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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.

Function(s) and Biological Relevance

is a matrix protein found in the bacteria biofilm matrix of Vibrio Cholerae. Vibrio Cholerae is a bacteria that is responsible for the disease Cholera. Cholera is a disease typically found in infectious water that rids the body of the necessary amount of liquids it needs via terrible diarrhea. If left untreated, this disease could kill a human.

Broader Implications

Understanding the structures of what makes up Vibrio Cholerae would be beneficial to treating the disease. Biofilms are extremely difficult to get rid of. Being able to break up the biofilm naturally and easily lead to less complications and less people dying from losing so much liquid.

Structural highlights and structure-function relationships

There are many key structures one can highlight for Bap1, such as its two different sized connected domains, 8-bladed β-propeller region, active site location outside of the central cavity, and carbohydrate binding site. When looking at the (secondary structure) of Bap1, the two different sized domains are easily seen. The larger domain of the protein is the 8-bladed β-propeller region. The smaller domain of the protein is a β-prism that is connected to the propeller region via a loop in between blade 6. When zooming in on what connects them, it is just two small strands. This makes the protein very flexible. When looking at a space-fill view of Bap1 and colored based on hydrophobicity, one can easily identify the binding pocket that carbohydrates bind to in the β-prism. Bap1 is known for its sugar binding properties.

It is important to note that this protein did not have a catalytic triad mentioned in the paper. Instead, highlighting the key amino acids that are important to the function of Bap1 should be mentioned. These amino acids are Gly 344, Ala 345, Val 346, Lys 501, Asp 348, and His 500.

Energy Transformation

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.