Dissertations, Theses, and Capstone Projects

Date of Degree


Document Type


Degree Name





Shaneen M. Singh

Subject Categories

Bioinformatics | Biology


computational analyses, ExoR, ExoS, Sinorhizobium meliloti


The Sinorhizobium meliloti periplasmic ExoR protein and the ExoS/ChvI two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. In the absence of crystal structures, understanding the molecular mechanism of interaction between ExoR and the ExoS sensor, which is thought to drive the key regulatory step in the invasion process, remains a major challenge. In this study, we present theoretical structural models of the active form of ExoR protein, ExoRm, as well as of the sensing domain of ExoS, ExoSp, generated using computational methods. Our model suggests that ExoRm possesses a super-helical fold comprising twelve α-helices forming six Sel1-like repeats, including two that were unidentified in previous studies. The structural model of ExoSp suggests that ExoSp is a single Per-ARNT-Sim (PAS) domain. Docking analysis was used to suggest models for ExoSp-ExoSp and ExoSp-ExoRm protein interactions and interfaces. Our studies reveal three novel insights: (a) a possible extended conformation of the ExoR third Sel1-like repeat that might be important for ExoR regulatory function (b) a buried proteolytic site that implies a unique mechanism of proteolysis, central to controlling ExoR function and (c) an elongated structure of helix H4 that is unique to ExoSp and might be crucial for the association with ExoRm. This study provides new and interesting insights into the structure of the S. meliloti ExoRm and ExoSp proteins, lays the groundwork for elaborating the molecular mechanism of ExoRm cleavage, ExoRm-ExoS interactions, and studies of ExoR homologs in other bacterial host interactions.