecular nanoelectronics applications, where complete control of the used SAM is needed. The different molecular dipole of each step of the process, which is verified by DFT calculations, supports the use of these SAMs as means to tune the electronic properties of semiconductors and for better synergism between SAMs and standard microelectronics processes and devices.

Accuracy and transferability of GAP models for tungsten

We introduce interatomic potentials for tungsten in the bcc crystal phase and its defects within the Gaussian Approximation Potential (GAP) framework, fitted to a database of first principles density functional theory (DFT) calculations. We investigate the performance of a sequence of models based on databases of increasing coverage in configuration space and showcase our strategy of choosing representative small unit cells to train models that predict properties only observable using thousands of atoms. The most comprehensive model is then used to calculate properties of the screw dislocation, including its structure, the Peierls barrier and the energetics of the vacancy-dislocation interaction. All software and raw data are available at www.libatoms.org.