Structure and stability of chiral beta-tapes: a computational coarse-grained approach

We present two coarse-grained models of different levels of detail for the description of beta-sheet tapes obtained from equilibrium self-assembly of short rationally designed oligopeptides in solution. Here we only consider the case of the homopolymer oligopeptides with the identical sidegroups attached, in which the tapes have a helicoid surface with two equivalent sides. The influence of the chirality parameter on the geometrical characteristics, namely the diameter, inter-strand distance and pitch, of the tapes have been investigated. The two models are found to produceequivalent results suggesting a considerable degree of universality in conformations of the tapes.Comment: 24 pages, 5 PS figures. Accepted to J. Chem. Phy

Room Temperature Magnetic Field Measurements as a Tool to Localize Inter-turns Electrical Short Circuits in the LHC Main Dipole coils

In this report the method for the localization of the electric shorts circuits in the main LHC dipoles using the magnetic measurements at room temperature is presented. The steps of the method are discussed, and two cases are studied in detail. A complete statistics of the 12 cases analyzed up to now is given

Short Circuit Localization in the LHC Main Dipole Coils by means of Room Temperature Magnetic Measurements

During the construction of the LHC main dipoles, 12 cases of short circuits between the cables of the superconducting coils have been detected. Some of them appeared only under the press, making impossible their localization after disassembly. In this paper we describe a method to locate electrical shorts through the use of room temperature magnetic measurements. An example case is discussed in detail to illustrate the features of the approach, and a statistic of the cases met during the production of more that 70% of the dipole total quantity is presented

Role of water in Protein Aggregation and Amyloid Polymorphism

A variety of neurodegenerative diseases are associated with the formation of amyloid plaques. Our incomplete understanding of this process underscores the need to decipher the principles governing protein aggregation. Most experimental and simulation studies have been interpreted largely from the perspective of proteins: the role of solvent has been relatively overlooked. In this Account, we provide a perspective on how interactions with water affect folding landscapes of A$\beta$ monomers, A$\beta_{16-22}$ oligomer formation, and protofilament formation in a Sup35 peptide. Simulations show that the formation of aggregation-prone structures (N$^*$) similar to the structure in the fibril requires overcoming high desolvation barrier. The mechanism of protofilament formation in a polar Sup35 peptide fragment illustrates that water dramatically slows down self-assembly. Release of water trapped in the pores as water wires creates protofilament with a dry interface. Similarly, one of the main driving force for addition of a solvated monomer to a preformed fibril is the entropy gain of released water. We conclude by postulating that two-step model for protein crystallization must also hold for higher order amyloid structure formation starting from N$^*$. Multiple N$^*$ structures with varying water content results in a number of distinct water-laden polymorphic structures. In predominantly hydrophobic sequences, water accelerates fibril formation. In contrast, water-stabilized metastable intermediates dramatically slow down fibril growth rates in hydrophilic sequences.Comment: 27 pages, 4 figures; Accounts of Chemical Research, 201

A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation

Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse the self- assembly of peptides into fibrillar structures. The simulation of a system of hundreds of peptides over the millisecond timescale enables us to show that the mechanism of aggregation involves a first phase in which small structurally disordered oligomers assemble onto the nanoparticle and a second phase in which they evolve into highly ordered beta-sheets as their size increases

Chrysomelidial in the Opisthonotal Glands of the Oribatid Mite, Oribotritia berlesei

Gas chromatographic–mass spectrometric analyses of whole body extracts of Oribotritia berlesei, a large-sized soil-dwelling oribatid mite, revealed a consistent chemical pattern of ten components, probably originating from the well-developed opisthonotal glands. The three major components of the extract were the iridoid monoterpene, (3S,8S)-chrysomelidial (about 45% of the extract), the unsaturated hydrocarbon 6,9-heptadecadiene, and the diterpene β-springene (the latter two, each about 20–25% of the extract). The remaining minor components (together about 10% of the extract) included a series of hydrocarbons (tridecene, tridecane, pentadecene, pentadecane, 8-heptadecene, and heptadecane) and the tentatively identified 9,17-octadecadienal. In contrast, analysis of juveniles showed only two compounds, namely a 2:1 mixture of (3S,8S)-chrysomelidial and its epimer, epi-chrysomelidial (3S,8R-chrysomelidial). Unexpectedly, neither adult nor juvenile secretions contained the so-called astigmatid compounds, which are considered characteristic of secretions of oribatids above moderately derived Mixonomata. The chrysomelidials, as well as β-springene and octadecadienal, are newly identified compounds in the opisthonotal glands of oribatid mites and have chemotaxonomic potential for this group. This is the first instance of finding chrysomelidials outside the Coleoptera

