Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin

Breaks in DNA strands recruit the protein PARP1 and its paralogue PARP2 to modify histones and other substrates through the addition of mono- and poly(ADP-ribose) (PAR)1-5. In the DNA damage responses, this post-translational modification occurs predominantly on serine residues6-8 and requires HPF1, an accessory factor that switches the amino acid specificity of PARP1 and PARP2 from aspartate or glutamate to serine9,10. Poly(ADP) ribosylation (PARylation) is important for subsequent chromatin decompaction and provides an anchor for the recruitment of downstream signalling and repair factors to the sites of DNA breaks2,11. Here, to understand the molecular mechanism by which PARP enzymes recognize DNA breaks within chromatin, we determined the cryo-electron-microscopic structure of human PARP2-HPF1 bound to a nucleosome. This showed that PARP2-HPF1 bridges two nucleosomes, with the broken DNA aligned in a position suitable for ligation, revealing the initial step in the repair of double-strand DNA breaks. The bridging induces structural changes in PARP2 that signal the recognition of a DNA break to the catalytic domain, which licenses HPF1 binding and PARP2 activation. Our data suggest that active PARP2 cycles through different conformational states to exchange NAD+ and substrate, which may enable PARP enzymes to act processively while bound to chromatin. The processes of PARP activation and the PARP catalytic cycle we describe can explain mechanisms of resistance to PARP inhibitors and will aid the development of better inhibitors as cancer treatments12-16.

Probing PARP1-inhibitor complexes for the development of novel inhibitors

Poly (ADP-ribose) polymerase 1 (PARP1) is the most important member of the PARP family which has been shown to have a direct involvement in the development of cancer. A strategy to rationalize the structure based drug discovery of PARP1 inhibitors has been discussed. So far studies regarding varied scaffold PARP1 inhibitors have been done, however the current study focus on how the available data from potent PARP1 inhibitors could be combined and utilized for developing a robust model for the development of novel inhibitors. Through detailed analyses of PARP1-inhibitor binding, a pharmacophore model has been developed followed by a virtual screen of potential inhibitors. The resulting high-affinity binding hits following the defined pharmacophore model and making the critical interactions were selected as final potential leads. Hence, using the approaches of pharmacophore design, docking based virtual screening and conformation alignment, we have identified important leads which satisfy all parameters of the screening process. The developed pharmacophore model as well as the strategy is very straightforward for screening novel inhibitors and could thus be used as a prototype for PARP1 structure based drug discovery.

Cryoelectron microscopy imaging of recombinant and tissue derived vaults: localization of the MVP N termini and VPARP

The vault is a highly conserved ribonucleoprotein particle found in all higher eukaryotes. It has a barrel-shaped structure and is composed of the major vault protein (MVP); vault poly(ADP-ribose) polymerase (VPARP); telomerase-associated protein 1 (TEP1); and small untranslated RNA (vRNA). Although its strong conservation and high abundance indicate an important cellular role, the function of the vault is unknown. In humans, vaults have been implicated in multidrug resistance during chemotherapy. Recently, assembly of recombinant vaults has been established in insect cells expressing only MVP. Here, we demonstrate that co-expression of MVP with one or both of the other two vault proteins results in their co-assembly into regularly shaped vaults. Particles assembled from MVP with N-terminal peptide tags of various length are compared. Cryoelectron microscopy (cryoEM) and single-particle image reconstruction methods were used to determine the structure of nine recombinant vaults of various composition, as well as wild-type and TEP1-deficient mouse vaults. Recombinant vaults with MVP N-terminal peptide tags showed internal density that varied in size with the length of the tag. Reconstruction of a recombinant vault with a cysteine-rich tag revealed 48-fold rotational symmetry for the vault. A model is proposed for the organization of MVP within the vault with all of the MVP N termini interacting non-covalently at the vault midsection and 48 copies of MVP forming each half vault. CryoEM difference mapping localized VPARP to three density bands lining the inner surface of the vault. Difference maps designed to localize TEP1 showed only weak density inside of the caps, suggesting that TEP1 may interact with MVP via a small interaction region. In the absence of atomic-resolution structures for either VPARP or TEP1, fold recognition methods were applied. A total of 21 repeats were predicted for the TEP1 WD-repeat domain, suggesting an unusually large beta-propeller fold.

Atomic force microscope imaging of DNA and DNA repair proteins: applications in radiobiological research

By using the atomic force microscope (AFM), three-dimensional structures of biological specimens may be imaged at nanometer resolution. Furthermore, samples can be imaged in air or in fluid environments. The tapping mode of AFM operation for imaging has offered a significant advance in visualizing soft biological structures, such as DNA, proteins, and membranes. Here, we review the principles underlying the application of this instrument to radiation biological investigations. We focus on examples of proteins involved in the processes of repair of damaged DNA, including poly(ADP-ribose) polymerase, Ku protein, and DNA protein kinase. Novel observations on the character of DNA damage and repair have been addressed by direct visualization of DNA and protein-DNA interactions, such as the observation that the Ku protein is capable of physically joining DNA fragments in vitro. The AFM offers a powerful tool for investigating biologically important molecular interactions that are relevant to DNA damage and repair processes.