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Welcome to Proteopedia ISSN 2310-6301The free, collaborative 3D-encyclopedia of proteins & other molecules
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HIV-1 protease
by David Canner
The X-ray structure of HIV-1 protease reveals that it is composed of two symmetrically related subunits which form a tunnel where they meet. This is critical because it contains the active site of the protease, consisting on two Asp-Thr-Gly conserved sequences, making it a member of the aspartyl protease family. The two catalytic Asp's either interact with the incoming water or protonate the carbonyl to make the carbon more electrophilic for the incoming water.
F Wang, Y Gu, JP O'Brien, SM Yi, SE Yalcin, V Srikanth, C Shen, D Vu, NL Ing, AI Hochbaum, EH Egelman, NS Malvankar. Cell 2019 doi: 10.1016/j.cell.2019.03.029 Bacteria living in anaerobic environments (no oxygen) need alternative electron acceptors in order to get energy from their food. An acceptor abundant in the earth's crust is red iron oxide ("rust"), which gets reduced to black iron oxide (magnetite). Many bacteria, such as Geobacter, get their metabolic energy by transferring electrons to acceptors that are multiple cell diameters distant, using protein nanowires. These were long thought to be pili. But when the structure of the nanowires was solved in 2019, to everyone's surprise, they turned out to be unprecedented linear polymers of multi-heme cytochromes. The hemes form an electrically conductive chain in the cores of these nanowires.
by Wayne Decatur
The 2025 Nobel Prize in Chemistry was awarded for studies of metal-organic frameworks. Against expectations, the building blocks of metal-organic frameworks turned out to form networks with large cavities and the materials have a wide range of far-reaching practical applications.