Protein stability in nanocages: a novel approach for influencing protein stability by molecular confinement

Confinement of a protein in a small inert space and microviscosity are known to increase its thermodynamic stability in a way similar to the mechanisms that stabilize protein fold in the cell. Here, to examine the influence of confinement on protein stability we choose four test cases of single domain proteins characterized by a wide range of melting temperatures, from approximately 73 degrees C of titin I27 to approximately 36 degrees C of yeast frataxin. All proteins are stabilized when confined in the gel, the most dramatic stabilization being that of yeast frataxin, whose melting temperature increased by almost 5 degrees C in the gel. In addition to being simple to use, this approach allows us to change the viscosity of the solvent without changing its composition or altering the structure of the proteins. The dimensions of the pores of the gels fall in the nanometer range, hence they are similar to those of the chaperone cavity. This method could therefore be used as a novel and powerful approach for protein folding studies.     

Compound Ex Vivo and In Silico Method for Hemodynamic Analysis of Stented Arteries

Hemodynamic factors such as low wall shear stress have been shown to influence endothelial healing and atherogenesis in stent-free vessels. However, in stented vessels, a reliable quantitative analysis of such relations has not been possible due to the lack of a suitable method for the accurate acquisition of blood flow. The objective of this work was to develop a method for the precise reconstruction of hemodynamics and quantification of wall shear stress in stented vessels. We have developed such a method that can be applied to vessels stented in or ex vivo and processed ex vivo. Here we stented the coronary arteries of ex vivo porcine hearts, performed vascular corrosion casting, acquired the vessel geometry using micro-computed tomography and reconstructed blood flow and shear stress using computational fluid dynamics. The method yields accurate local flow information through anatomic fidelity, capturing in detail the stent geometry, arterial tissue prolapse, radial and axial arterial deformation as well as strut malapposition. This novel compound method may serve as a unique tool for spatially resolved analysis of the relationship between hemodynamic factors and vascular biology. It can further be employed to optimize stent design and stenting strategies.     

Mixing and modes of mass transfer in the third cerebral ventricle: a computational analysis

Anatomic, velocimetric, and brain motion MRI scans were combined with a computational fluid dynamics model to investigate cerebrospinal fluid (CSF) mixing in the third cerebral ventricle of a healthy male adult. It was found that advection dominates over diffusion in most of the third ventricle. Three zones where diffusion plays an important role in the mixing process were identified. One of these zones, consisting of recessus infundibulus, recessus opticus and the adjacent regions up to commissura anterior, is likely to exist in the general population. We hypothesize that this zone may act as a buffer to flatten concentration peaks of pituitary gland hormones released into the CSF of the third ventricle. We further hypothesize that this zone may facilitate the communication between hypothalamus and the pituitary gland through the third ventricle cerebrospinal fluid by prolonging residence times of the communicated hormones.     

Hemodynamics in coronary arteries with overlapping stents

Coronary artery stenosis is commonly treated by stent placement via percutaneous intervention, at times requiring multiple stents that may overlap. Stent overlap is associated with increased risk of adverse clinical outcome. While changes in local blood flow are suspected to play a role therein, hemodynamics in arteries with overlapping stents remain poorly understood. In this study we analyzed six cases of partially overlapping stents, placed ex vivo in porcine left coronary arteries and compared them to five cases with two non-overlapping stents. The stented vessel geometries were obtained by micro-computed tomography of corrosion casts. Flow and shear stress distribution were calculated using computational fluid dynamics. We observed a significant increase in the relative area exposed to low wall shear stress (WSS<0.5 Pa) in the overlapping stent segments compared both to areas without overlap in the same samples, as well as to non-overlapping stents. We further observed that the configuration of the overlapping stent struts relative to each other influenced the size of the low WSS area: positioning of the struts in the same axial location led to larger areas of low WSS compared to alternating struts. Our results indicate that the overlap geometry is by itself sufficient to cause unfavorable flow conditions that may worsen clinical outcome. While stent overlap cannot always be avoided, improved deployment strategies or stent designs could reduce the low WSS burden.     

Non-extensitivity and criticality of atomic hydropathicity around a voltage-gated sodium channel’s pore: a modeling study

Voltage-gated sodium channels (NavChs) are pore-forming membrane proteins that regulate the transport of sodium ions through the cell membrane. Understanding the structure and function of NavChs is of major biophysical, as well as clinical, importance given their key role in cellular pathophysiology. In this work, we provide a computational framework for modeling system-size-dependent, i.e., cumulative, atomic properties around a NavCh’s pore. We illustrate our methodologies on the bacterial NavAb channel captured in a closed-pore state where we demonstrate that the atomic environment around its pore exhibits a bi-phasic spatial organization dictated by the structural separation of the pore domains (PDs) from the voltage-sensing domains (VSDs). Accordingly, a mathematical model describing packing of atoms around NavAb’s pore is constructed that allows—under certain conservation conditions—for a power-law approximation of the cumulative hydropathic dipole field effect acting along NavAb’s pore. This verified the non-extensitivity hypothesis for the closed-pore NavAb channel and revealed a long-range hydropathic interactions law regulating atom-packing around the NavAb’s selectivity filter. Our model predicts a PDs-VSDs coupling energy of ∼282.1 kcal/mol corresponding to a global maximum of the atom-packing energy profile. Crucially, we demonstrate for the first time how critical phenomena can emerge in a single-channel structure as a consequence of the non-extensive character of its atomic porous environment.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10867-021-09565-w.