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Because life has more than 2D, Proteopedia helps to understand relationships between structure and function. Proteopedia is a free, collaborative 3D-encyclopedia of proteins & other molecules. ISSN 2310-6301

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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.

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Opening a Gate to Human Health

by Alice Clark (PDBe)
In the 1970s, an exciting discovery of a family of medicines was made by the Japanese scientist Satoshi Ōmura. One of these molecules, ivermectin, is shown in this artwork bound in the ligand binding pocket of the Farnesoid X receptor, a protein which helps regulate cholesterol in humans. This structure showed that ivermectin induced transcriptional activity of FXR and could be used to regulate metabolism.

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Geobacter pili: surprising function.

Y Gu, V Srikanth, AI Salazar-Morales, R Jain, JP O'Brien, SM Yi, RK Soni, FA Samatey, SE Yalcin, NS Malvankar. Nature 2021 doi: 10.1038/s41586-021-03857-w
Geobacter pili were long thought to be electrically conductive protein nanowires composed of PilA-N. Nanowires are crucial to the energy metabolism of bacteria flourishing in oxygen-deprived environments. To everyone's surprise, in 2019, the long-studied nanowires were found to be linear polymers of multi-heme cytochromes, not pili. The first cryo-EM structure of pili (2021) reveals a filament made of dimers of PilA-N and PilA-C, shown. Electrical conductivity of pili is much lower than that of cytochrome nanowires. Evidence suggests that PilA-NC filaments are periplasmic pseudopili crucial for exporting cytochrome nanowires onto the cell surface, rather than the pili serving as nanowires themselves.

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Tutorial: Ramachandran Plot Inspection

by Angel Herráez
Side-by-side display of dihedral angles in a 3D model of a tripeptide and its Ramachandran plot. Users can interact with any of them and the other will change accordingly. Includes animated rotations with display of clashes.

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Proteopedia Page Contributors and Editors (what is this?)

Joel L. Sussman, Jaime Prilusky

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