Modern rational modulator design and structure-function characterization often concentrate on concave regions of biomolecular surfaces, ranging from well-defined small-molecule binding sites to large protein-protein interaction interfaces. Here, we introduce a β-cluster as a pseudomolecular representation of fragment-centric pockets detected by AlphaSpace [. , , 1585], a recently developed computational analysis tool for topographical mapping of biomolecular concavities.
View Article and Find Full Text PDFA long-standing mystery shrouds the mechanism by which catalytically repressed receptor tyrosine kinase domains accomplish transphosphorylation of activation loop (A-loop) tyrosines. Here we show that this reaction proceeds via an asymmetric complex that is thermodynamically disadvantaged because of an electrostatic repulsion between enzyme and substrate kinases. Under physiological conditions, the energetic gain resulting from ligand-induced dimerization of extracellular domains overcomes this opposing clash, stabilizing the A-loop-transphosphorylating dimer.
View Article and Find Full Text PDFAn autoinhibitory network of hydrogen bonds located at the kinase hinge (referred to as the "molecular brake") regulates the activity of several receptor tyrosine kinases. The mechanism whereby mutational disengagement of the brake allosterically activates the kinase in human disease is incompletely understood. We used a combination of NMR, bioinformatics, and molecular dynamics simulation to show that mutational disruption of the molecular brake triggers localized conformational perturbations that propagate to the active site.
View Article and Find Full Text PDFNi(I)-mediated single-electron oxidative activation of alkyl halides has been extensively proposed as a key step in Ni-catalyzed cross-coupling reactions to generate radical intermediates. There are four mechanisms through which this step could take place: oxidative addition, outer-sphere electron transfer, inner-sphere electron transfer, and concerted halogen-atom abstraction. Despite considerable computational studies, there is no experimental study to evaluate all four pathways for Ni(I)-mediated alkyl radical formation.
View Article and Find Full Text PDFNi-catalyzed cross-coupling reactions have found important applications in organic synthesis. The fundamental characterization of the key steps in cross-coupling reactions, including C-C bond-forming reductive elimination, represents a significant challenge. Bimolecular pathways were invoked in early proposals, but the experimental evidence was limited.
View Article and Find Full Text PDFInhibition of protein-protein interactions (PPIs) is emerging as a promising therapeutic strategy despite the difficulty in targeting such interfaces with drug-like small molecules. PPIs generally feature large and flat binding surfaces as compared to typical drug targets. These features pose a challenge for structural characterization of the surface using geometry-based pocket-detection methods.
View Article and Find Full Text PDFFur protein plays key roles in regulating numerous genes in bacteria and is essential for intracellular iron concentration regulation. However, atomic level pictures of the iron binding site and its functional mechanism remain to be established. Here we present results of the first quantum chemical investigation of various first- and second-shell models and experimental Mössbauer data of E.
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