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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 the binding pocket of the β-prism, it is hard to really see the depth of the pocket itself. A good view of it can be seen here at top right of the molecule. The is shown.

When looking at a space-fill view of Bap1 and colored based on , one can easily identify the binding pocket that carbohydrates bind to in the β-prism. Bap1 is known for its sugar binding properties. The hydrophobic molecules are colored in dark gray. The charged molecules are colored in white. The neutral molecules are colored in dark green. Anionic polysaccharides, sugars that are negative, want their amino acid to be negative to bind to. Lysine, which makes up a large portion of the binding pocket is critical to identify when talking about the function of this protein. It is colored in orange.

, which is found on the beta-prism of Bap1, plays a crucial role in binding to citrate and carbohydrates. Mutation of aspartic acid to alanine results in a missense mutation of Bap1. Since Ala has a much smaller side chain than Asp, it becomes too many Å away to interact. Asp 348 is colored in dark red and the rest of the molecule is colored in a faded teal.

It is important to note that this protein did not have a catalytic triad mentioned in the paper. Instead, highlighting the 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. The actual ligand was not mentioned in the paper either, but citrate was bound near the sites and can be used for important functionality of the protein. Gly 344, Ala 345, Val 346, Lys 501 all interact with citrate via hydrogen bonding. Asp 348 and His 500 interact with citrate via van der Waals interactions. The protein is colored in a light tan and the amino acids are highlighted in CPK to be able to visualize the hydrogen bonding areas.

Because bap1 is known for holding together a biofilm, there may not be a energy transformation involved with it.