Dynamic Rearrangement Research Articles

Arl4A‐PAK1 complex establishes a positive‐feedback loop contributing to PAK1 activation for cell migration

Cell migration requires coordination of multiple signaling pathways involving in membrane dynamic and cytoskeleton rearrangement. Arf‐like small GTPase Arl4A has been shown to modulate the Golgi organization and actin cytoskeleton remodeling. However, the evidences for Arl4A function in cell migration are insufficient. Here, we report that Arl4A acts with a serine/threonine protein kinase PAK1 to modulate cell migration. We first observe that Arl4A directly interacts with PAK1, and recruits PAK1 to the plasma membrane in a GTP‐dependent manner. Unexpectedly, we found that PAK1 can recruit a cytoplasmic myristoylation‐deficient Arl4A‐G2A mutant, but not GTP‐binding defective Arl4A‐T34N mutant, to the plasma membrane. Thus, these results suggest that there is a positive feedback loop between Arl4A and PAK1, which mutually recruit each other to the plasma membrane. Furthermore, we found that Arl4A promotes cell migration in a GTP‐dependent manner and Arl4A‐PAK1 interaction is critical for Arl4A‐induced cell migration, which is independent of Rac‐PAK1 interaction. Overall, this study shows that Arl4A plays important role for cell migration through direct interaction of PAK1 without effecting Rac1 activation. Our data presented here provide evidence for a novel mechanism for PAK1 regulation and activation.Support or Funding InformationThis work was supported by grants from the NHRI in Taiwan (NHRI‐EX106‐10601B1) to F.‐J. S. LeeThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Pak1 Kinase Promotes Activated T Cell Trafficking by Regulating the Expression of L-Selectin and CCR7.

Normal function of the adaptive immune system requires trafficking of T cells between the blood and lymphoid organs. Lymphocyte homing to lymph nodes requires that they cross endothelial barriers present in blood vessels and lymphatics. This multi-step process requires a remodeling of the lymphocyte plasma membrane, which is mediated by the dynamic re-arrangement of the actin cytoskeleton. Pak1 plays a central role in cell morphology, adhesion and migration in various cell types. Here we demonstrate that Pak1 is required for activated CD4+ T cell trafficking to lymph nodes. Pak1 deficiency in T cells causes a defect in the transcription of CCR7 and L-selectin, thereby altering lymphocyte trafficking. Additionally, we report an increase in L-selectin shedding in Pak1-deficient T cells, which correlates with a decrease in the recruitment of calmodulin to the cytoplasmic tail of L-selectin during T cell activation. Overall, our findings demonstrate that by regulating the expression of two major lymph node homing molecules, L-selectin and CCR7, Pak1 mediates activated CD4+ T cell trafficking.

Fast Pareto Front Exploration for Design of Reconfigurable Energy Storage

Advancement in energy storage technologies has enabled the emergence of new applications, such as grid-scale and domestic energy storage and electric vehicles (EVs). Despite the advances, the loss of energy during operation is one of the major challenges in improving the energy efficiency and the lifetime of storage systems. Reconfigurable energy storage allows the dynamic rearrangement of the unit cells to reduce voltage variations and therefore increase energy efficiency, but the introduction of switching circuit increases the upfront cost of the systems. Therefore, determining the granularity of reconfiguration that achieves high energy efficiency at a reasonable cost is a crucial design decision. However, the design space exploration for finding the optimal granularity often involves time-consuming evaluation of numerous feasible solutions. In this paper, we propose a novel algorithm to accelerate the design space exploration for reconfigurable energy storage in a branch-and-bound manner. The proposed algorithm finds a set of Pareto front solutions in terms of cost and energy efficiency with a reduced amount of computation. We apply the proposed algorithm to the design of supercapacitor energy storage for an EV, and the experimental result shows a reduction in computation by 45.4% on average with only 6.1% of non-Pareto (but still near-optimal) solutions included in the suggested solutions.

