Allosteric Regulation of Serine Protease HtrA2 through Novel Non-Canonical Substrate Binding Pocket

Pruthvi Raj Bejugam,G Madhavi Sastry,Nikhil Gadewal,Lalith K Chaganti,Nitu Singh,Raja R Kuppili,Kakoli Bose,Srinivasa M Srinivasula

doi:10.1371/journal.pone.0055416

Pruthvi Raj Bejugam, G Madhavi Sastry + Show 6 more

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https://doi.org/10.1371/journal.pone.0055416

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Abstract

HtrA2, a trimeric proapoptotic serine protease is involved in several diseases including cancer and neurodegenerative disorders. Its unique ability to mediate apoptosis via multiple pathways makes it an important therapeutic target. In HtrA2, C-terminal PDZ domain upon substrate binding regulates its functions through coordinated conformational changes the mechanism of which is yet to be elucidated. Although allostery has been found in some of its homologs, it has not been characterized in HtrA2 so far. Here, with an in silico and biochemical approach we have shown that allostery does regulate HtrA2 activity. Our studies identified a novel non-canonical selective binding pocket in HtrA2 which initiates signal propagation to the distal active site through a complex allosteric mechanism. This non-classical binding pocket is unique among HtrA family proteins and thus unfolds a novel mechanism of regulation of HtrA2 activity and hence apoptosis.

Highlights

Multidomain proteins due to their structural complexity require different levels of regulatory mechanisms for executing cellular functions efficiently within a specified time period
While in some other cases, minimal structural perturbation helps in propagation of the signal in an energy efficient way to the functional domain where movement is mainly restricted to the side chains, loops and linker regions and which occur within picosecond to nanosecond timescales [1]
Among the five possible putative binding sites that were identified, Site2 or selective binding pocket (SBP) (Figure 1c) that encompasses the groove generated by SPD-PDZ linker, protease and PDZ domains attained the best score (Table 1)

Summary

Introduction

Multidomain proteins due to their structural complexity require different levels of regulatory mechanisms for executing cellular functions efficiently within a specified time period. While in some other cases, minimal structural perturbation helps in propagation of the signal in an energy efficient way to the functional domain where movement is mainly restricted to the side chains, loops and linker regions and which occur within picosecond to nanosecond timescales [1]. PDZ (postsynaptic density-95/discs large/zonula occludens-1) domains that are involved in myriads of protein-protein interactions [2,3] exhibit minimal structural changes during allosteric propagation. These domains have multiple ligand docking sites and are known to possess unique dynamics that regulate conformation of the functional site from a distal region

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