Finite Size Effects in Simulations of Protein Aggregation

It is becoming increasingly clear that the soluble protofibrillar species that proceed amyloid fibril formation are associated with a range of neurodegenerative disorders such as Alzheimer's and Parkinson diseases. Computer simulations of the processes that lead to the formation of these oligomeric species are starting to make significant contributions to our understanding of the determinants of protein aggregation. We simulate different systems at constant concentration but with a different number of peptides and we study the how the finite number of proteins affects the underlying free energy of the system and therefore the relative stability of the species involved in the process. If not taken into account, this finite size effect can undermine the validity of theoretical predictions regarding the relative stability of the species involved and the rates of conversion from one to the other. We discuss the reasons that give rise to this finite size effect form both a probabilistic and energy fluctuations point of view and also how this problem can be dealt by a finite size scaling analysis

Performance of the Main Dipole Magnet Circuits of the LHC during Commissioning

During hardware commissioning of the Large Hadron Collider (LHC), 8 main dipole circuits are tested at 1.9 K and up to their nominal current. Each dipole circuit contains 154 magnets of 15 m length, and has a total stored energy of up to 1.3 GJ. All magnets are wound from Nb-Ti superconducting Rutherford cables, and contain heaters to quickly force the transition to the normal conducting state in case of a quench, and hence reduce the hot spot temperature. In this paper the performance of the first three of these circuits is presented, focussing on quench detection, heater performance, operation of the cold bypass diodes, and magnet-to-magnet quench propagation. The results as measured on the entire circuits will be compared to the test results obtained during the reception tests of the individual magnets

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

We present an extension of the coarse-grained MARTINI model for proteins and apply this extension to amyloid- and elastin-like peptides. Atomistic simulations of tetrapeptides, octapeptides, and longer peptides in solution are used as a reference to parametrize a set of pseudodihedral potentials that describe the internal flexibility of MARTINI peptides. We assess the performance of the resulting model in reproducing various structural properties computed from atomistic trajectories of peptides in water. The addition of new dihedral angle potentials improves agreement with the contact maps computed from atomistic simulations significantly. We also address the question of which parameters derived from atomistic trajectories are transferable between different lengths of peptides. The modified coarse-grained model shows reasonable transferability of parameters for the amyloid- and elastin-like peptides. In addition, the improved coarse-grained model is also applied to investigate the self-assembly of β-sheet forming peptides on the microsecond time scale. The octapeptides SNNFGAIL and (GV)4 are used to examine peptide aggregation in different environments, in water, and at the water–octane interface. At the interface, peptide adsorption occurs rapidly, and peptides spontaneously aggregate in favor of stretched conformers resembling β-strands

Performance of the Superconducting Corrector Magnet Circuits during the Commissioning of the LHC

The LHC is a complex machine requiring more than 7400 superconducting corrector magnets distributed along a circumference of 26.7 km. These magnets are powered in 1446 different electrical circuits at currents ranging from 60 A up to 600 A. Among the corrector circuits the 600 A corrector magnets form the most diverse and differentiated group. All together, about 60000 high current connections had to be made. A fault in a circuit or one of the superconducting connections would have severe consequences for the accelerator operation. All magnets are wound from various types of Nb-Ti superconducting strands, and many contain parallel protection resistors to by-pass the current still flowing in the other magnets of the same circuit when they quench. In this paper the performance of these magnet circuits is presented, focussing on the quench behaviour of the magnets. Quench detection and the performance of the electrical interconnects will be dealt with. The results as measured on the entire circuits are compared to the test results obtained at the reception of the individual magnets