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Reader's Corner Archive

12 Mar

Solid-state NMR spectroscopy (Nature Reviews Methods Primers)

Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method to determine the chemical structure, 3D structure and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR spectroscopy as applied to the wide range of solid systems. The nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins in solid-state NMR are the same as in liquid-state NMR spectroscopy. However, because of the orientation dependence of the nuclear spin interactions in the solid state, the majority of high-resolution solid-state NMR spectra are measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. Mei Hong et. al. describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials and inorganic solids. Continuing development of sensitivity-enhancement NMR approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization and experiments in ultra-high magnetic fields, is described. They highlight recent applications of solid-state NMR spectroscopy to biological and materials chemistry. The Primer ends with a discussion of current limitations as well as areas of development of solid-state NMR spectroscopy and points to emerging areas of applications of this sophisticated spectroscopy.

19 Feb

Computational modeling of dynein motor proteins at work (Chem. Commun.)

Along with various experimental methods, a combination of theoretical and computational methods is essential to explore different length-scale and time-scale processes in the biological system. The functional mechanism of a dynein, an ATP-fueled motor protein, working in a multiprotein complex, involves a wide range of length/time-scale events. It generates mechanical force from chemical energy and moves on microtubules towards the minus end direction while performing a large number of biological processes including ciliary beating, intracellular material transport, and cell division. Like in the cases of other conventional motor proteins, a combination of experimental techniques including X-crystallography, cryo-electron microscopy, and single molecular assay have provided a wealth of information about the mechanochemical cycle of a dynein. Dyneins have a large and complex structural architecture and therefore, computational modeling of different aspects of a dynein is extremely challenging. As the process of dynein movement involves varying length and timescales, it demands, like in experiments, a combination of computational methods covering such a wide range of processes for the comprehensive investigation of the mechanochemical cycle. In this review article, M. Dutta and B.Jama summarize how the use of state-of-the-art computational methods can provide a detailed molecular understanding of the mechanochemical cycle of the dynein. They implemented all-atom molecular dynamics simulations and hybrid quantum-mechanics/molecular-mechanics simulations to explore the ATP hydrolysis mechanisms at the primary ATPase site (AAA1) of dynein. To investigate the large-scale conformational changes They employed coarse-grained structure-based molecular dynamics simulations to capture the domain motions. Here they explored the conformational changes upon binding of ATP at AAA1, nucleotide state-dependent regulation of the mechanochemical cycle, and inter-head coordination by inter-head tension. Additionally, implementing a phenomenological theoretical model we explore the force-dependent detachment rate of a motorhead from the microtubule and the principle of multi-dynein cooperation during cargo transport.

19 Feb

Human species D adenovirus hexon capsid protein mediates cell entry through a direct interaction with CD46 (PNAS)

Human adenovirus species D (HAdV-D) types are currently being explored as vaccine vectors for coronavirus disease 2019 (COVID- 19) and other severe infectious diseases. The efficacy of such vector-based vaccines depends on functional interactions with re- ceptors on host cells. Adenoviruses of different species are assumed to enter host cells mainly by interactions between the knob domain of the protruding fiber capsid protein and cellular receptors. Using a cell-based receptor-screening assay, N. Amberg et.al. identi- fied CD46 as a receptor for HAdV-D56. The function of CD46 was validated in infection experiments using cells lacking and overex- pressing CD46, and by competition infection experiments using soluble CD46. Remarkably, unlike HAdV-B types that engage CD46 through interactions with the knob domain of the fiber pro- tein, HAdV-D types infect host cells through a direct interaction between CD46 and the hexon protein. Soluble hexon proteins (but not fiber knob) inhibited HAdV-D56 infection, and surface plasmon analyses demonstrated that CD46 binds to HAdV-D hexon (but not fiber knob) proteins. Cryoelectron microscopy analysis of the HAdV-D56 virion–CD46 complex confirmed the interaction and showed that CD46 binds to the central cavity of hexon trimers. Fi- nally, soluble CD46 inhibited infection by 16 out of 17 investigated HAdV-D types, suggesting that CD46 is an important receptor for a large group of adenoviruses. In conclusion, this study identifies a noncanonical entry mechanism used by human adenoviruses, which adds to the knowledge of adenovirus biology and can also be useful for development of adenovirus-based vaccine vectors.

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