3D architecture of DNA Pol α reveals the functional core of multi-subunit replicative polymerases

Eukaryotic DNA replication requires the coordinated activity of the multi-subunit DNA polymerases: Pol α, Pol δ and Pol ɛ. The conserved catalytic and regulatory B subunits associate in a constitutive heterodimer that represents the functional core of all three replicative polymerases. Here, we combine X-ray crystallography and electron microscopy (EM) to describe subunit interaction and 3D architecture of heterodimeric yeast Pol α. The crystal structure of the C-terminal domain (CTD) of the catalytic subunit bound to the B subunit illustrates a conserved mechanism of accessory factor recruitment by replicative polymerases. The EM reconstructions of Pol α reveal a bilobal shape with separate catalytic and regulatory modules. Docking of the B–CTD complex in the EM reconstruction shows that the B subunit is tethered to the polymerase domain through a structured but flexible linker. Our combined findings provide a structural template for the common functional architecture of the three major replicative DNA polymerases

The High Radiosensitizing Efficiency of a Trace of Gadolinium-Based Nanoparticles in Tumors

International audienceWe recently developed the synthesis of ultrasmall gadolinium-based nanoparticles (GBN), (hydrodynamic diameter <5 nm) characterized by a safe behavior after intravenous injection (renal clearance, preferential accumulation in tumors). Owing to the presence of gadolinium ions, GBN can be used as contrast agents for magnetic resonance imaging (MRI) and as radiosensitizers. The attempt to determine the most opportune delay between the intravenous injection of GBN and the irradiation showed that a very low content of radiosensitizing nanoparticles in the tumor area is sufficient (0.1 μg/g of particles, i.e. 15 ppb of gadolinium) for an important increase of the therapeutic effect of irradiation. Such a promising and unexpected result is assigned to a suited distribution of GBN within the tumor, as revealed by the X-ray fluorescence (XRF) maps

Transient Protein-Protein Interaction of the SH3-Peptide Complex via Closely Located Multiple Binding Sites

Protein-protein interactions play an essential role in cellular processes. Certain proteins form stable complexes with their partner proteins, whereas others function by forming transient complexes. The conventional protein-protein interaction model describes an interaction between two proteins under the assumption that a protein binds to its partner protein through a single binding site. In this study, we improved the conventional interaction model by developing a Multiple-Site (MS) model in which a protein binds to its partner protein through closely located multiple binding sites on a surface of the partner protein by transiently docking at each binding site with individual binding free energies. To test this model, we used the protein-protein interaction mediated by Src homology 3 (SH3) domains. SH3 domains recognize their partners via a weak, transient interaction and are therefore promiscuous in nature. Because the MS model requires large amounts of data compared with the conventional interaction model, we used experimental data from the positionally addressable syntheses of peptides on cellulose membranes (SPOT-synthesis) technique. From the analysis of the experimental data, individual binding free energies for each binding site of peptides were extracted. A comparison of the individual binding free energies from the analysis with those from atomistic force fields gave a correlation coefficient of 0.66. Furthermore, application of the MS model to 10 SH3 domains lowers the prediction error by up to 9% compared with the conventional interaction model. This improvement in prediction originates from a more realistic description of complex formation than the conventional interaction model. The results suggested that, in many cases, SH3 domains increased the protein complex population through multiple binding sites of their partner proteins. Our study indicates that the consideration of general complex formation is important for the accurate description of protein complex formation, and especially for those of weak or transient protein complexes

Speciation of Al-III in blood serum - The Al-III-citrate-phosphate ternary system

Time-dependent speciation studies have been carried out on the ternary Al-III-citrate (A)-phosphate (B) system in order to clarify the solution state of Al-III in blood serum. The potentiometric results indicate that ternary complexes predominate both in freshly prepared mixtures and at equilibrium. The ternary species AlAB and AlABH(-1) and the binary species AlAH(-1) and AlBH-1 are present at physiological pH. As the solution ages the amount of the trinuclear species [Al-3(AH(-1))(3)(OH)](4-) increases at the expense of the mononuclear binary and ternary complexes. P-31 NMR spectra measured at neutral pH provide corroborating evidence of the formation of the ternary complexes ALAB and AlABH(-1) and binary species AlBH-1 and Al2BH-3 found potentiometrically. Time-dependent H-1 NMR measurements show that monodentate phosphate can slowly displace citrate from the otherwise very stable structure of the trinuclear species [Al-3(AH(-1))(3)(OH)](4-). At blood serum concentrations [c(Al-III) = 3 muM], Al-III is mostly bound to citrate either in binary species or in the ternary species formed with phosphate. However, with increasing Al-III concentrations binding to phosphate becomes more important