Identification of the Conformational transition pathway in PIP2 Opening Kir Channels

The gating of Kir channels depends critically on phosphatidylinositol 4,5-bisphosphate (PIP2), but the detailed mechanism by which PIP2 regulates Kir channels remains obscure. Here, we performed a series of Targeted molecular dynamics simulations on the full-length Kir2.1 channel and, for the first time, were able to achieve the transition from the closed to the open state. Our data show that with the upward motion of the cytoplasmic domain (CTD) the structure of the C-Linker changes from a loop to a helix. The twisting of the C-linker triggers the rotation of the CTD, which induces a small downward movement of the CTD and an upward motion of the slide helix toward the membrane that pulls the inner helix gate open. At the same time, the rotation of the CTD breaks the interaction between the CD- and G-loops thus releasing the G-loop. The G-loop then bounces away from the CD-loop, which leads to the opening of the G-loop gate and the full opening of the pore. We identified a series of interaction networks, between the N-terminus, CD loop, C linker and G loop one by one, which exquisitely regulates the global conformational changes during the opening of Kir channels by PIP2

Visualization of Allostery in P-Selectin Lectin Domain Using MD Simulations

Allostery of P-selectin lectin (Lec) domain followed by an epithelial growth factor (EGF)-like domain is essential for its biological functionality, but the underlying pathways have not been well understood. Here the molecular dynamics simulations were performed on the crystallized structures to visualize the dynamic conformational change for state 1 (S1) or state 2 (S2) Lec domain with respective bent (B) or extended (E) EGF orientation. Simulations illustrated that both S1 and S2 conformations were unable to switch from one to another directly. Instead, a novel S1' conformation was observed from S1 when crystallized B-S1 or reconstructed “E-S1” structure was employed, which was superposed well with that of equilibrated S1 Lec domain alone. It was also indicated that the corresponding allosteric pathway from S1 to S1' conformation started with the separation between residues Q30 and K67 and terminated with the release of residue N87 from residue C109. These results provided an insight into understanding the structural transition and the structure-function relationship of P-selectin allostery

Mechanokinetics of receptor–ligand interactions in cell adhesion

Receptor-ligand interactions in blood flow are crucial to initiate such biological processes as inflammatory cascade, platelet thrombosis, as well as tumor metastasis. To mediate cell adhesion, the interacting receptors and ligands must be anchored onto two apposing surfaces of two cells or a cell and a substratum, i.e., two-dimensional (2D) binding, which is different from the binding of a soluble ligand in fluid phase to a receptor, i.e., three-dimensional (3D) binding. While numerous works have been focused on 3D kinetics of receptor-ligand interactions in the immune system, 2D kinetics and its regulations have been less understood, since no theoretical framework or experimental assays were established until 1993. Not only does the molecular structure dominate 2D binding kinetics, but the shear force in blood flow also regulates cell adhesion mediated by interacting receptors and ligands. Here, we provide an overview of current progress in 2D binding and regulations, mainly from our group. Relevant issues of theoretical frameworks, experimental measurements, kinetic rates and binding affinities, and force regulations are discussed. A neutrophil undergoes capture and rolling (or tethering) on the endothelium through selectin-PSGL-1 bonds, followed by slow rolling and firm adhesion through the -integrins LFA-1 and Mac-1 as well as intraluminal crawling and transmigration through the endothelium to the inflamed tissue

Mechanically Regulated Outside-In Activation of an I-Domain-Containing Integrin

Integrins are heterodimeric transmembrane proteins that mediate cellular adhesion and bidirectional mechanotransductions through their conformational allostery. The allosteric pathway of an I-domain-containing integrin remains unclear because of its complexity and lack of effective experiments. For a typical I-domain-containing integrin alpha(x)beta(2), molecular dynamics simulations were employed here to investigate the conformational dynamics in the first two steps of outside-in activation, the bindings of both the external and internal ligands. Results showed that the internal ligand binding is a prerequisite to the allosteric transmission from the alpha- to beta-subunits and the exertion of external force to integrin-ligand complex. The opening state of alpha l domain with downward movement and lower half unfolding of alpha(7)-helix ensures the stable intersubunit conformational transmission through external ligand binding first and internal ligand binding later. Reverse binding order induces a, to our knowledge, novel but unstable swingout of beta-subunit Hybrid domain with the retained close states of both alpha l and beta l domains. Prebinding of external ligand greatly facilitates the following internal ligand binding and vice versa. These simulations furthered the under-standing in the outside-in activation of I-domain-containing integrins from the viewpoint of internal allosteric pathways

Multi-scale molecular dynamics simulations and applications on mechanosensitive proteins of integrins*

Molecular dynamics simulation (MDS) is a powerful technology for investigating evolution dynamics of target proteins, and it is used widely in various fields from materials to biology. This mini-review introduced the principles, main preforming procedures, and advances of MDS, as well as its applications on the studies of conformational and allosteric dynamics of proteins especially on that of the mechanosensitive integrins. Future perspectives were also proposed. This review could provide clues in understanding the potentiality of MD simulations in structure-function relationship investigation of biological proteins

