Posts Tagged PDB

Anna and Shalanda – PyMol Visualization of 1OAC

Using the Protein Data Bank, we located the protein 1OAC, otherwise known as copper amine oxidase of E. coli.  It is a dimer and has two active sites which are buried away from the solvent.  The enzyme has an inactive and an active form. 1OAC has a single copper ion and a covalently bonded cofactor.  The formation of this cofactor is done post-translationally by modifying a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). (Information taken from Proteopedia)  A great summary of the enzyme is available at PDBsum.  To access that information, input the PDB code for the enzyme (1OAC).

This gallery shows two images.  The first was generated in PyMol and shows the dimer chains in two different colors.  The second image, generated by Consurf, shows the conservation of the residues of chain a (purple being most conserved, blue being most variable, and yellow representing no data available).

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Anastasia and Thomas’s Investigation of Prion Structural Simularities in Rabbits (3O79), Mice and Humans

Prions are a destructive family of proteins, due to a transformational (mis-folding) of a alpha helix to a beta sheet. The beta sheets only represent 3% of the proteins secondary structure (Fig. 1) This minor change in protein conformation is enough to turn a useful protein into a highly destructive stable force.

Figure 1. 56% helical (5 helices; 59 residues) 3% beta sheet (2 strands; 4 residues) of 3070 rabbit prion

Its amino acid sequence (95% match in sheep) as well as its 3-D structure ( 97% similarity to humans) is highly conserved through different species. What makes misfolding such a problem is its ability to perpetuate misfolding of the surrounding proteins. It has been found that rabbits have a helix capping motif the dramatically lowers the propensity of prion formation (Fig. 2)



Figure 2: Mouse vs Rabbit 3-D cartoon structure using Pymol

In conclusion prions have a highly conserved structure that is both minor yet destructive.

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Protein visualization (Rachel / Thomas)

Solved crystal structure of BRCA1 BRCT (made in Jmol):

Electrostatic map of BRCA1 BRCT (made in Pymol):

Sequence of BRCA1 BRCT showing features such as beta strands and alpha helices:

The structure has a diameter of ~27 A.  ~55 A in length.

There are a variety of secondary structures including beta turns, beta strands and alpha helices.

BRCA1 is composed of 215 residues.

Conserf run (MSA):

Dark purple regions are conserved.  Notice ligands binding in that region.

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