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ISSN 2310-6301

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.


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The ribosome

by Wayne Decatur
The 2009 Nobel Prize in Chemistry was awarded for studies of the ribosome. The ribosome is the machine in your cells that accurately and efficiently decodes the genetic information stored in your genome and synthesizes the corresponding polypeptide chain one amino acid at a time in the process of translation. These structures are considered landmarks for the fact they showed clearly the major contributions to decoding and peptide bond synthesis come from RNA and not protein, as well as for the sheer size of the structures determined.

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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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Structural flexibility of the periplasmic protein, FlgA, regulates flagellar P-ring assembly in Salmonella enterica.

H Matsunami, YH Yoon, VA Meshcheryakov, K Namba, FA Samatey. Scientific Reports 2016 doi: 10.1038/srep27399
A periplasmic flagellar chaperone protein, FlgA, is required for P-ring assembly in bacterial flagella of taxa such as Salmonella enterica or Escherichia coli. Here we present the open and closed crystal structures of FlgA from Salmonella enterica serovar Typhimurium, grown under different crystallization conditions. An intramolecular disulfide cross-linked form of FlgA caused a dominant negative effect on motility of the wild-type strain.

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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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Joel L. Sussman, Jaime Prilusky

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