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ISSN 2310-6301

As life is more than 2D, Proteopedia helps to bridge the 3D relationships between function & structure of biomacromolecules


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Self-assembling Nano-Cages

Huddy, Hsia, Kibler, Xu & 27 others in the Nobel Prize winning group of David Baker have designed standardized protein building blocks that self assemble into a wide range of nanostructures. The building blocks attach to each other at engineered sites and angles, and come in various sizes.

>>> Get a quick overview! >>>

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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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Make Your Own Electrostatic Potential Maps

Positive (+) and Negative (-) charges on the surface of a protein molecule play crucial roles in its interactions with other molecules, and hence in its functions. Electrostatic potential maps coloring the surface of a protein molecule are a popular way to visualize the distribution of surface charges. Easy to use free software is available to to create these surface maps. Above is an integral membrane potassium channel protein. One of its 4 identical chains is removed so you can see the Negative (-) protein surface contacting the 3 K+ ions.

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List of Art on Science pages in Proteopedia

About Interactive 3D Complements - I3DCs

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Joel L. Sussman, Jaime Prilusky

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