Journal of structural biology最新文献

The Helicase-Like Transcription Factor (HLTF) is member of the SWI/SNF-family of ATP dependent chromatin remodellers known primarily for maintaining genome stability. Biochemical and cellular assays support its multiple roles in DNA Damage Tolerance. However, the lack of sufficient structural data limits the comprehension of the molecular basis of its modes of action. In this work we have modelled and characterized the HLTF ATPase remodeling domain by using bioinformatic tools and all-atoms molecular dynamics simulations. In-silico results suggested that its binding to dsDNA is mainly mediated by the positively charged residues Arg563 and Lys913, found conserved in HLTF homologs, and Arg620 and Lys999, found only in HLTF. Interestingly, these residues are mutated in cancer cells. During translocation on dsDNA, HLTF remains persistently bound through the N-terminal ATPase subunit. However, DNA advancement occurs only in the presence of the synergic-anticorrelated action of both motor lobes. In contrast, the C-terminal facilitates substrate remodeling through DNA deformation and generation of bulges according to a wave-model. Finally, the large conformational change suggested between the two motor-remodeling subunits might be activated upon the release of PARP1 on stalled fork and be responsible for the intervention of HLTF-HIRAN in the formation of D-loop and 4-way junction DNA structures.

Calcific deposits in the arterial media have been associated with a number of metabolic and genetic disorders including diabetes, chronic kidney disease and generalized arterial calcification of infancy. The loss of Matrix Gla protein (MGP) leads to medial elastic lamina calcification (elastocalcinosis) in both humans and animal models. While MGP-deficient (Mgp^-/-) mice have been used as a reliable model to study medial elastocalcinosis, these mice are difficult to maintain because of their fragility. Also, these mice are unsuitable for long-term calcification studies in relation to age and sex as most often they die prematurely. In order to circumvent these problems we generated Mgp^-/-;ApoE-FGF23 mice, which in addition to the ablation of Mgp alleles, carries a transgene expressing the phosphaturic hormone FGF23. Increased FGF23 levels in the circulation and ensuing hypophosphatemia in these mice lead to a complete prevention of medial calcification until late adulthood. Interestingly, upon feeding a high phosphorus diet for 10 days, we were able to induce medial calcification in 3-week-old Mgp^-/-;ApoE-FGF23 mice. Our mineral analyses showed that the calcific deposits in these mice were Our mineral analyses showed that the Ca/P % in the calcific deposits in these mice were comparable to that of 5-week-old Mgp^-/- mice although the level of crystallinity differed. The aorta explants from Mgp^-/-;ApoE-FGF23 mice resulted in elastocalcinosis in the presence of 2mM phosphate in the culture medium which was completely prevented by pyrophosphate analogue alendronate. Mgp^-/-;ApoE-FGF23 mice will be suitable for future in vivo or ex vivo studies examining the effects of age, sex and mineralization inhibitors on medial elastocalcinosis.

Osteogenesis imperfecta (OI) is a genetic bone disease occurring in approximately 1 in 10,000 births, usually as a result of genetic mutation. OI patients suffer from increased fracture risk and - depending on the severity of the disease - deformation of the limbs, which can even lead to perinatal death. Despite extensive studies, the way in which the genetic mutation is translated into structural and compositional anomalies of the tissue is still an open question. Different observations have been reported, ranging from no structural (or chemical) differences to completely chaotic bone structure and composition. Here, we investigated bone samples from two adolescent OI-IV patients, focusing on the bone structure and chemistry in naturally occurring fractures. The exposed fracture plane allows the investigation of the structure and composition of the weakest bone plane. We do so by combining scanning electron microscopy (SEM) imaging with chemical information from Raman microscopy. The exposed fracture planes show different regions within the same tissue, displaying normal osteonal structures next to disorganized osteons and totally disordered structures, while the collagen mineralization in all cases is similar to that of a healthy bone. In addition, we also detected significant amounts of depositions of glycogen-rich, organic, globules of 250-1000 nm in size. These depositions point to a role of cellular disfunction in the disorganization of the collagen in qualitative OI. Overall, our results unite multiple, sometimes contradicting views from the literature on qualitative OI.

In human, mutations in the gene encoding the enamel matrix protein ameloblastin (Ambn) have been identified in cases of amelogenesis imperfecta. In mouse models, perturbations in the Ambn gene have caused loss of enamel and dramatic disruptions in enamel-making ameloblast cell function. Critical roles for Ambn in ameloblast cell signaling and polarization as well as adhesion to the nascent enamel matrix have been supported. Recently, we have identified a multitargeting domain (MTD) in Ambn that interacts with cell membrane, with the majority enamel matrix protein amelogenin, and with itself. This domain includes an amphipathic helix (AH) motif that directly interacts with cell membrane. In this study, we analyzed the sequence of the MTD for evolutionary conservation and found high conservation among mammals within the MTD and particularly within the AH motif. We computationally predicted that the AH motif lost its hydrophobic moment upon deleting hydrophobic but not hydrophilic residues from the motif. Furthermore, we rationally designed peptides that encompassed the Ambn MTD and contained deletions of largely hydrophobic or hydrophilic stretches of residues. To assess their AH-forming and membrane-binding abilities, we combined those peptides with synthetic phospholipid membrane vesicles and performed circular dichroism, membrane leakage, and vesicle clearance measurements. Circular dichroism showed retention of α-helix formation in all peptides except the one with the largest deletion of eleven amino acids including seven that were hydrophobic. This same peptide variant failed to cause leakage or clearance of synthetic membranes, while smaller deletions yielded intermediate membrane interaction as measured by leakage and clearance assays. Our data revealed that deletion of key hydrophobic residues from the AH leads to the most dramatic loss of Ambn-membrane interaction. Pinpointing roles of residues within the MTD has important implications for the multifunctionality of Ambn.