Spectroscopy and molecular docking approach for investigation on the binding of nocodazole to human serum albumin

The interaction between nocodazole (Nz) and human serum albumin (HSA) under controlled physiological condition (pH 7.4) is examined using absorption, emission, fluorescence lifetime (FLT) and circular dichroism (CD) spectroscopic techniques. The binding constant (order of 10⁵ M^-1) from UV-vis and fluorescence spectroscopy reveals a strong interaction between Nz and HSA. Fluorescence quenching study shows that Nz binds with HSA through static quenching process. It is induced by formation of Nz-HSA complex because the Stern-Volmer quenching constant is inversely correlated with the temperature which is further verified by time-resolved fluorescence spectroscopy. The thermodynamic parameters at different temperatures indicate that the binding process is spontaneous where hydrogen bonding interactions and Van der Waals forces play major roles during the interaction between Nz and HSA. By means of spectroscopy and molecular modeling, we have discovered and interpreted the alteration of the secondary structure of HSA by Nz complexation. Synchronous, three-dimensional fluorescence and CD spectroscopic results reveal that the addition of Nz to HSA affects changes in the micro-environment and conformation of HSA. According to Förster Resonance Energy Transfer (FRET), the binding distance (r) between Nz and residue of HSA is <8 nm with excellent energy efficiency. The docking study suggests that nocodazole binds at Domain IIA in the hydrophobic pocket of human serum albumin.

Microtubule and Actin Interplay Drive Intracellular c-Src Trafficking

The proto-oncogene c-Src is involved in a variety of signaling processes. Therefore, c-Src spatiotemporal localization is critical for interaction with downstream targets. However, the mechanisms regulating this localization have remained elusive. Previous studies have shown that c-Src trafficking is a microtubule-dependent process that facilitates c-Src turnover in neuronal growth cones. As such, microtubule depolymerization lead to the inhibition of c-Src recycling. Alternatively, c-Src trafficking was also shown to be regulated by RhoB-dependent actin polymerization. Our results show that c-Src vesicles primarily exhibit microtubule-dependent trafficking; however, microtubule depolymerization does not inhibit vesicle movement. Instead, vesicular movement becomes both faster and less directional. This movement was associated with actin polymerization directly at c-Src vesicle membranes. Interestingly, it has been shown previously that c-Src delivery is an actin polymerization-dependent process that relies on small GTPase RhoB at c-Src vesicles. In agreement with this finding, microtubule depolymerization induced significant activation of RhoB, together with actin comet tail formation. These effects occurred downstream of GTP-exchange factor, GEF-H1, which was released from depolymerizing MTs. Accordingly, GEF-H1 activity was necessary for actin comet tail formation at the Src vesicles. Our results indicate that regulation of c-Src trafficking requires both microtubules and actin polymerization, and that GEF-H1 coordinates c-Src trafficking, acting as a molecular switch between these two mechanisms.

Cell Synchronization Techniques to Study the Action of CDK Inhibitors

Cell synchronization techniques have been used for the studies of mechanisms involved in cell cycle regulation. Synchronization involves the enrichment of subpopulations of cells in specific stages of the cell cycle. These subpopulations are then used to study regulatory mechanisms of the cell cycle such as DNA synthesis, gene expression, protein synthesis, protein phosphorylation, protein degradation, and development of new drugs (e.g., CDK inhibitors). Here, we describe several protocols for synchronization of cells from different phases of the cell cycle. We also describe protocols for determining cell viability and mitotic index and for validating the synchrony of the cells by flow cytometry.

The golgin tether giantin regulates the secretory pathway by controlling stack organization within Golgi apparatus

Golgins are coiled-coil proteins that play a key role in the regulation of Golgi architecture and function. Giantin, the largest golgin in mammals, forms a complex with p115, rab1, GM130, and soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), thereby facilitating vesicle tethering and fusion processes around the Golgi apparatus. Treatment with the microtubule destabilizing drug nocodazole transforms the Golgi ribbon into individual Golgi stacks. Here we show that siRNA-mediated depletion of giantin resulted in more dispersed Golgi stacks after nocodazole treatment than by control treatment, without changing the average cisternal length. Furthermore, depletion of giantin caused an increase in cargo transport that was associated with altered cell surface protein glycosylation. Drosophila S2 cells are known to have dispersed Golgi stacks and no giantin homolog. The exogenous expression of mammalian giantin cDNA in S2 cells resulted in clustered Golgi stacks, similar to the Golgi ribbon in mammalian cells. These results suggest that the spatial organization of the Golgi ribbon is mediated by giantin, which also plays a role in cargo transport and sugar modifications.

