Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites

NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, “closed” conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes

Gelation behavior of polysaccharide-based interpenetrating polymer network (IPN) hydrogels

We report the preparation and rheological characterization of interpenetrating polymer network (IPN) hydrogels made from alginate and hydrophobically modified ethyl hydroxyl ethyl cellulose (HMEHEC). To our knowledge, there have been no studies of the gelation behavior of IPNs. We found that the rheology of these systems can be easily tuned, with the elastic modulus of the IPN strongly dependent on the relative ratio of HMEHEC to alginate. The sol-gel transition of these systems was found to satisfy the Winter-Chambon criterion for gelation at various crosslinker densities. From the power law relationship of the dynamic moduli (G (') similar to G (aEuro3) similar to omega (n)), the exponent n appears to be dependent on both the crosslinker density and relative amount of two polymers. The value of n was found to be similar to 0.5 for all samples for stoichiometric amounts of crosslinker. The effect of molecular weight of HMEHEC on the gel point and viscoelastic exponent has also been reported. Alginate seems to dominate the kinetics of the process but the effect of high molecular weight HMEHEC on the gel point, especially at lower proportion was also evident