Meters of HtrA2. Graph representing relative activity of wild type HtrA2 and its mutants and variants with FITC labelled b-casein as the substrate. The graph for two mutants (F16D and G230A) is shown in inset. doi:10.1371/journal.pone.0055416.gdeath pathways through its serine protease activity [5,12]. Association of HtrA2 with cancer and neurodegenerative disorders makes it a promising therapeutic target. For example, overexpression of HtrA2 substrates such as IAPs and the Wilms’s tumor suppressor protein WT1 in Title Loaded From File several cancers suggests modulation of HtrA2 protease activity can effectively regulate their relative levels in the cells [24,25,26,27]. Out of several approaches that can be used to regulate HtrA2 activity, allosteric modulation is one of the simplest and most efficient ways. However, modulating HtrA2 functions with desired characteristics for disease intervention will require a detailed understanding of its mode of activation and the underlying conformational plasticity that controls it. Table 4. Steady state kinetic parameters for HtrA2 wild type, variants and mutants with b-casein as the substrate.HtrA2 ProteinsWild type N216A, S219A E292A E296A N-SPD F16D G230AKm (mM)4.59 5.43 5.15 4.68 3.02 9.3 9.Vmax (M/s)4.08361029 1.93761029 1.90361029 3.29kcat (1/s)0.02041 0.00968 0.00951 0.01868 0.0039 0.000025 0.kcat/Km (1/M.s)4.4526103 1.7886103 1.8496103 3.9956103 1.296103 0.00266103 0.0.7851610 4.08610 1.doi:10.1371/journal.pone.0055416.tPeptide design using site complementarity followed by MDS of the docked peptide-macromolecular complex is an extremely useful tool to study subtle conformational changes and protein dynamics. HtrA2 has a complex network of flexible loops surrounding the active site pocket and a linker at the PDZprotease interface whose relative orientations and crosstalk with different domains might be critical in defining HtrA2 functions. With partially missing loops and the flexible linker region, the solved structure of HtrA2 [4] could not fully explain the dynamics and allostery that regulate its activity and specificity. Here, with an in silico and biochemical approach, we have shown that like few other HtrA family proteins, allosteric propagation does regulate HtrA2 activity. In this study, peptide binding to SBP showed conformational changes in the distal flexible regions of HtrA2 such as the PDZprotease interface, loops L1, LD and LA that rearrange to form a more Title Loaded From File catalytically efficient active site thus establishing the role of SBP as an allosteric site in HtrA2. A close look at and around the active site pocket shows that in the bound form, the N atom of Gly (22 position) faces the oxyanion hole to form an H-bond whereas in the unbound form it flips in the opposite direction to form a malformed oxyanion hole [12,28]. Moreover, keeping in trend with other HtrA proteases, the phenylalanine ring of 23 position moves closer to the imidazole ring of His65 while in the unbound form, it moves outward as observed from Figures 6b and Movie S1. All these subtle structural rearrangements along with making and breaking of bonds at sites away from the active site might stabilize the peptide bound form such that it shifts the equilibrium toward catalysis. Enzymology studies with b-casein that has a putative SBP binding sequence (GPFPIIV) as shown in Table 4 show significantAllosteric Regulation of HtrAFigure 6. Structural changes at the oxyanion hole and YIGV groove upon peptide binding. a. Overlay of the oxyanion h.Meters of HtrA2. Graph representing relative activity of wild type HtrA2 and its mutants and variants with FITC labelled b-casein as the substrate. The graph for two mutants (F16D and G230A) is shown in inset. doi:10.1371/journal.pone.0055416.gdeath pathways through its serine protease activity [5,12]. Association of HtrA2 with cancer and neurodegenerative disorders makes it a promising therapeutic target. For example, overexpression of HtrA2 substrates such as IAPs and the Wilms’s tumor suppressor protein WT1 in several cancers suggests modulation of HtrA2 protease activity can effectively regulate their relative levels in the cells [24,25,26,27]. Out of several approaches that can be used to regulate HtrA2 activity, allosteric modulation is one of the simplest and most efficient ways. However, modulating HtrA2 functions with desired characteristics for disease intervention will require a detailed understanding of its mode of activation and the underlying conformational plasticity that controls it. Table 4. Steady state kinetic parameters for HtrA2 wild type, variants and mutants with b-casein as the substrate.HtrA2 ProteinsWild type N216A, S219A E292A E296A N-SPD F16D G230AKm (mM)4.59 5.43 5.15 4.68 3.02 9.3 9.Vmax (M/s)4.08361029 1.93761029 1.90361029 3.29kcat (1/s)0.02041 0.00968 0.00951 0.01868 0.0039 0.000025 0.kcat/Km (1/M.s)4.4526103 1.7886103 1.8496103 3.9956103 1.296103 0.00266103 0.0.7851610 4.08610 1.doi:10.1371/journal.pone.0055416.tPeptide design using site complementarity followed by MDS of the docked peptide-macromolecular complex is an extremely useful tool to study subtle conformational changes and protein dynamics. HtrA2 has a complex network of flexible loops surrounding the active site pocket and a linker at the PDZprotease interface whose relative orientations and crosstalk with different domains might be critical in defining HtrA2 functions. With partially missing loops and the flexible linker region, the solved structure of HtrA2 [4] could not fully explain the dynamics and allostery that regulate its activity and specificity. Here, with an in silico and biochemical approach, we have shown that like few other HtrA family proteins, allosteric propagation does regulate HtrA2 activity. In this study, peptide binding to SBP showed conformational changes in the distal flexible regions of HtrA2 such as the PDZprotease interface, loops L1, LD and LA that rearrange to form a more catalytically efficient active site thus establishing the role of SBP as an allosteric site in HtrA2. A close look at and around the active site pocket shows that in the bound form, the N atom of Gly (22 position) faces the oxyanion hole to form an H-bond whereas in the unbound form it flips in the opposite direction to form a malformed oxyanion hole [12,28]. Moreover, keeping in trend with other HtrA proteases, the phenylalanine ring of 23 position moves closer to the imidazole ring of His65 while in the unbound form, it moves outward as observed from Figures 6b and Movie S1. All these subtle structural rearrangements along with making and breaking of bonds at sites away from the active site might stabilize the peptide bound form such that it shifts the equilibrium toward catalysis. Enzymology studies with b-casein that has a putative SBP binding sequence (GPFPIIV) as shown in Table 4 show significantAllosteric Regulation of HtrAFigure 6. Structural changes at the oxyanion hole and YIGV groove upon peptide binding. a. Overlay of the oxyanion h.
