A modified active Brownian dynamics model using asymmetric energy conversion and its application to the molecular motor system.

We consider a modified energy depot model in the overdamped limit using an asymmetric energy conversion rate, which consists of linear and quadratic terms in an active particle's velocity. In order to analyze our model, we adopt a system of molecular motors on a microtubule and employ a flashing ratchet potential synchronized to a stochastic energy supply. By performing an active Brownian dynamics simulation, we investigate effects of the active force, thermal noise, external load, and energy-supply rate. Our model yields the stepping and stalling behaviors of the conventional molecular motor. The active force is found to facilitate the forwardly processive stepping motion, while the thermal noise reduces the stall force by enhancing relatively the backward stepping motion under external loads. The stall force in our model decreases as the energy-supply rate is decreased. Hence, assuming the Michaelis-Menten relation between the energy-supply rate and the an ATP concentration, our model describes ATP-dependent stall force in contrast to kinesin-1.

A splice variant of the C(2)H(2)-type zinc finger protein, ZNF268s, regulates NF-kappaB activation by TNF-alpha.

IkappaB kinase (IKK), the pivotal kinase in signal-dependent activation of nuclear factor-kappaB (NF-kappaB), is composed of multiple protein components, including IKK alpha/beta/gamma core subunits. To investigate the regulation of the IKK complex, we immunoaffinity purified the IKK complex, and by MALDI-TOF mass spectrometry identified a splice variant of zinc finger protein 268 (ZNF268) as a novel IKK-interacting protein. Both the full-length and the spliced form of the ZNF268 protein were detected in a variety of mammalian tissues and cell lines. The genes were cloned and expressed by in vitro transcription/translation. Several deletion derivatives, such as KRAB domain (KRAB) on its own, the KRAB/spacer/4-zinc fingers (zF4), and the spacer/ 4-zinc fingers (zS4), were ectopically expressed in mammalian cells and exhibited had different subcellular locations. The KRAB-containing mutants were restricted to the nucleus, while zS4 was localized in the cytosol. TNF-alpha-induced NF-kappaB activation was examined using these mutants and only zS4 was found to stimulate activation. Collectively, the results indicate that a spliced form of ZNF268 lacking the KRAB domain is located in the cytosol, where it seems to play a role in TNF-alpha-induced NF-kappaB activation by interacting with the IKK complex.

Energetics of rotational gating mechanisms of an ion channel induced by membrane deformation.

We consider the gating mechanisms of an ion channel which has a conical structure for a closed state and a cylindrical or a bottleneck structure for an open state depending on the gating mechanisms. Applying the simplified continuum model of the membrane in the presence of a strong hydrophobic interaction between the channel proteins and the nearby lipid molecules of the membrane, we obtain energy differences between closed and open states for two known and one newly proposed rotational gating mechanism. We compare the energetics of three gating mechanisms and find out the most favorable mechanism under the given biological conditions such as hydrophobic mismatch, spontaneous curvature of a monolayer, and membrane moduli in our approach. Our results show that spontaneous curvature plays more important role in these gating mechanisms than surface tension does. Introducing spontaneous curvature to the inner or outer layer of the membrane affects the gating mechanism. We also discuss an effect of membrane thickness change due to the channel's conformational transition during gating.

Effects of hydrophobic mismatch and spontaneous curvature on ion channel gating with a hinge.

We analyze the energetics of an ion-channel gating, focusing on effects of hydrophobic mismatch between the channel protein and the nearby lipid molecules, spontaneous curvature of monolayers, and thickness change of membranes. For the analysis we consider recently proposed open and closed conformations of a potassium channel which has a gating hinge, using the elastic continuum model of membranes. Gating energy, defined as the difference of deformation free energies for open and closed conformations, is quantitatively evaluated for various values of moduli related to the deformation of membranes and spontaneous curvature of monolayer imposing a strong hydrophobic boundary condition. We show that the gating mechanism with a hinge can work successfully even in a continuum model that considers hydrophobic mismatch and spontaneous curvature. When the energy cost for the thickness change of the membrane is neglected, the surface tension is not necessarily strong enough to open the channel. Otherwise, a relatively strong surface tension is required to open the channel.

Walking motion of an overdamped active particle in a ratchet potential.

An active particle can convert its internal energy into mechanical work. We study a generalized energy-depot model of an overdamped active particle in a ratchet potential. Using well-known biological parameters for kinesin-1 and modeling ATP influx as a pulsed energy supply, we apply our model to the molecular motor system. We find that our simple model can capture the essential properties of the kinesin motor such as forward stepping, stalling, backward stepping, dependence on ATP concentration, and stall force. Our model might be quite universal in the sense that it is able to describe dynamics of various types of motors as long as realistic parameters for each motor species are adopted.

