Validation methods for low-resolution fitting of atomic structures to electron microscopy data

A new method to statistically describe microcatheter tip position in patient-specific aneurysm models

BACKGROUND AND PURPOSE

Evidence on how to select microcatheters to facilitate aneurysm catheterization during coil embolization is sparse. We developed a new method to define microcatheter tip location inside a patient-specific aneurysm model as a 3-dimensional probability map. We hypothesized that precision and accuracy of microcatheter tip positioning depend on catheter tip shape and aneurysmal geometry.

MATERIALS AND METHODS

Under fluoroscopic guidance two to three operators introduced differently shaped microcatheters (straight, 45°, 90°) into eight aneurysm models targeting the anatomic center of the aneurysm. Each microcatheter position was recorded with flat-panel CT, and 3-dimensional probability maps of the microcatheter tip positions were generated. Maps were assessed with histogram analyses and compared between tip shapes, aneurysm locations and operators.

RESULTS

Among a total of 530 microcatheter insertions, the precision (mean distance between catheter positions) and accuracy (mean distance to target position) were significantly higher for the 45° tip (1.10±0.64 mm, 3.81±1.41 mm, respectively) than for the 90° tip (1.27±0.57 mm, p=0.010; 4.21±1.60 mm p=0.014, respectively). Accuracy was significantly higher in posterior communicating artery aneurysms (3.38±1.20 mm) than in aneurysms of the internal carotid artery (4.56±1.54 mm, p<0.001).

CONCLUSION

Our method can be used tostatistically describe statistically microcatheter behavior in patient-specific anatomy, which may improve the available evidence guiding microcatheter shape selection. Experience increases the ability to reach the intended position with a microcatheter (accuracy) that is also dependent on the aneurysm location, whereas catheter tip choice determines the variability of catheter tip placements versus each other (precision). Clinical validation is required.

Three-Dimensional Structures of Full-Length, Membrane-Embedded Human α(IIb)β(3) Integrin Complexes

Integrins are bidirectional, allosteric transmembrane receptors that play a central role in hemostasis and arterial thrombosis. Using cryo-electron microscopy, multireference single-particle reconstruction methods, and statistics-based computational fitting approaches, we determined three-dimensional structures of human integrin αIIbβ3 embedded in a lipid bilayer (nanodiscs) while bound to domains of the cytosolic regulator talin and to extracellular ligands. We also determined the conformations of integrin in solution by itself to localize the membrane and the talin-binding site. To our knowledge, our data provide unprecedented three-dimensional information about the conformational states of intact, full-length integrin within membrane bilayers under near-physiological conditions and in the presence of cytosolic activators and extracellular ligands. We show that αIIbβ3 integrins exist in a conformational equilibrium clustered around four main states. These conformations range from a compact bent nodule to two partially extended intermediate conformers and finally to a fully upright state. In the presence of nanodiscs and the two ligands, the equilibrium is significantly shifted toward the upright conformation. In this conformation, the receptor extends ∼20 nm upward from the membrane. There are no observable contacts between the two subunits other than those in the headpiece near the ligand-binding pocket, and the α- and β-subunits are well separated with their cytoplasmic tails ∼8 nm apart. Our results indicate that extension of the ectodomain is possible without separating the legs or extending the hybrid domain, and that the ligand-binding pocket is not occluded by the membrane in any conformations of the equilibrium. Further, they suggest that integrin activation may be influenced by equilibrium shifts.

Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling

Protein-protein interactions carry out a large variety of essential cellular processes. Cryo-electron microscopy (cryo-EM) is a powerful technique for the modeling of protein-protein interactions at a wide range of resolutions, and recent developments have caused a revolution in the field. At low resolution, cryo-EM maps can drive integrative modeling of the interaction, assembling existing structures into the map. Other experimental techniques can provide information on the interface or on the contacts between the monomers in the complex. This inevitably raises the question regarding which type of data is best suited to drive integrative modeling approaches. Systematic comparison of the prediction accuracy and specificity of the different integrative modeling paradigms is unavailable to date. Here, we compare EM-driven, interface-driven, and contact-driven integrative modeling paradigms. Models were generated for the protein docking benchmark using the ATTRACT docking engine and evaluated using the CAPRI two-star criterion. At 20 Å resolution, EM-driven modeling achieved a success rate of 100%, outperforming the other paradigms even with perfect interface and contact information. Therefore, even very low resolution cryo-EM data is superior in predicting heterodimeric and heterotrimeric protein assemblies. Our study demonstrates that a force field is not necessary, cryo-EM data alone is sufficient to accurately guide the monomers into place. The resulting rigid models successfully identify regions of conformational change, opening up perspectives for targeted flexible remodeling.