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The complex pathways followed by a polypeptide chain. As expressed succinctly in the central dogma expression of the gene produces RNA, which is translated by the ribosome to yield a polypeptide chain. In the normal function the unfolded protein folds spontaneously, executes the designed function, and is ultimately degraded as indicated in the upper right corner. If the folding channel does not operate as planned the unfolded protein can form N*, an aggregation-prone species, which can then form toxic oligomers eventually resulting in the form of insoluble amyloid fibrils, as displayed in the lower right hand corner.
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The viral capsid of the AIDS-causing virus (HIV-1) unveiled at the atomic level by a combination of experimental techniques and computation. The capsid protects the viral RNA, reverse-transcriptase, and other auxiliary proteins essential to the infective cycle of the virus. The capsid has to be stable enough to protect its content, yet also brittle upon a chemical trigger, to release its content after the capsid enters a cell. The architecture of the virus follows a theorem of Euler according to which a fully enclosed encasing can be realized through hexagonal and pentagonal elements where one needs exactly 12 pentagons (some visible in green), but can adopt any number of hexagons (here 216, shown in blue). The number of hexagons determines the size, the distribution of pentagons the shape. The capsid is made of only protein CA that can accommodate a distribution of surface curvatures. There are about 1300 CAs in the capsid. The image is based on an atomic model derived through crystallography and nuclear magnetic resonance (NMR) structure analysis of isolated CA dimers, pentamers and hexamers, through electron microscopy of hexameric surfaces, and through data-guided molecular dynamics simulations (pdb code 3J3Q). Capsid structure and dynamics pose a new challenge to chemical physics. The model and a first molecular dynamics simulation (involving 64 × 106 atoms) of a solvated capsid have been reported in Ref. 86 .
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A random walk from Ref. 96 in this issue. Continuous time random walks (CTRWs) are stochastic models for anomalous diffusion (AD) processes. AD is characterized by pronounced trapping periods, during which the particle cannot move. This may happen, for instance, when small tracer particles are successively caged in a matrix of semiflexible biopolymers, such as the ultrastructure in living cells. Such environments are intrinsically noisy: the matrix itself evolves in time and fluctuates thermally, rattling the particle during trapping periods. Noisy CTRWs can account for such rattling effects. The red line shows the case when the thermal noise only weakly disturbs the trapping events (horizontal plateaus between sudden changes in position). In the blue line strong noise completely changes the trajectory with the same initial condition, highlighting the importance of an evolving environment for the single particle dynamics.
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