Mechanical Stability of Microtubule Lattices - Molecular Dynamic Indentation Studies

Microtubules (MTs) are made of αβ-tubulin heterodimers joined longitudinally into protofilaments (PFs). PFs associate laterally to form the hollow cylinder of an MT. Most MTs in cells contain 13 PFs, however the most common in vitro MTs have 13 or/and 14 PFs. The B-lattice (where two adjacent PFs are laterally connected by interactions between the same type of tubulin monomers: α-α/β-β) is dominant in the MT cylinder structure. Additionally, each MT cylinder contains a single lateral interaction created by the A-lattice (where two adjacent PFs are connected through α-β and β-α interactions) and called the seam. The proper functioning of MTs has a key role in the process of cell division, cell motility and cell development due to the fact that MTs are responsible for cell morphology, cell interior organization and intracellular cargo transport. Dynamic MTs rearrangements by breaking and healing are crucial for accomplishing and maintaining their cellular functions. MT breakage can occur through one of two mechanisms: breaking from high frequency buckling of PFs and breaking induced by microtubule-severing enzymes. Due to the high complexity of MTs, experimental techniques are not able to fully answer the question which of the A/B MT lattices is the “sweet spot” for the binding of microtubule-severing enzymes. Therefore, a combination of experimental and theoretical techniques is required to solve this problem. We use computational methods to probe and compare the mechanical stability of the both MTs lattices using coarse-grained indenting molecular dynamics. With the knowledge of how the B-lattice behaves (with/without defects) we can compare its mechanical stability with that of the A-lattice. Furthermore, for both lattices computationally predicted breaking forces, bending angles distributions and MTs length factors are comparable with experimental data obtained from in vitro severing assays and AFM experiments.

Dynamic Actin Reorganization and Vav/Cdc42-Dependent Actin Polymerization Promote Macrophage Aggregated LDL (Low-Density Lipoprotein) Uptake and Catabolism.

Objective- During atherosclerosis, LDLs (low-density lipoproteins) accumulate in the arteries, where they become modified, aggregated, and retained. Such deposits of aggregated LDL (agLDL) can be recognized by macrophages, which attempt to digest and clear them. AgLDL catabolism promotes internalization of cholesterol and foam cell formation, which leads to the progression of atherosclerosis. Therapeutic blockade of this process may delay disease progression. When macrophages interact with agLDL in vitro, they form a novel extracellular, hydrolytic compartment-the lysosomal synapse (LS)-aided by local actin polymerization to digest agLDL. Here, we investigated the specific regulators involved in actin polymerization during the formation of the LS. Approach and Results- We demonstrate in vivo that atherosclerotic plaque macrophages contacting agLDL deposits polymerize actin and form a compartment strikingly similar to those made in vitro. Live cell imaging revealed that macrophage cortical F-actin depolymerization is required for actin polymerization to support the formation of the LS. This depolymerization is cofilin-1 dependent. Using siRNA-mediated silencing, pharmacological inhibition, genetic knockout, and stable overexpression, we elucidate key roles for Cdc42 Rho GTPase and GEF (guanine nucleotide exchange factor) Vav in promoting actin polymerization during the formation of the LS and exclude a role for Rac1. Conclusions- These results highlight critical roles for dynamic macrophage F-actin rearrangement and polymerization via cofilin-1, Vav, and Cdc42 in LS formation, catabolism of agLDL, and foam cell formation. These proteins might represent therapeutic targets to treat atherosclerotic disease.

Cocaine addicted to cytoskeletal change and a fibrosis high.

Cocaine is one of the most widely abused illicit drugs due to its euphoric and addictive properties. Cocaine-mediated cognitive impairments are the result of dynamic cytoskeletal rearrangements involved in mediating structural and behavioural plasticity. Cytoskeletal changes initiated following cocaine abuse are regulated by the Rho family of GTPases with significant downstream activity in key actin binding proteins. Moreover, signalling via the endoplasmic reticulum chaperone protein, sigma-1 receptor has highlighted the possibility of cocaine regulated pathology in other organ systems. However, the question of whether upstream stimulation of such a high affinity binding receptor is directly involved in cocaine-mediated cytoskeletal changes at present remains unknown. In this review, we describe the functional role of key cytoskeletal regulators in response to cocaine-induced signalling cues. In addition, we ascertain the extent of whether global cytoskeletal modulators involved in cocaine-induced neurological stimulation can be used as a platform for future studies into elucidating its fibrotic potential within the hepatic microenvironment. A focus on aspects still poorly understood relating to the nonneuronal pathological impact of cocaine is discussed in the sphere of hepatic dysregulation. Lastly, we suggest that cocaine may mediate its pathological capacity via the sigma1 receptor in regulating hepatoxicity, hepatic stellate cells activity, cytoskeletal dynamics, and the transcriptional regulation of key hepato-fibrogenic modulators.

The Periplasmic Chaperones Skp and SurA.

