Biology subjects

Padmini Rangamani

Publications and source records attributed to Padmini Rangamani.

5 recordsLinked to original sources

bioRxiv2016

Pulsatile lipid vesicles under osmotic stress

The response of lipid bilayers to osmotic stress is an important part of cellular function. Previously, in (Oglecka et al., 2014), we reported that cell-sized giant unilamellar vesicles (GUVs) exposed to hypotonic media, respond to the osmotic assault by undergoing a cyclical sequence of swelling and bursting events, coupled to the membranes compositional degrees of freedom. Here, we seek to deepen our quantitative understanding of the essential pulsatile behavior of GUVs under hypotonic conditions, by advancing a comprehensive theoretical model for vesicle dynamics. The model quantitatively captures our experimentally measured swell-burst parameters for single-component GUVs, and reveals that thermal fluctuations enable rate dependent pore nucleation, driving the dynamics of the swell-burst cycles. We further identify new scaling relationships between the pulsatile dynamics and GUV properties. Our findings provide a fundamental framework that has the potential to guide future investigations on the non-equilibrium dynamics of vesicles under osmotic stress.

Biophysics↗

bioRxiv2016

An introduction to linear stability analysis for deciphering spatial patterns in signaling networks

Mathematical modeling is now used commonly in the analysis of signaling networks. With advances in high resolution microscopy, the spatial location of different signaling molecules and the spatio-temporal dynamics of signaling microdomains are now widely acknowledged as key features of biochemical signal transduction. Reaction-diffusion mechanisms are commonly used to model such features, often with a heavy reliance on numerical simulations to obtain results. However, simulations are parameter dependent and may not be able to provide an understanding of the full range of the system responses. Analytical approaches on the other hand provide a framework to study the entire phase space. In this tutorial, we provide a largely analytical method for studying reaction-diffusion models and analyzing their stability properties. Using two representative biological examples, we demonstrate how this approach can guide experimental design.

Systems Biology↗

bioRxiv2016

Shear-induced nitric oxide production by endothelial cells

We present a biochemical model of the wall shear stress (WSS)-induced activation of endothelial nitric oxide synthase (eNOS) in an endothelial cell (EC). The model includes three key mechanotransducers: mechanosensing ion channels, integrins and G-protein-coupled receptors. The reaction cascade consists of two interconnected parts. The first is rapid activation of calcium, which results in formation of calcium-calmodulin complexes, followed by recruitment of eNOS from caveolae. The second is phosphoryaltion of eNOS by protein kinases PKC and AKT. The model also includes a negative feedback loop due to inhibition of calcium influx into the cell by cyclic guanosine monophosphate (cGMP). In this feedback, increased nitric oxide (NO) levels cause an increase in cGMP levels, so that cGMP inhibition of calcium influx can limit NO production. The model was used to predict the dynamics of NO production by an EC subjected to a step increase of WSS from zero to a finite physiologically relevant value. Among several experimentally observed features, the model predicts a highly nonlinear, bipha-sic transient behavior of eNOS activation and NO production: a rapid initial activation due to the very rapid influx of calcium into the cytosol (occurring within 1 to 5 minutes) is followed by a sustained period of activation due to protein kinases.\n\nAcronymsAKT, protein kinase B; [Ca2+]c, [Ca2+]s, [Ca2+]e and [Ca2+]b, cytosolic, stored, external and buffer concentrations of calcium ions, respectively; Ca3-CaM and Ca4-CaM, calcium-calmodulin complexes with 3 and 4 calcium ions bound to CaM, respectively; CaM, calmodulin; CCE, capacitative calcium entry; cGMP, cyclic guanosine monophosphate; EC, endothelial cell; ECM, extracellular matrix; eNOS, endothelial nitric oxide synthase; eNOScav, eNOS bound to caveolin; eNOS*, eNOS-CaM complex phosphorylated at Ser-1197; eNOS0, caveolin-bound eNOS phosphorylated at Thr-495; ER, endoplasmic reticulum; FAK, focal adhesion kinase; G, active G proteins; Gt, total G proteins; GPCR, G-protein-coupled receptors; Hsp90, heat shock protein 90; GTP, guanosine triphosphate; IP3, inositol triphosphate; L-Arg, L-form of arginine; MSIC, mechanosensing ion channel; NO, nitric oxide; O2, oxygen; PIP2, phosphatidylinositol 4,5-bisphosphate; PIP3, phos-phatidylinositol (3,4,5)-triphosphate; PI3K, phosphatidylinositide 3-kinases; PKC, protein kinase C; RBC, red blood cell; sGC, soluble guanylate cyclase; WSS, wall shear stress