Inhibition of the proliferation and invasion of hepatocellular carcinoma cells by lipocalin 2 through blockade of JNK and PI3K/Akt signaling.

Lipocalin 2 (Lcn2) has been reported to induce cellular proliferation based on its expression in a variety of proliferative cells. Consistent with these findings, the present study demonstrates a significant increase in Lcn2 levels in human hepatocellular carcinoma (HCC) tissues compared with non-tumor liver tissues. However, the role of Lcn2 in hepatocarcinogenesis is far from clear. To investigate the effects of Lcn2 expression on hepatocarcinogenesis, Chang liver and SK-Hep1 HCC cell lines were genetically manipulated to express Lcn2, and the effects on the proliferation and invasion of HCC cells were analyzed. Ectopic expression of Lcn2 in HCC cells significantly inhibited the growth of HCC cells in vitro and in vivo, reduced the invasive potential of cells, and inhibited the expression of matrix metalloproteinase 2 (MMP-2). Lcn2 may exert its function partly through the inhibition of the c-Jun N-terminal kinase (JNK) and phospha-tidyl inositol 3'-kinase (PI3K)/Akt signaling pathways in HCC cells. The selective inhibition of these pathways using pharmacological inhibitors significantly inhibited proliferation, invasion and MMP-2 expression, whereas Lcn2 expression suppressed the JNK and PI3K/Akt pathways. Collectively, these results clearly indicate that Lcn2 may play a protective role against the progression of HCCs by suppressing cell proliferation and invasion. The clinical significance of the present findings should be evaluated further.

Resultant pressure distribution pattern along the basilar membrane in the spiral shaped cochlea.

The cochlea is an important auditory organ in the inner ear. In most mammals, it is coiled as a spiral. Whether this specific shape influences hearing is still an open problem. By employing a three-dimensional fluid model of the cochlea with an idealized geometry, the influence of the spiral geometry of the cochlea is examined. We obtain solutions of the model through a conformal transformation in a long-wave approximation. Our results show that the net pressure acting on the basilar membrane is not uniform along its spanwise direction. Also, it is shown that the location of the maximum of the spanwise pressure difference in the axial direction has a mode dependence. In the simplest pattern, the present result is consistent with the previous theory based on the Wentzel-Kramers-Brillouin-like approximation (Manoussaki et al., Phys Rev Lett 96:088701, 2006). In this mode, the pressure difference in the spanwise direction is a monotonic function of the distance from the apex and the normal velocity across the channel width is zero. Thus, in the lowest-order approximation, we can neglect the existence of the Reissner's membrane in the upper channel. However, higher responsive modes show different behavior and, thus, the real maximum is expected to be located not exactly at the apex but at a position determined by the spiral geometry of the cochlea and the width of the cochlear duct. In these modes, the spanwise normal velocities are not zero. Thus, it indicates that one should take into account the detailed geometry of the cochlear duct for a more quantitative result. The present result clearly demonstrates that the spiral geometry and the geometry of the cochlear duct play decisive roles in distributing the wave energy.

Ectopic expression of neutrophil gelatinase-associated lipocalin suppresses the invasion and liver metastasis of colon cancer cells.

Neutrophil gelatinase-associated lipocalin (NGAL), also known as lipocalin 2, is a 25-kDa lipocalin initially purified from neutrophil granules. It is thought to play a role in regulating cellular growth since its expression is highly upregulated in a variety of proliferative cells such as cancer cells. However, experimental evidence showing a clear causal relationship between NGAL expression and the proliferation of tumor cells is lacking. Here, we found NGAL expression in highly and poorly metastatic colon cancer cell lines of the same genetic origin correlated inversely with the metastatic potential of these cells, which suggests NGAL participates in the metastatic process. To explore the role NGAL plays in tumor growth and metastasis, the KM12SM human colon cancer cell line, which is highly metastatic while showing decreased NGAL expression, was genetically manipulated to overexpress NGAL. The effects of this on tumor growth and liver metastasis were then analyzed using experimental animal models established by injecting BALB/c nude mice with tumor cells subcutaneously or intrasplenically. Ectopic expression of NGAL in the colon cancer cells had little effect on the growth and viability of the tumor cells both in vitro and in vivo. However, NGAL expression not only suppressed the ability of the colon carcinoma cells to invade Matrigel in vitro, it also substantially inhibited liver metastasis in an experimental animal model. Collectively, these results indicate that NGAL may be a candidate metastasis suppressor in colon cancer cells.