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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 ^[1] . 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 and more than twenty thousand humans are killed each year because of this disease. ^[2]

Broader Implications

Understanding the structures of what makes up Vibrio Cholerae would be beneficial to treating the Cholera. The bacteria is made up of a biofilm ^[3]. Biofilms are extremely difficult to get rid of because of their overlapping structures. 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 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 ^[4]. A greek key fold motif is a specific structural fold in a protein consisting of four adjacent anti-parallel strands and their three respective linking loops ^[5]. When zooming in on what connects them, it is just two small strands. This makes the protein very flexible. The function of the alpha helix itself was never specified. The color of beta is light blue, the alpha is light pink and the remainder is white.

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. 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 ^[6]. The hydrophobic molecules are colored in dark gray. These molecules are important to biofilms because once they attach and intertwine onto a colony, removal is extremely hard to achieve ^[7]. 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 ^[8]. It is colored in orange.

, which is found on the beta-prism of Bap1, plays a crucial role in binding to citrate and carbohydrates. Sugars and citrate both bind to this site via the amino acids, Gly 344, Ala 345, Val 346, Lys 501, Asp 348, and His 500. ^[9] 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 ^[10]. 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 < are highlighted in CPK to be able to visualize the hydrogen bonding areas. A zoomed-out view of the amino acids is important to show where in the protein they are located.

Energy Transformations

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