Transport properties of the mesothelium and interstitium measured in rabbit pericardium

The contribution of the pleural mesothelium to pleural liquid and protein transport is still vigorously debated. Recent in vitro studies of stripped pleural membrane and free-standing pericardium have demonstrated active ion solute coupled transport of liquid and transcytosis of protein. However, the relative contribution of the passive transport properties of the pleural mesothelium compared to the pleural interstitium has not been extensively studied. In in vitro studies, we measured the albumin diffusion coefficient, reflection coefficient, hydraulic conductivity and electrical resistance of rabbit pericardium. We used two techniques, treatment with 40 muM nocodazole and a 1-min hypotonic cell lysis with distilled water, to eliminate the effect of the two mesothelial layers on diffusional and hydraulic resistances. Each technique increased the albumin diffusion coefficient and hydraulic conductivity 3- to 4-fold. In hydraulic conductivity experiments using tracer 125I-albumin, nocodazole reduced the reflection coefficient to zero, rendering the pericardium completely permeable to albumin. We applied the cell-lysis technique to the pleural and pericardial mesothelium in sequence to evaluate the separate contribution of each mesothelium. Both diffusional and hydraulic resistances, but not electrical resistance, of the mesothelium were overestimated by the cell-lysis technique. The pleural mesothelium contributed at most 30% of diffusional resistance, 10% of hydraulic resistance and 14% of electrical resistance of the total pericardial resistances. We conclude that the pleural mesothelium is not the primary barrier to protein diffusion or bulk flow of liquid from the pericardial microcirculation to the pleural liquid.

A common pharmacophore for a diverse set of colchicine site inhibitors using a structure-based approach

Modulating the structure and function of tubulin and microtubules is an important route to anticancer therapeutics, and therefore, small molecules that bind to tubulin and cause mitotic arrest are of immense interest. A large number of synthetic and natural compounds with diverse structures have been shown to bind at the colchicine site, one of the major binding sites on tubulin, and inhibit tubulin assembly. Using the recently determined X-ray structure of the tubulin:colchicinoid complex as the template, we employed docking studies to determine the binding modes of a set of structurally diverse colchicine site inhibitors. These binding models were subsequently used to construct a comprehensive, structure-based pharmacophore that in combination with molecular dynamics simulations confirms and extends our understanding of binding interactions at the colchicine site.

LIM kinase 1 coordinates microtubule stability and actin polymerization in human endothelial cells

Microtubule (MT) destabilization promotes the formation of actin stress fibers and enhances the contractility of cells; however, the mechanism involved in the coordinated regulation of MTs and the actin cytoskeleton is poorly understood. LIM kinase 1 (LIMK1) regulates actin polymerization by phosphorylating the actin depolymerization factor, cofilin. Here we report that LIMK1 is also involved in the MT destabilization. In endothelial cells endogenous LIMK1 co-localizes with MTs and forms a complex with tubulin via the PDZ domain. MT destabilization induced by thrombin or nocodazole resulted in a decrease of LIMK1 colocalization with MTs. Overexpression of wild type LIMK1 resulted in MT destabilization, whereas the kinase-dead mutant of LIMK1 (KD) did not affect MT stability. Importantly, down-regulation of endogenous LIMK1 by small interference RNA resulted in abrogation of the thrombin-induced MTs destabilization and the inhibition of thrombin-induced actin polymerization. Expression of Rho kinase 2, which phosphorylates and activates LIMK1, dramatically decreases the interaction of LIMK1 with tubulin but increases its interaction with actin. Interestingly, expression of KD-LIMK1 or small interference RNA-LIMK1 prevents thrombin-induced microtubule destabilization and F-actin formation, suggesting that LIMK1 activity is required for thrombin-induced modulation of microtubule destabilization and actin polymerization. Our findings indicate that LIMK1 may coordinate microtubules and actin cytoskeleton.