Sandbox 35: Difference between revisions

==Structure==

Papain's single polypeptide chain consists of 212 amino acid residues which fold to form a groove containing the active site between its two domains. Its

<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 name="Kamphuis">PMID: 6502713</ref>  

Located in the cleft between its domains, the active site consists of seven subsites (S1-S4 and S1’-S3’) each accommodating one amino acid residue of a substrate (P1-P4 and P1’-P3’). <ref>Schechter and Berger 1967</ref> The specificity of the active site is controlled by the S2 subsite which is a hydrophobic pocket that accommodates the P2 side chain of the substrate. Particularly at this subsite, papain shows specific substrate preferences for bulky hydrophobic or aromatic residues. On the other hand, outside of the S2 subsite preferences, the active site appears to exhibit a lack of clearly defined residue selectivity from within. <ref>Kimmel and Smith 1954</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>  

Except for valine, papain prefers to cleave at hydrophobic residues alanine, leucine, isoleucine, phenylalanine, tryptophan, or tyrosine <ref>[http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410606] Papain Sigma Aldrich </ref>. In light of the describe catalytic mechanism it makes sense that substances such as cysteine, sulfide/sulfite, heavy metal chelating agents like EDTA, and N-bromosuccinimide act as activators of the enzyme while PMSF, Hg2+ and other heavy metals, cystatin, leupeptin, sulfhydryl binding agents, carbonyl reagents, and alkylating agents serve as inhibitors.