New molecular interaction of IIANtr and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies

High-resolution protein-protein docking by global optimization: recent advances and future challenges

A computational protein-protein docking method that predicts atomic details of protein-protein interactions from protein monomer structures is an invaluable tool for understanding the molecular mechanisms of protein interactions and for designing molecules that control such interactions. Compared to low-resolution docking, high-resolution docking explores the conformational space in atomic resolution to provide predictions with atomic details. This allows for applications to more challenging docking problems that involve conformational changes induced by binding. Recently, high-resolution methods have become more promising as additional information such as global shapes or residue contacts are now available from experiments or sequence/structure data. In this review article, we highlight developments in high-resolution docking made during the last decade, specifically regarding global optimization methods employed by the docking methods. We also discuss two major challenges in high-resolution docking: prediction of backbone flexibility and water-mediated interactions.

Phosphotransferase protein EIIANtr interacts with SpoT, a key enzyme of the stringent response, in Ralstonia eutropha H16

EIIA(Ntr) is a member of a truncated phosphotransferase (PTS) system that serves regulatory functions and exists in many Proteobacteria in addition to the sugar transport PTS. In Escherichia coli, EIIA(Ntr) regulates K(+) homeostasis through interaction with the K(+) transporter TrkA and sensor kinase KdpD. In the β-Proteobacterium Ralstonia eutropha H16, EIIA(Ntr) influences formation of the industrially important bioplastic poly(3-hydroxybutyrate) (PHB). PHB accumulation is controlled by the stringent response and induced under conditions of nitrogen deprivation. Knockout of EIIA(Ntr) increases the PHB content. In contrast, absence of enzyme I or HPr, which deliver phosphoryl groups to EIIA(Ntr), has the opposite effect. To clarify the role of EIIA(Ntr) in PHB formation, we screened for interacting proteins that co-purify with Strep-tagged EIIA(Ntr) from R. eutropha cells. This approach identified the bifunctional ppGpp synthase/hydrolase SpoT1, a key enzyme of the stringent response. Two-hybrid and far-Western analyses confirmed the interaction and indicated that only non-phosphorylated EIIA(Ntr) interacts with SpoT1. Interestingly, this interaction does not occur between the corresponding proteins of E. coli. Vice versa, interaction of EIIA(Ntr) with KdpD appears to be absent in R. eutropha, although R. eutropha EIIA(Ntr) can perfectly substitute its homologue in E. coli in regulation of KdpD activity. Thus, interaction with KdpD might be an evolutionary 'ancient' task of EIIA(Ntr) that was subsequently replaced by interaction with SpoT1 in R. eutropha. In conclusion, EIIA(Ntr) might integrate information about nutritional status, as reflected by its phosphorylation state, into the stringent response, thereby controlling cellular PHB content in R. eutropha.