User talk:Brian Ochoa/Sandbox 1

This is a default text for your page Brian Ochoa/Sandbox 1. Click above on edit this page to modify. Be careful with the < and > signs.

You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Structural Highlights

BRCA1 is an 1,863 amino acid long protein that contains a ring finger motif from position 24 to 64. The ring motif is part of a larger domain spanning the first one hundred amino acid residues, which is required for the formation of its stable structure. This N-terminus domain is of the most highly conserved region of the BRCA1 gene and several cancer-predisposition mutations have been identified in this region. The ring motif is also a C3HC4 zinc-binding motif, named so for the conserved pattern of cysteine and histidines residues that bind the zinc ions. Ultimately, the ring motif of BRCA1 forms a heterodimer with the ring motif of BARD1 to assemble the functional protein complex. The solution structure of this complex shows that long alpha helices border the zinc binding residues in the ring motif. These alpha helices from the ring motif’s of BRCA1 and BARD1 combine to form a four-helix bundle that stabilizes the heterodimer and positions the zinc binding regions next to one another.

Function

The two main functions of the ring finger domain of BRCA1 are to mediate heterodimer formation with BARD1 and to catalyze ubiquination of lysine residue using ubiquitin from E2 enzymes. BRCA1 also moves to areas within the cell containing damaged DNA and acts as scaffolding for repair complexes to sit. BARD1 and BRCA1 are able to form a heterodimer because they both contain ring finger domains that interact with each other. Ubiquination of lysine-48 is a means of marking a protein for degradation by the proteasome. Ubiquination of lysine-63 on the over hand, controls DNA repair pathways as well as activate protein kinases by sending out non-proteolytic signals.

Disease

Relevance

Critical Amino Acids

Abbreviations

^[3]

Structural highlights

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.