The periplasm of Gram-negative bacteria contains a specialized chaperone network that facilitates the transport of unfolded membrane proteins to the outer membrane as its primary functional role. The network, involving the chaperones Skp and SurA as key players and potentially additional chaperones, is indispensable for the survival of the cell. Structural descriptions of the apo forms of these molecular chaperones were initially provided by X-ray crystallography. Subsequently, a combination of experimental biophysical methods including solution NMR spectroscopy provided a detailed understanding of full-length chaperone-client complexes . The data showed that conformational changes and dynamic re-organization of the chaperones upon client binding, as well as client dynamics on the chaperone surface are crucial for function. This chapter gives an overview of the structure-function relationship of the dynamic conformational rearrangements that regulate the functional cycles of the periplasmic molecular chaperones Skp and SurA.

Молекулярная организация клеточной поверхности дрожжей

This review summarizes the main achievements of recent years in molecular organization research of yeast cell surface, i.e., the compartment that consists of the coordinately functioning plasma membrane, periplasmic space, and cell wall. There are data on vesicular transport to the external environment through the cell wall and the formation of channels in the wall, which indicate the possibility of dynamic rearrangements of the molecular structure of the yeast cell wall. There is an idea about the mosaic arrangement of the compartments of the plasma membrane. The hypothesis has been suggested on the heterogeneity of the molecular structure of the cell wall, which is usually considered as uniform except for the budding zones. The groups of proteins that form the molecular assembly of the yeast cell surface have been described. Special attention has been paid for proteins with amyloid properties, including Bgl2p glucanosyltransglycosylase, which is important for virulence in pathogenic yeast, and Gas1p, the first of the studied proteins of the cell surface, which is involved in the regulation of ribosomal DNA transcriptional silencing. The data on the structure of receptors localized on the cell surface and the "moonlight" proteins, involved in the cell stress response of yeasts, have been given.

Dielectric Environment-Robust Ultrafast Charge Transfer Between Two Atomic Layers.

Understanding electron transfer across two-dimensional (2D) van der Waals (vdW) interfaces especially the effect of dielectric environment not only contributes to the rational design of high performance optoelectronic and photo/electrocatalytic devices but also unravels the nature of charge motion. Herein, we investigated the electron transfer process between two atomic thin layered materials coupled by vdW force at ultimate proximity. Despite their susceptible electronic properties, we show electron transfer at 2D vdW interface is robust and ultrafast (∼30 fs), regardless of the surrounding dielectrics and solvents. Considering the static energy landscape and dynamic nuclear rearrangements, our result suggests the electronic coupling at 2D vdW heterointerfaces is sufficiently strong such that electron transfers adiabatically in a barrierless and ultrafast manner where energetics and solvent relaxation are not that relevant. The robust ultrafast electron transfer against the variation of dielectric environment is highly encouraging for 2D optoelectronic and photo/electrocatalytic devices.

Analysis for Remodeling of Hepatic Tissue Structures in 3D During Regeneration.

It has been demonstrated that the liver remarkably alter its tissue structures during regeneration, and various types of liver stem or progenitor cells locating in specific areas in the liver tissue contribute to regeneration. Therefore, it is important to analyze the dynamic rearrangement of the liver tissue structures in 3D for better understanding the process and mechanism of liver regeneration. Here we describe a macroscopic analysis method to visualize the whole 3D structure of the vasculatures and the biliary tree, which are dynamically remodeled during regeneration, and a microscopic analysis method to visualize detailed structures at the cellular level, which can compensate what cannot be detected in the macroscopic analysis.

A structural and dynamic model for the assembly of Replication Protein A on single-stranded DNA

Replication Protein A (RPA), the major eukaryotic single stranded DNA-binding protein, binds to exposed ssDNA to protect it from nucleases, participates in a myriad of nucleic acid transactions and coordinates the recruitment of other important players. RPA is a heterotrimer and coats long stretches of single-stranded DNA (ssDNA). The precise molecular architecture of the RPA subunits and its DNA binding domains (DBDs) during assembly is poorly understood. Using cryo electron microscopy we obtained a 3D reconstruction of the RPA trimerisation core bound with ssDNA (∼55 kDa) at ∼4.7 Å resolution and a dimeric RPA assembly on ssDNA. FRET-based solution studies reveal dynamic rearrangements of DBDs during coordinated RPA binding and this activity is regulated by phosphorylation at S178 in RPA70. We present a structural model on how dynamic DBDs promote the cooperative assembly of multiple RPAs on long ssDNA.

Dynamic structural rearrangements and functional regulation of voltage-sensing phosphatase.