Mechanical Point Loading Induces Cortex Stiffening and Actin Reorganization

Global cytoskeleton reorganization is well-recognized when cells are exposed to distinct mechanical stimuli, but the localized responses at a specified region of a cell are still unclear. In this work, we mapped the cell-surface mechanical property of single cells in situ before and after static point loading these cells using atomic force microscopy in PeakForce-Quantitative Nano Mechanics mode. Cell-surface stiffness was elevated at a maximum of 1.35-fold at the vicinity of loading site, indicating an enhanced structural protection of the cortex to the cell. Mechanical modeling also elucidated the structural protection from the stiffened cell cortex, in which 9-15% and 10-19% decrease of maximum stress and strain of the nucleus were obtained. Furthermore, the flat-ended atomic force microscopy probes were used to capture cytoskeleton reorganization after point loading quantitatively, revealing that the larger the applied force and the longer the loading time are, the more pronounced cytoskeleton reorganization is. Also, point loading using a microneedle combined with real-time confocal microscopy uncovered the fast dynamics of actin cytoskeleton reorganization for actin-stained live cells after point loading (<10 s). These results furthered the understandings in the transmission of localized mechanical forces into an adherent cell

Biphasic flow dynamics and polarized mass transportation in branched hepatic sinusoids

In fatty liver diseases, such as liver fibrosis and liver cirrhosis, blood flow in hepatic sinusoids, an elementary building block of the liver lobule, tends to bypass through collateral vessels inside sinusoids and presents distinct sinusoidal flows compared to normal physiological flows. It remains unclear in those flow characteristics in branched sinusoids and the correlation of pathological flows with liver lesions, mainly due to the difficulty of direct hemodynamics measurements in the sinusoids. Here, we developed a dual-branched theoretical model of hepatic sinusoidal flow to elucidate the relevant flow dynamics and mass transport. Numerical simulations, based on the lattice Boltzmann method, indicated that the flow velocity distribution in hepatic sinusoids is mainly dominated by endothelium permeability and presents a non-monotonic variation with the permeability at the fusion segment of these branched sinusoids. Flow-induced shear stress on the endothelium at the side of the Disse space exhibited a biphasic pattern, yielding a low shear stress region at the junctional site. Meanwhile, a highly polarized distribution of lipoproteins concentration was also presented at the low shear stress region, indicating a localized accumulation of typical hepatic serum proteins. Thus, this work provides the basic understanding of blood flow features and mass transport regulations in branched hepatic sinusoids. Published under an exclusive license by AIP Publishing

E-selectin negatively regulates polymorphonuclear neutrophil transmigration through altered endothelial junction integrity

Transendothelial migration (TEM) of neutrophils under blood flow is critical in the inflammatory cascade. However, the role of endothelial plasticity in this process is not fully understood. Therefore, we used an in vitro model to test the dynamics of human polymorphonuclear neutrophil (PMN) TEM across lipopolysaccharide-treated human umbilical vein endothelial cell (HUVEC) monolayers. Interestingly, shRNA-E-selectin knockdown in HUVECs destabilized endothelial junctional integrity by reducing actin branching and increasing stress fiber at cell-cell junctions. This process is accomplished by downregulating the activation of cortactin and Arp2/3, which in turn alters the adhesive function of VE-cadherin, enhancing PMN transmigration. Meanwhile, redundant P-selectins possess overlapping functions in E-selectin-mediated neutrophil adhesion, and transmigration. These results demonstrate, to our knowledge, for the first time, that E-selectins negatively regulate neutrophil transmigration through alterations in endothelial plasticity. Furthermore, it improves our understanding of the mechanisms underlying actin remodeling, and junctional integrity, in endothelial cells mediating leukocyte TEM

Influence of microflow on hepatic sinusoid blood flow and red blood cell deformation

Hepatic sinusoids present complex anatomical structures such as the endothelial sieve pores and the Disse space, which govern the microscopic blood flow in the sinusoids and are associated with structural variations in liver fibrosis and cirrhosis. However, the contributions of the permeability of endothelial and collagen layers and the roughness of hepatocyte microvilli to the features of this microflow remain largely unknown. Here, an immersed boundary method coupled with a lattice Boltzmann method was adopted in an in vitro hepatic sinusoidal model, and flow field and erythrocyte deformation analyses were conducted by introducing three new source terms including permeability of the endothelial layer, resistance of hepatocyte micro-villi and collagen layers, and deformation of red blood cells (RBCs). Numerical calculations indicated that alterations in endothe-lial permeability could significantly affect the flow velocity and flow rate distributions in hepatic sinusoids. Interestingly, a biphasic regulating pattern of shear stress occurred simultaneously on the surface of hepatocytes and the lower side of endothelium, i.e., the shear stress increased with increased thickness of hepatocyte microvilli and collagen layer when the endothelial permeability was high but decreased with the increase of the thickness at low endothelial permeability. Additionally, this specified microflow manipulates typical RBC deformation inside the sinusoid, yielding one-third of the variation of deformable index with varied endo-thelial permeability. These simulations not only are consistent with experimental measurements using in vitro liver sinusoidal chip but also elaborate the contributions of endothelial and collagen layer permeability and wall roughness. Thus, our results provide a basis for further characterizing this microflow and understanding its effects on cellular migration and deformation in the hepatic sinusoids