Correlative 3D cryo X-ray imaging reveals intracellular location and effect of designed antifibrotic protein-nanomaterial hybrids.

Revealing the intracellular location of novel therapeutic agents is paramount for the understanding of their effect at the cell ultrastructure level. Here, we apply a novel correlative cryo 3D imaging approach to determine the intracellular fate of a designed protein-nanomaterial hybrid with antifibrotic properties that shows great promise in mitigating myocardial fibrosis. Cryo 3D structured illumination microscopy (cryo-3D-SIM) pinpoints the location and cryo soft X-ray tomography (cryo-SXT) reveals the ultrastructural environment and subcellular localization of this nanomaterial with spatial correlation accuracy down to 70 nm in whole cells. This novel high resolution 3D cryo correlative approach unambiguously locates the nanomaterial after overnight treatment within multivesicular bodies which have been associated with endosomal trafficking events by confocal microscopy. Moreover, this approach allows assessing the cellular response towards the treatment by evaluating the morphological changes induced. This is especially relevant for the future usage of nanoformulations in clinical practices. This correlative super-resolution and X-ray imaging strategy joins high specificity, by the use of fluorescence, with high spatial resolution at 30 nm (half pitch) provided by cryo-SXT in whole cells, without the need of staining or fixation, and can be of particular benefit to locate specific molecules in the native cellular environment in bio-nanomedicine.

Supramolecular attack particles are autonomous killing entities released from cytotoxic T cells.

Cytotoxic T lymphocytes (CTLs) kill infected and cancerous cells. We detected transfer of cytotoxic multiprotein complexes, called supramolecular attack particles (SMAPs), from CTLs to target cells. SMAPs were rapidly released from CTLs and were autonomously cytotoxic. Mass spectrometry, immunochemical analysis, and CRISPR editing identified a carboxyl-terminal fragment of thrombospondin-1 as an unexpected SMAP component that contributed to target killing. Direct stochastic optical reconstruction microscopy resolved a cytotoxic core surrounded by a thrombospondin-1 shell of ~120 nanometer diameter. Cryo-soft x-ray tomography analysis revealed that SMAPs had a carbon-dense shell and were stored in multicore granules. We propose that SMAPs are autonomous extracellular killing entities that deliver cytotoxic cargo targeted by the specificity of shell components.

ARP/wARP and molecular replacement.

The aim of ARP/wARP is improved automation of model building and refinement in macromolecular crystallography. Once a molecular-replacement solution has been obtained, it is often tedious to refine and rebuild the initial (search) model. ARP/wARP offers three options to automate that task to varying extents: (i) autobuilding of a completely new model based on phases calculated from the molecular-replacement solution, (ii) updating of the initial model by atom addition and deletion to obtain an improved map and (iii) docking of a structure onto a new (or mutated) sequence, followed by rebuilding and refining the side chains in real space. A few examples are presented where ARP/wARP made a considerable difference in the speed of structure solution and/or made possible refinement of otherwise difficult or uninterpretable maps. The resolution range allowing complete autobuilding of protein structures is currently 2.0 A, but for map improvement considerable advances over more conventional refinement techniques are evident even at 3.2 A spacing.

Crystallization and preliminary crystallographic analysis of deoxyuridine 5'-triphosphate nucleotidohydrolase from Bacillus subtilis.

Single crystals of purified homotrimeric deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) from Bacillus subtilis have been grown under several different conditions using vapour diffusion. X-ray diffraction data have been collected using synchrotron radiation from three crystal forms of the unliganded enzyme and from enzyme cocrystallized with a substrate analogue and inhibitor, dUDP, and a metal ion, Sr(2+). The three crystal forms of unliganded enzyme belong to hexagonal (P6(3)), orthorhombic (P2(1)2(1)2) and cubic (P2(1)3) space groups and data have been recorded to 1.75, 1.90 and 2.50 A spacing, respectively. Crystals grown in the presence of dUDP and Sr(2+) belong to the orthorhombic space group P2(1)2(1)2(1) and data were measured to 1.90 A spacing. Solution of the hexagonal crystal form by molecular replacement using the dUTPase from feline immunodeficiency virus as a search model is in progress.

New crystal forms of Trypanosoma cruzi dUTPase.

The dUTPase from Trypanosoma cruzi has been crystallized in two crystal forms, both belonging to space group P6(3)22, with unit-cell parameters a = b = 134.67, c = 148.66 A (form I, two molecules per asymmetric unit) and a = b = 136.43, c = 68.71 A (form II, one molecule per asymmetric unit). Single-wavelength data have been collected using synchrotron radiation to 3.0 A for crystal form I and to 2.4 A for crystal form II and structure solution is under way. T. cruzi dUTPase is a potential target for anti-protozoan drug design.