The voltage-sensing phosphatase (VSP) consists of a voltage sensor domain (VSD) and a cytoplasmic catalytic region. The latter contains a phosphatase domain and a C2 domain, showing remarkable similarity to the tumour suppressor enzyme PTEN. In VSP, membrane depolarization induces a conformational change in the VSD, which activates the phosphoinositide phosphatase. The final outcome in VSP is enzymatic activity in the cytoplasmic region, unlike in voltage-gated ion channels where conformational change of the transmembrane pore is induced by the VSD. Therefore, it is crucial to detect structural change in the cytoplasmic catalytic region to gain insights into the operating mechanisms of VSP. This review summarizes a recent study in which a method of genetic incorporation of a non-canonical amino acid, Anap, was used to detect dynamic membrane voltage-controlled rearrangements of the structure of the catalytic region of sea squirt VSP (Ci-VSP). Upon membrane depolarization, both the phosphatase domain and the C2 domain move in a similar time frame, suggesting that the two regions are coupled to each other. Measurement of Förster resonance energy transfer (FRET) between Anap introduced into the C2 domain of Ci-VSP and dipicrylamine in the cell membrane suggested no large movement of the enzyme towards the membrane. Fluorescence changes in Anap induced by different membrane potentials indicate the presence of multiple conformations of the active enzyme.

PKA-dependent phosphorylation of IP3K-A at Ser119 regulates a binding affinity with EB3.

Microtubule-associated end-binding protein 3 (EB3) accumulates asymmetrically at the tip-end of growing microtubules, providing a central platform for linking various cellular components. EB3 orchestrates microtubule dynamics and targeting, enabling diverse processes within neurons. Inositol 1, 4, 5-trisphosphate 3-kinase A (IP3K-A; also known as ITPKA) is a neuron-enriched protein that binds to microtubules by PKA-dependent manners. In this study, we found that IP3K-A binds to EB3 and their binding affinity is precisely regulated by protein kinase A (PKA)-dependent phosphorylation of IP3K-A at Ser119 (pSer119). We also revealed that the complex of IP3K-A and EB3 dissociates and reassociates rapidly during chemically induced LTP (cLTP) condition. This dynamic rearrangement of IP3K-A and EB3 complex will contribute remodeling of microtubule cytoskeleton allowing effective structural plasticity in response to synaptic stimulations.

Actin dynamics during Ca2+-dependent exocytosis of endothelial Weibel-Palade bodies

Weibel-Palade bodies (WPBs) are specialized secretory organelles of endothelial cells that serve important functions in the response to inflammation and vascular injury. WPBs actively respond to different stimuli by regulated exocytosis leading to full or selective release of their contents. Cellular conditions and mechanisms that distinguish between these possibilities are only beginning to emerge. To address this we analyzed dynamic rearrangements of the actin cytoskeleton during histamine-stimulated, Ca2+-dependent WPB exocytosis. We show that most WPB fusion events are followed by a rapid release of von-Willebrand factor (VWF), the large WPB cargo, and that this occurs concomitant with a softening of the actin cortex by the recently described Ca2+-dependent actin reset (CaAR). However, a considerable fraction of WPB fusion events is characterized by a delayed release of VWF and observed after the CaAR reaction peak. These delayed VWF secretions are accompanied by an assembly of actin rings or coats around the WPB post-fusion structures and are also seen following direct elevation of intracellular Ca2+ by plasma membrane wounding. Actin ring/coat assembly at WPB post-fusion structures requires Rho GTPase activity and is significantly reduced upon expression of a dominant-active mutant of the formin INF2 that triggers a permanent CaAR peak-like sequestration of actin to the endoplasmic reticulum. These findings suggest that a rigid actin cortex correlates with a higher proportion of fused WPB which assemble actin rings/coats most likely required for efficient VWF expulsion and/or stabilization of a WPB post-fusion structure.This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech.

Membrane-binding domains in autophagy.

Autophagy is an intracellular degradation system conserved among eukaryotes that mediates the degradation of various biomolecules and organelles. During autophagy, a double membrane-bound organelle termed an autophagosome is synthesized de novo and delivers targets from the cytoplasm to the lysosomes for degradation. Autophagosome formation involves complex and dynamic membrane rearrangements, which are regulated by dozens of autophagy-related (Atg) proteins. In this review, we summarize our current knowledge of membrane-binding domains and motifs in Atg proteins and discuss their roles in autophagy.

Dynamic and Responsive DNA-like Polymers.

The synthesis of thiolactone monomers that mimic natural nucleosides and engage in robust ring opening polymerizations (ROP) is herein described. As each repeat unit contains a thioester functional group, dynamic rearrangement of the polymer is feasible via thiol-thioester exchange, demonstrated here by depolymerization of the polymers and coalescing of two polymers of different molecular weight or chemical composition. This approach constitutes the first step toward a platform that enables for the routine synthesis of sequence controlled polymers via dynamic template directed synthesis.

