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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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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.

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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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Interconversion of the specificities of human lysosomal enzymes associated with Fabry and Schindler diseases.

IB Tomasic, MC Metcalf, AI Guce, NE Clark, SC Garman. J. Biol. Chem. 2010 doi: 10.1074/jbc.M110.118588
The human lysosomal enzymes α-galactosidase and α-N-acetylgalactosaminidase share 46% amino acid sequence identity and have similar folds. Using a rational protein engineering approach, we interconverted the enzymatic specificity of α-GAL and α-NAGAL. The engineered α-GAL retains the antigenicity but has acquired the enzymatic specificity of α-NAGAL. Conversely, the engineered α-NAGAL retains the antigenicity but has acquired the enzymatic specificity of the α-GAL enzyme. Comparison of the crystal structures of the designed enzyme to the wild-type enzymes shows that active sites superimpose well, indicating success of the rational design. The designed enzymes might be useful as non-immunogenic alternatives in enzyme replacement therapy for treatment of lysosomal storage disorders such as Fabry disease.

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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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