The remarkable efficiency of a Pin-II proteinase inhibitor sans two conserved disulfide bonds is due to enhanced flexibility and hydrogen-bond density in the reactive loop
Rakesh S. Joshi, Manasi Mishra, Vaijayanti A. Tamhane, Anirban Ghosh, Uddhavesh Sonavane, C. G. Suresh, Rajendra Joshi, Vidya S. Gupta and Ashok P. Giri [1]
Molecular Tour
Background: Plant proteinase Inhibitors (PIs) are ubiquitous in the plant kingdom and have been extensively studied as plant defense molecules, which inhibit hydrolytic enzymes of the insect gut [2]. Among various PI families, Serine PI Pin-II/Pot-II family displays a remarkable structural and functional diversity at the gene and protein level [3]. Wound, herbivory and stress induced up-regulation of these PIs clearly link them to plant defense [2]. Previous studies using transgenic systems or in vivo assays have positively correlated the advantage offered by Pin-II PI expression in plants against insect attack [4] [5]. Precursor proteins of Pin-II PIs consist of 1- to 8- inhibitory repeat domains (IRDs) connected by proteolytic-sensitive linkers, which releases IRD units upon cleavage. Each IRD is a peptide of around 50 aa length with a molecular mass of ~6 KDa. The aa sequence of IRDs shows variations, at the same time the 8 cysteine residues that form disulfide bridge are conserved [6] [7] [8] [9]. One structural feature of Pin-II IRD is a disordered loop with triple stranded β sheet scaffold. The disordered solvent exposed reactive loop is anchored by the four conserved disulfide bonds (C4-C41, C7-C25, C8-C37 and C14-C50) [10] [11]. Among the four disulfide bonds, C8-C37 has been found to be very crucial for maintaining active conformation, whereas C4-C41 has an important role in maintaining the flexibility of the reactive loop [12]. Thus, any selective loss of disulfide bond is expected to have evolutionary significance leading to functional differentiation of inhibitors (Li et al., 2011).
[A] Functionality: To assess the effect of aa variations on activity and structural stability different biochemical studies and 20 ns MD simulations was performed on IRD structures. Inhibition kinetic studies displayed a sigmoidal pattern with increasing concentrations of the inhibitors suggesting reversible and competitive inhibition with tight binding. IRD-9 turned out to be a stronger inhibitor of bovine trypsin (IC50 ~0.0022 mM) than IRD-7 (IC50 ~0.135 mM) and IRD-12 (IC50 ~0.065 mM).
[B] Structural Variability: In accordance with the structure of a typical IRD belonging to Pin-II PI family, the predicted structures of CanPI also have three antiparallel β sheets joined by disordered loops containing the reactive site and stabilized by four disulfide bonds. It was thought that the disulfide bonds act as structural scaffold to hold the reactive site in a relatively rigid conformation and provide thermal and proteolytic stability. A single 310, helix of one turn is also present in the structure, the disordered loop is held by disulfide bond in IRD-7 and -12 whereas by a network of intra molecular hydrogen bonds in IRD-9. Furthermore, Post-simulation analysis of the intramolecular hydrogen bonds illustrated that IRD-9 with two disulfide bonds (C7-C25 and C8-C37) less, has a relatively higher density of intra-molecular hydrogen bonds as compared to IRD-7 and -12. These intramolecular hydrogen bonds might be substituting the two lost disulfide bonds of IRD-9 to stabilize the protein structure in the active conformation and might be protecting the molecules from a hydrophobic collapse. The replaced serine residues in the place of two cysteines C7 and C8 in IRD-9 may be contributing to the increased number of hydrogen bonds.
[C] Molecular Tour: The molecular models of the IRD bound HaTry predicted several atomic interactions with a reactive loop of inhibitors that also explained the contribution of the solvent exposed reactive loop. In IRD-9-HaTry interaction, carbonyl oxygen atoms of MET-92, and SER-207 of HaTry active site formed hydrogen bonds with inhibitor side chain of LYS-39 and ASN-40, while side chains of MET-92, ASP-192 and SER-191 from HaTry form hydrogen bond with side chain of LYS-39, ASN-40 residues of IRD-9, respectively. ARG-39 from IRD-12 reactive site formed three hydrogen bond between SER-207 and HIS-50 of the HaTry active site. In case of IRD-7, side chain of LYS-39 residue of reactive loop form one hydrogen bond each, with carboxyl oxygen atom of HIS-50. There are additional hydrogen bond exist between side chain of CYS-37 form reactive loop of IRD-9 and -12, with carboxyl oxygen atom of ILE-210 and ARG-109 residue from HaTry. Although the interaction of active site of enzymes with all the three inhibitors were similar in nature, significant differences were observed in making the weak interaction like hydrogen bonding and van der Waal’s interactions, which resulted in differential binding free energy of the complexes. IRD-9 forms the maximum number of stable hydrogen bonds with the active site residues (HIS-50, ASP-95 and SER-207) of the HaTry and which were maintained for longer duration. Although IRD-12 forms relatively more hydrogen bonds, but they are very unstable as reflected by their fluctuating nature. MD simulations provides structural insight into an importance of inter/intra molecular hydrogen bonds and its effect on the interaction between protease and PIs. The results of this analysis were corroborated with previous reports. Post simulation analysis also explained experimentally observed increase in binding affinity, hence activity of IRD-9 towards proteases.
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