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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

Bap1 (Biofilm-Associated protein 1) is an extracellular matrix protein from the bacterium Vibrio cholerae that aids in biofilm architecture and adhesion affinity to living surfaces. Bap1 is also responsible for the biofilm resistance to aqueous environments, acid conditions, antibiotics and the human immune system making the V. cholerae biofilm very versatile and difficult to eradicate. Vibrio cholerae biofilms are made up of Vibrio polysaccharides, nucleic acids and matrix proteins RBmA, RbmC, and Bap1. V. cholerae biofilms are linked to increased transmission, virulence and resistance to various environments, which resulted in pandemic cholera. The biofilm resistance and adhesion affinity promote survival in a multitude of environments including mammalian stomachs. The increased resistance and adhesion affinity increase the virulence of the bacterium resulting in a greater probability of contraction, infection and disease.

Broader Implications

It is important for medical professionals and scientists alike to understand how Vibrio cholerae interact with the host they are infecting. According to the CDC, “Cholera is a disease spread by drinking water or eating food contaminated with cholera bacteria.” The main implication cholera causes in humans is dehydration from loose stools. Pushing fluids to maintain hydration will lower your risk of death below 1%. The main implication of treating cholera is breaking down the V. cholerae biofilms which are resistant to antibiotics, stomach acid and antibiotics. Understanding how to break down this resistant biofilm could help many 3rd world countries and travelers avoid illness.

Structural highlights and structure-function relationships

(57 amino acid deletion) Bap1 is an insoluble protein at full length and requires a deletion of a hydrophobic 57-amino acid chain, which forms the beta-prism domain within blade-six of the eight-bladed beta-propeller.

(Two-Domain arrangement) Bap1 is formed by a two-domain structure, which is made up of an eight-bladed beta-propeller with a beta-prism domain within the sixth blade by a flexible linker.

(8-bladed beta propeller) The eight-bladed beta-propeller has a four-stranded antiparallel beta-sheet making up each blade.

(Beta-Prism) The beta-prism is an insertion domain within blade six via a flexible linker.

(Ion Binding sites) Blade six and blade eight don’t appear to be ion binding sites, however all sites appear to bind calcium ions. During purification of the protein, all cations were replaced by sodium ions.

(All Binding Sites) Bap1 active site appears to be outside of the central cavity of the eight-bladed beta-propeller.

(Citrate Binding Site figure 4, not actual ligand) The citrate molecule in Bap1 binds in the carbohydrate-binding site in the beta-prism domains. Citrate is required to produce optimal crystal form due to the extensive crystal contacts in the area.

(No Catalytic Triad) There doesn’t seem to be a catalytic triad within 6MLT.

(Lectin = protein that binds to carbohydrates) The beta-propeller utilizes lectins, called PropLecs, which are found in the beta-propeller folds that contain carbohydrate-binding sites. Asp348 forms essential contacts with bound carbohydrates in the beta-prism lectin domain on blade-six of the eight-bladed beta-propeller.

Energy Transformation

Bap1 does not transform energy as its main purpose is binding and promote structural integrity of the Vibrio cholerae biofilm.

References

1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644