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Register a new userMechanical properties of the two-filament insulin amyloid fibril: a theoretical study
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Authors
Chiu Fan Lee
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We study the two-filament insulin fibrils structure by incorporating recent simulation results and mechanical measurements. Our investigation suggests that the persistence length measurement correlates well with the previously proposed structural model, while the elasticity measurement suggests that stretching the fibril may involve hydrogen bond breakage. Our work illustrates an attempt to correlate nanoscale measurements with microscopic information on the quaternary protein structure.
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Many proteins have the potential to aggregate into amyloid fibrils, which are associated with a wide range of human disorders including Alzheimers and Parkinsons disease. In contrast to that of folded proteins, the thermodynamic stability of amyloid fibrils is not well understood: specifically the balance between entropic and enthalpic terms, including the chain entropy and the hydrophobic effect, are poorly characterised. Using simulations of a coarse-grained protein model we delineate the enthalpic and entropic contributions dominating amyloid fibril elongation, predicting a characteristic temperature-dependent enthalpic signature. We confirm this thermodynamic signature by performing calorimetric experiments and a meta-analysis over published data. From these results, we can also elucidate the necessary conditions to observe cold denaturation of amyloid fibrils. Overall, we show that amyloid fibril elongation is associated with a negative heat capacity, the magnitude of which correlates closely with the hydrophobic surface area that is buried upon fibril formation, highlighting the importance of hydrophobicity for fibril stability.
We investigate the elastic and yielding properties of two dimensional defect-free mono-crystals made of highly monodisperse droplets. Crystals are compressed between two parallel boundaries of which one acts as a force sensor. As the available space between boundaries is reduced, the crystal goes through successive row-reduction transitions. For small compression forces, the crystal responds elastically until a critical force is reached and the assembly fractures in a single catastrophic global event. Correspondingly there is a peak in the force measurement associated with each row-reduction. The elastic properties of ideal mono-crystal samples are fully captured by a simple analytical model consisting of an assembly of individual capillary springs. The yielding properties of the crystal are captured with a minimal bond breaking model.
By means of ab-initio calculations we investigate the optical properties of pure a-SiN$_x$ samples, with $x in [0.4, 1.8]$, and samples embedding silicon nanoclusters (NCs) of diameter $0.5 leq d leq 1.0$ nm. In the pure samples the optical absorption gap and the radiative recombination rate vary according to the concentration of Si-N bonds. In the presence of NCs the radiative rate of the samples is barely affected, indicating that the intense photoluminescence of experimental samples is mostly due to the matrix itself rather than to the NCs. Besides, we evidence an important role of Si-N-Si bonds at the NC/matrix interface in the observed photoluminescence trend.
The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of linkers in the solution modifies the effective inter-rod interaction and can lead to inter-filament attraction. Depending on the systems composition and physical properties such as linker binding energies, filaments will either orient perpendicular or parallel to each other, leading to network-like or bundled structures. We show that such a system can have one of three generic phase diagrams, one dominated by bundles, another by networks, and the third containing both bundle and network-like phases. The first two diagrams can be found over a wide range of interaction energies, while the third occurs only for a narrow range. These results provide theoretical understanding of the classification of linker proteins as bundling proteins or crosslinking proteins. In addition, they suggest possible mechanisms by which the cell may control cytoskeletal morphology.
Antiferromagnetism in stacked nanographite is investigated with using the Hubbard-type model. We find that the open shell electronic structure can be an origin of the decreasing magnetic moment with the decrease of the inter-graphene distance, as experiments on adsorption of molecules suggest. Next, possible charge-separated states are considered using the extended Hubbard model with nearest-neighbor interactions. The charge-polarized state could appear, when a static electric field is present in the graphene plane for example. Finally, superperiodic patterns with a long distance in a nanographene sheet observed by STM are discussed in terms of the interference of electronic wave functions with a static linear potential theoretically. In the analysis by the k-p model, the oscillation period decreases spatially in agreement with experiments.
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