Prediction of substrate specificity and preliminary kinetic characterization of the hypothetical protein PVX_123945 from Plasmodium vivax

On the importance of composite protein multiple ligand interactions in protein pockets

“…Binding of the diaminopyrroloquinazoline and diaminopteridine classes of molecules to E. coli DHFR (EcDHFR) was tested by differential scanning fluorimetry (DSF). The experiments were carried out following previously reported protocols from our lab . Briefly, the reactions were carried out in 96 well plates on the RealPlex quantitative PCR instrument (Eppendorf, NY).…”

“…The interactions of small molecules with functional groups in a protein's pocket underlie most in silico approaches to drug discovery. Identification, comparison and analyses of binding pockets are pivotal for structure‐based drug design endeavors, hit identification in virtual ligand screening, detection of secondary binding sites, annotation of functions in orphan hypothetical proteins, and efforts at predicting drug side‐effects by assessing off‐target interactions …”

Catalytic and substrate promiscuity: distinct multiple chemistries catalysed by the phosphatase domain of receptor protein tyrosine phosphatase

“…Jensen proposed that modern day enzymes, often assumed to be highly specialized for the reactions that they catalyze, have evolved from broad specificity ancestors (5). Further, instances of promiscuity have been extensively reported from members belonging to the haloacid dehalogenase superfamily (1, 6), thioesterases from the hotdog fold superfamily (1) and others (7, 8). Demonstration of the limited number of distinct ligand binding pockets and the emergence of catalytic pockets in proteins without selection for function has further strengthened the understanding that promiscuity and catalysis are inherent features of proteins and that it is very likely (and certainly not surprising) that the tremendous rate accelerations that we see with present day enzymes results from evolutionary selection from a significant random background (9, 10).…”

Metabolic proof-reading in Plasmodium berghei: essentiality of phosphoglycolate phosphatase

“…Studies on HADSF members have focused on identifying their physiological substrates by screening a wide range of metabolites that include sugar phosphates, lipid phosphates, nucleotides as well as phosphorylated amino acids and co-factors. This approach has helped understand the physiological relevance of these enzymes in various cellular processes such as cell wall synthesis, catabolic and anabolic pathways, salvage pathways, signaling pathways and detoxification [3,4,5,6,7,8,9,10,11,12,13]. Apart from dephosphorylating metabolites, HADSF members have also been know to dephosphorylate proteins and such members are characterized by the absence of the cap domain [1,2].…”

“…A large scale study reported by Huang et al, has identified a HADSF member from Salmonella enterica that catalyzes dephosphorylation of more than 100 phosphorylated substrates [5]. This extended substrate specificity is a common observation in HADSF members and often leads to a confounding situation where determining the physiological substrate of such promiscuous enzymes becomes a challenging task.Recent studies have identified and characterised HADSF members from the apicomplexan parasite, Plasmodium [ 4,10,13,14,15,16]. HADSF members from Plasmodium have been found to be involved in processes that lead to the development of resistance to the drug fosmidomycin, which inhibits isoprenoid biosynthesis [4].…”