Systems Biology↗

bioRxiv2016

Membrane tension is a key determinant of bud morphology in clathrin-mediated endocytosis

A critical step in cellular trafficking pathways is the budding of membranes by protein coats, which recent experiments have demonstrated can be inhibited by elevated membrane tension. The robustness of processes like clathrin-mediated endocytosis (CME) across a diverse range of organisms and mechanical environments suggests that the protein machinery in this process has evolved to take advantage of some set of physical design principles to ensure robust vesiculation against opposing forces like membrane tension. Using a theoretical model for membrane mechanics and membrane protein interaction, we have systematically investigated the influence of membrane rigidity, curvature induced by the protein coat, area covered by the protein coat, membrane tension and force from actin polymerization on bud formation. Under low tension, the membrane smoothly evolves from a flat to budded morphology as the coat area or spontaneous curvature increases, whereas the membrane remains essentially flat at high tensions. At intermediate, physiologically relevant, tensions, the membrane undergoes a snapthrough instability in which small changes in the coat area, spontaneous curvature or membrane tension cause the membrane to \"snap\" from an open, U-shape to a closed bud. This instability can be smoothed out by increasing the bending rigidity of the coat, allowing for successful budding at higher membrane tensions. Additionally, applied force from actin polymerization can bypass the instability by inducing a smooth transition from an open to a closed bud. Finally, a combination of increased coat rigidity and force from actin polymerization enables robust vesiculation even at high membrane tensions.\n\nSignificance statementPlasma membrane tension plays an important role in various biological processes. In particular, recent experimental studies have shown that membrane tension inhibits membrane budding processes like clathrin-mediated endocytosis (CME). We have identified a mathematical relationship between the curvature-generating capability of the protein coat and membrane tension that can predict whether the coat alone is sufficient to produce closed buds. Additionally, we show that a combination of increased coat rigidity and applied force from actin polymerization can produce closed buds at high membrane tensions. These findings are general to any membrane budding process, suggesting that biology has evolved to take advantage of a set of physical design principles to ensure robust vesicle formation across a range of organisms and mechanical environments.\n\nAuthor ContributionsJ.E.H., G.O., and P.R. designed research. J.E.H. performed research. J.E.H., D.G.D., and P.R. analyzed data. J.E.H., G.O., D.G.D., and P.R. wrote the paper.

Biophysics↗

bioRxiv2016

Paradoxical signaling regulates structural plasticity in dendritic spines

Transient spine enlargement (3-5 min timescale) is an important event associated with the structural plasticity of dendritic spines. Many of the molecular mechanisms associated with transient spine en{-}largement have been identified experimentally. Here, we use a systems biology approach to construct a mathematical model of biochemical signaling and actin-mediated transient spine expansion in response to calcium-influx due to NMDA receptor activation. We have identified that a key feature of this signaling network is the paradoxical signaling loop. Paradoxical components act bifunctionally in signaling net{-}works and their role is to control both the activation and inhibition of a desired response function (protein activity or spine volume). Using ordinary differential equation (ODE)-based modeling, we show that the dynamics of different regulators of transient spine expansion including CaMKII, RhoA, and Cdc42 and the spine volume can be described using paradoxical signaling loops. Our model is able to capture the experimentally observed dynamics of transient spine volume. Furthermore, we show that actin remod{-}eling events provide a robustness to spine volume dynamics. We also generate experimentally testable predictions about the role of different components and parameters of the network on spine dynamics.

Neuroscience↗