Abstract
BackgroundAmong the diverse roles of the Type III secretion-system (T3SS), one of the notable functions is that it serves as unique nano machineries in gram-negative bacteria that facilitate the translocation of effector proteins from bacteria into their host. These effector proteins serve as potential targets to control the pathogenicity conferred to the bacteria. Despite being ideal choices to disrupt bacterial systems, it has been quite an ordeal in the recent times to experimentally reveal and establish a concrete sequence-structure-function relationship for these effector proteins. This work focuses on the disease-causing spectrum of an effector protein, HopS2 secreted by the phytopathogen Pseudomonas syringae pv. tomato DC3000.ResultsThe study addresses the structural attributes of HopS2 via a bioinformatics approach to by-pass some of the experimental shortcomings resulting in mining some critical regions in the effector protein. We have elucidated the functionally important regions of HopS2 with the assistance of sequence and structural analyses. The sequence based data supports the presence of important regions in HopS2 that are present in the other functional parts of Hop family proteins. Furthermore, these regions have been validated by an ab-initio structure prediction of the protein followed by 100 ns long molecular dynamics (MD) simulation. The assessment of these secondary structural regions has revealed the stability and importance of these regions in the protein structure.ConclusionsThe analysis has provided insights on important functional regions that may be vital to the effector functioning. In dearth of ample experimental evidence, such a bioinformatics approach has helped in the revelation of a few structural regions which will aid in future experiments to attain and evaluate the structural and functional aspects of this protein family.
Highlights
Among the diverse roles of the Type III secretion-system (T3SS), one of the notable functions is that it serves as unique nano machineries in gram-negative bacteria that facilitate the translocation of effector proteins from bacteria into their host
Type III secretion systems (T3SS) are specialized molecular apparatus found in gram negative bacteria which facilitate the direct injection of effector proteins into their respective animal or plant hosts [1]
It is reported that the translocation of effector from plant pathogens through the T3SS is assisted by a signalling information that resides in the N-terminal sequence in effector proteins [7, 8]
Summary
Sequence analysis of hop proteins The physicochemical properties evaluated from the HopS2 protein sequence are tabulated in the Additional file 1: Table S1. This region markedly corresponds to the identified helix and beta motif region, with low probability of disorder stated by PrDOS. As a result of preliminary sequence analysis and long simulations, we report about the probable stretches of residues vital to the effector protein structure and interaction. This information may be experimentally verified and further used in structural determination of these proteins. Such an analysis can be used with other members of the Hop protein family to provide introductory hints to the structure of these effector proteins which otherwise are limited by experimental techniques
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