Differential basal-to-apical accessibility of lamin A/C epitopes in the nuclear lamina regulated by changes in cytoskeletal tension.

Nuclear lamins play central roles at the intersection between cytoplasmic signalling and nuclear events. Here, we show that at least two N- and C-terminal lamin epitopes are not accessible at the basal side of the nuclear envelope under environmental conditions known to upregulate cell contractility. The conformational epitope on the Ig-domain of A-type lamins is more buried in the basal than apical nuclear envelope of human mesenchymal stem cells undergoing osteogenesis (but not adipogenesis), and in fibroblasts adhering to rigid (but not soft) polyacrylamide hydrogels. This structural polarization of the lamina is promoted by compressive forces, emerges during cell spreading, and requires lamin A/C multimerization, intact nucleoskeleton-cytoskeleton linkages (LINC), and apical-actin stress-fibre assembly. Notably, the identified Ig-epitope overlaps with emerin, DNA and histone binding sites, and comprises various laminopathy mutation sites. Our findings should help decipher how the physical properties of cellular microenvironments regulate nuclear events.

Multiple steps to activate FAK's kinase domain: adaptation to confined environments?

Protein kinases regulate cell signaling by phosphorylating their substrates in response to environment-specific stimuli. Using molecular dynamics, we studied the catalytically active and inactive conformations of the kinase domain of the focal adhesion kinase (FAK), which are distinguished by displaying a structured or unstructured activation loop, respectively. Upon removal of an ATP analog, we show that the nucleotide-binding pocket in the catalytically active conformation is structurally unstable and fluctuates between an open and closed configuration. In contrast, the pocket remains open in the catalytically inactive form upon removal of an inhibitor from the pocket. Because temporal pocket closures will slow the ATP on-rate, these simulations suggest a multistep process in which the kinase domain is more likely to bind ATP in the catalytically inactive than in the active form. Transient closures of the ATP-binding pocket might allow FAK to slow down its catalytic cycle. These short cat naps could be adaptions to crowded or confined environments by giving the substrate sufficient time to diffuse away. The simulations show further how either the phosphorylation of the activation loop or the activating mutations of the so-called SuperFAK influence the electrostatic switch that controls kinase activity.

Structural Insights How PIP2 Imposes Preferred Binding Orientations of FAK at Lipid Membranes.

Focal adhesion kinase (FAK) is a multidomain protein (FERM-kinase-FAT) with important signaling functions in the regulation of cell-substrate adhesions. Its inactive, autoinhibited form is recruited from the cytoplasm to the plasma membrane, where it becomes activated at PIP2 enriched regions. To elucidate the molecular basis of activation, we performed a systematic screening of binding orientations of FAK's autoinhibited FERM-kinase complex, as well as of the dissociated FERM and kinase domains alone, on model plasma membranes using coarse-grained scFix MARTINI simulations, partially corroborated by atomistic MD simulations. The proteins adopted many more different orientations than previously thought. The presence of PIP2 tuned and narrowed the complex map of competing interfacial orientations. The dissociated FERM domain most frequently interacted with the membrane through its autoinhibitory interface rather than with the "basic patch" residues. These findings suggest a PIP2-dependent activation mechanism in which membrane binding of the dissociated FERM domain competes with the rebinding of the kinase domain. This competition could promote FAK autophosphorylation on Y397 and subsequent Src binding. The orientation of peripheral proteins at membranes is crucial to understand cell adhesion processes and is furthermore required to exploit steered molecular dynamics to predict how tensile forces might switch their active states.

Improved Side Chain Dynamics in MARTINI Simulations of Protein-Lipid Interfaces.

Specific interactions of protein side chains and lipid membranes regulate the localization, orientation, and activity of many peripheral proteins. Here, we introduce a modification of the coarse-grained MARTINI protein model, called 'side chain fix' (scFix), that was necessary and sufficient to correctly sample the side chain dynamics of ß-strands in several globular proteins. When compared to µs long atomistic simulations or previous experimental findings, scFix MARTINI simulations reproduced all key interactions between the well-studied PLC-δ1 pleckstrin homology domain and a phosphatidylinositol-4,5-bisphosphate (PIP2) containing lipid membrane. Moreover, the extended runtime and higher sampling speed enabled the systematic mapping of the protein's rolling motion at the membrane, the identification of short-lived and stable binding orientations, as well as the verification and prediction of already known and of novel transient PIP2 binding sites. scFix also showed promise to maintain proper side chain orientation in other secondary structural motifs of the α-spectrin SH3 domain, the B1 domain of protein G, and the villin headpiece. This suggests that scFix improves on the predictive power of MARTINI simulations regarding protein-lipid and protein-ligand interactions.

An experimental and computational analysis of primary cilia deflection under fluid flow.

In this study we have developed a novel model of the deflection of primary cilia experiencing fluid flow accounting for phenomena not previously considered. Specifically, we developed a large rotation formulation that accounts for rotation at the base of the cilium, the initial shape of the cilium and fluid drag at high deflection angles. We utilised this model to analyse full 3D data-sets of primary cilia deflecting under fluid flow acquired with high-speed confocal microscopy. We found a wide variety of previously unreported bending shapes and behaviours. We also analysed post-flow relaxation patterns. Results from our combined experimental and theoretical approach suggest that the average flexural rigidity of primary cilia might be higher than previously reported (Schwartz et al. 1997, Am J Physiol. 272(1 Pt 2):F132-F138). In addition our findings indicate that the mechanics of primary cilia are richly varied and mechanisms may exist to alter their mechanical behaviour.