Sandbox 35: Difference between revisions

<scene name='Sandbox_35/Secondary_structure_papain/2'>secondary structure</scene> consists of 17 <scene name='Sandbox_35/2nd_struc_papain_beta/2'>beta sheet</scene> strands and 7 <scene name='Sandbox_35/2nd_struc_papain_helix/2'>alpha helices</scene> giving it a composition 21% and 25% respectively. <ref name="9PAP PDB">[http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP]9PAP PDB</ref> The hydrogen bonds within the alpha helices are shorter than the typical alpha helix because of C=O being directed further away from the helical axis. Moreover, the beta sheet hydrogen bonding constraints and structural angles show great variation; hydrogen bonds in the sheets' central tend to be shorter than on the fringes. Three disulfide bonds, like <scene name='Sandbox_35/Papain_cys_bond/1'>Cys 22-Cys 63</scene>, serve to hold papain's tertiary structure together. <ref>PMID: 6502713</ref>  

The <scene name='Sandbox_35/Active_site_papain/4'>active site</scene> primarily consist of three main residues Cys25-His159-Asn175 holding resemblance to the catalytic triad of chymotrypsin <ref>PMID: 8140097</ref><ref>PMID: 2397208</ref>. However, growing studies are showing that the mechanism behind catalysis may actually involve a double catalytic site - consisting of Cys25-His159-Asn175 '''and''' Cys25-His159-

<scene name='Sandbox_35/Active_site_papain/5'>Asp 158</scene>! It is postulated that "a two-state mechanism" takes place instead of a "single steric mechanism." <ref>PMID: 8140097</ref> In addition, replacement of Asn 175 with other residues such as Ala mutants, reveals a decrease in kcat (less efficiency). Despite this, the rate of hydrolysis is still significantly larger than non-catalytic rates, suggesting a less essential role the Asn 175 plays than originally thought. It should be noted however, that alteration to the 175 side chain resulted in less thermal stability lending thought that Asn 175 plays a more structural conservative role rather than catalytic. <ref>[http://www.jbc.org/content/270/28/16645.abstract] The Journal of Biological Chemistry </ref>

Papain is said to have 29 identifiable methanol molecules that encircle around it as <scene name='Sandbox_35/Papain_ligand/1'>ligands</scene>. The polarity of the ligands result in hydrogen bonding interactions, possibly providing further stability for papain structure. <ref>PMID: 6502713</ref>

<scene name='Sandbox_35/Cathepsin_l_specific_inhibitor/3'>Cathepsin L specific inhibitor</scene> is part of a series known as CLIK inhibitors and was used on papain as an assessment of inhibition specificity for cathepsin enzymes. Structural differences between Papain-CLIK 148 complex and original papain is not very drastic. Minute changes result primarily from alterations in surface proteins except where a covalent bond is formed between the C2 on <scene name='Sandbox_35/Clik_cys/1'>CLIK 148 and Cys 25 residue</scene>. The primary <scene name='Sandbox_35/Cathepsin_interaction/3'>interactions</scene> between pseudo-substrate/inhibitor and papain were non-water hydrogen bonds and mostly hydrophobic interactions. CLIK 148's binding to the active site of papain is in a non-substrate mode with the main site showing pyrimidine ring interaction between <scene name='Sandbox_35/Clik_trp_177/1'>Trp 177 and CLIK 148</scene>. Hydrogen bonding is observed between the oxygens in <scene name='Sandbox_35/Clik_gly_gln/1'>CLIK 148 to Gln 19 and Gly 66 residues</scene>. Moreover, a water molecule has been observed to be near the His 159 residue enabling greater hydrogen bonding, once again highlighting solvents role in stability. <ref>PMID: 10600517</ref>  

Papain's catalytic mechanism is like serine proteases. Its catalytic triad of residues Cys 25- His159- Arg-175 appear to work with a fourth residue, Gln-19, suspected to be involved in oxyanion hole formation. When a peptide binds to the active site, His-159 deprotonates  Cys-25 which in turn attacks the substrate carbonyl carbon. The oxyanion hole then stabilizes the resulting covalent, tetrahedral intermediate. Subsequently, nitrogen in the peptide bond is protonated by His-159 (acting as an acid). This action frees the C-terminal portion of the peptide so that it is released. The entrance of water into the active site then attacks the carbonyl carbon while it is deprotonated by His-159, resulting in another tetrahedral covalent intermediate once again stabilized through the oxyanion hole. At the end, carbonyl reformation and the Cys-25 sulfur action as the leaving group releases the N-terminal portion of the peptide. The enzyme is regenerated for the cycle to begin again. <ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>  

Remember the 2002 SARS (Severe Acute Respiratory Syndrome) epidemic that placed global health, particularly in Southeast Asia, in a precarious state? On-going research is happening to further understand the mechanisms of this coronavirus, so that future steps can be taken for prevention. Its been found that the replication of RNA for this virus is mediated by two viral proteases that have many papain-like characteristics! <ref>PMID: 16306590 </ref>