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Function

The protein being studied in this article is ^[1]. This cysteine peptidase is a major virulence factor for the periodontopathogen Porphyromonas gingivalis. KGP works by cleaving many constituents of human connective tissue which leads to decreased bacterial activity and chronic inflammation in the gums. It contains a catalytic triad of cysteine, histidine, and aspartic acid. The histidine and aspartic acid residues in the catalytic triad use acid base chemistry catalysis to form a covalent intermediate with the cysteine. The intermediate formed is L-lysinylmethyl which is found in the specificity pocket. KGP uses cysteine to cleave proteins containing Lys-X. KGP always cuts after lysine residues ^[2]. The substrate is any peptide that contains a Lysine. Substrate XXLXX and the product would be XXL + XX.

Disease

Porphyromonas gingivalis is a Gram-Negative oral anaerobe that leads to periodontitis. It invades periodontal tissues, and evades the host defense mechanisms by a series of virulence factors, such as KGP, that deregulate innate immune and inflammatory responses. This bacteria and its products can enter circulation and contribute to the development of diabetes^[3], cardiovascular disease^[4], and rheumatoid arthritis^[5].

Relevance

Bacteria are typically beneficial to maintaining a healthy mouth, however, if they are a susceptible host they can become pathogenic ^[6]. Once they become pathogenic they can invade tissues and lead to infection and disease. Resistant strains are currently responsible for half of all infections, and resistant pathogens infect over 2 million people annually in the United States^[7]. The only way to keep up with these resistant pathogens is by developing new antimicrobials, but the pharmaceutical industry is failing to keep up^[8]. By studying KGP, scientists hope to find a suitable inhibitor to eliminate KGP activity, and thus prevent periodontal disease in humans.

Structural highlights

The of KGP is made up of about equal amounts of alpha helices and antiparallel beta sheets. The secondary structure is important to understand because it provides detail about how the protein is folded due to interactions between amino acids. For example, alpha helices shown in pink contain hydrophilic amino acids facing the solvent and hydrophobic amino acids facing inside, but the center of the helices is too small for even a hydrogen atom to fit through. Alpha helices and beta sheets cannot contain proline or glycine in their structure, so by simply knowing what the secondary structures are you already have insight into what types of amino acids are found in certain areas of the protein. For KGP, the secondary structure elements are generally connected by tight loops. The structure of KGP is broken up into a catalytic domain and an IGSF. The globular CD contains four cation binding sites (two sodium and two calcium ions) that generally contribute to the integrity of the. It is subdivided into a smaller A subdomain that contains the N-terminus which is highlighted in pink. It also contains a larger, B subdomain that contains the C-terminus which is shown in orange. The light blue portion of the protein represents the IGSF, which is essential for folding of KGP. The IGSF fold corresponds to typical IGSF like domains, which usually function as cell adhesion molecules. By viewing KGP under the view you can see that the protein is very tightly packed and there is little to no room for other molecules to reach the center. The space-fill view also gives you a better idea of the size and shape of the protein. The view of KGP shows the protein contains both hydrophilic (shown in purple) and hydrophobic (shown in grey) amino acid residues. Viewing under the space fill view and coloring by hydrophobicity at the same time allows you to see the hydrophobicity on the outside of the protein. Since there are about equal amounts of purple and grey, the surface of the protein contains both hydrophobic and hydrophilic regions. The 'CKC' is a lysine mimic that binds to KGP and is recognized by the cysteine peptidase to cleave Lys-X. KGP contains a : Cys-477, His-444, Asp-388. The catalytic triad interacts with the ligand, CKC, shown highlighted in red in the scene. Histidine and aspartic acid use acid base chemistry catalysis to form a covalent intermediate with Cysteine 477. The intermediate formed is L-lysinylmethyl (LM) group in the specificity pocket. The is shown with the ligand, CKC, highlighted and labeled in red. The catalytic triad is labeled and colored in green, and other amino acid residues that interact in the specificity pocket are colored by element. An interesting fact about KGP is that it contains a set of alpha helices that are interrupted by a segment of the protein containing the amino acids glycine and proline. The portion of the protein containing these , highlighted in red, are alpha helix breakers as glycine is too small and proline contains a ring structure that prevent alpha helices from forming. These interrupted alpha helices are exceedingly rare in protein structures. The CSD domain of the protein contains an internal channel that vertically traverses the molecule over 20 Angstroms from the bottom of the specificity pocket in the active site to the lower outer surface of the subdomain. The channel emerges through a formed by proline-595, Asparagine-551, and arginine-597 shown in space-fill view to help visualize the crater. KGP interacts with various through solvent channels. This JSmol shows various amino acid residues interacting with a calcium ion.