Rational Design of Superhydrophilic/Superoleophobic Surfaces for Oil-Water Separation via Thiol-Acrylate Photopolymerization.

We report a simple, rapid, and scalable strategy to fabricate surfaces exhibiting in-air superoleophobic/superhydrophilic wetting via sequential spray deposition and photopolymerization of nanoparticle-laden thiol–acrylate resins comprising both hydrophilic and oleophobic chemical constituents. The combination of spray deposition with nanoparticles provides hierarchical surface morphologies with both micro- and nanoscale roughness. Mapping the wetting behavior as a function of resin composition using high- and low-surface-tension liquid probes enabled facile identification of coatings that exhibit a range of wetting behavior, including superhydrophilic/superoleophilic, superhydrophobic/superoleophobic, and in-air superhydrophilic/superoleophobic wetting. In-air superhydrophilic/superoleophobic wetting was realized by a dynamic rearrangement of the interface to expose a greater fraction of hydrophilic moieties in response to contact with water. We show that these in-air superoleophobic/superhydrophilic coatings deposited onto porous supports enable separation of model oil–water emulsions with separation efficiencies up to 99.9% with 699 L·m–2 h–1 permeate flux when the superhydrophilic/superoleophobic coatings are paired with 0.45 μm nylon membrane supports.

Cell-Instructive Alginate Hydrogels Targeting RhoA.

Cellular processes involve dynamic rearrangement of the cytoskeleton. The GTPase RhoA plays a fundamental role in controlling cytoskeletal architecture. The phenotypic stability of chondrocytes is enhanced through inhibition of RhoA, whereas RhoA activation leads to dedifferentiation. We hypothesized that local inhibition of this pathway could induce chondrogenesis and cartilage regeneration. In this study, a novel alginate-derived hydrogel system was developed for sustained RhoA targeting. Specifically, an engineered variant of C. botulinum C3 transferase, a potent RhoA inhibitor, was immobilized onto a hydrogel to achieve sustained release and enzymatic activity. Chondrocytes encapsulated within this fully biocompatible, mechanically stable scaffold produced a stable collagen type II-rich matrix in vitro which matured over a six-week period. Samples were implanted subcutaneously in mice, and similar production of a collagen type II-rich matrix was observed. The intrinsically versatile system has the potential to treat a number of clinical disorders, including osteoarthritis, linked with RhoA dysregulation.

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes.

RNA-binding proteins (RBPs) play key roles in the post-transcriptional control of gene expression. Therefore, biochemical characterization of mRNA-protein complexes is essential to understanding mRNA regulation inferred by interacting proteins or non-coding RNAs. Herein, we describe a tandem RNA isolation procedure (TRIP) that enables the purification of endogenously formed mRNA-protein complexes from cellular extracts. The two-step protocol involves the isolation of polyadenylated mRNAs with antisense oligo(dT) beads and subsequent capture of an mRNA of interest with 3'-biotinylated 2'-O-methylated antisense RNA oligonucleotides, which can then be isolated with streptavidin beads. TRIP was used to recover in vivo crosslinked mRNA-ribonucleoprotein (mRNP) complexes from yeast, nematodes and human cells for further RNA and protein analysis. Thus, TRIP is a versatile approach that can be adapted to all types of polyadenylated RNAs across organisms to study the dynamic re-arrangement of mRNPs imposed by intracellular or environmental cues.

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

RNA-binding proteins (RBPs) play key roles in the post-transcriptional control of gene expression. Therefore, biochemical characterization of mRNA-protein complexes is essential to understanding mRNA regulation inferred by interacting proteins or non-coding RNAs. Herein, we describe a tandem RNA isolation procedure (TRIP) that enables the purification of endogenously formed mRNA-protein complexes from cellular extracts. The two-step protocol involves the isolation of polyadenylated mRNAs with antisense oligo(dT) beads and subsequent capture of an mRNA of interest with 3'-biotinylated 2'-O-methylated antisense RNA oligonucleotides, which can then be isolated with streptavidin beads. TRIP was used to recover in vivo crosslinked mRNA-ribonucleoprotein (mRNP) complexes from yeast, nematodes and human cells for further RNA and protein analysis. Thus, TRIP is a versatile approach that can be adapted to all types of polyadenylated RNAs across organisms to study the dynamic re-arrangement of mRNPs imposed by intracellular or environmental cues.