scholarly journals Insights into the cooperative nature of ATP hydrolysis in actin filaments

2018 ◽  
Author(s):  
Harshwardhan H. Katkar ◽  
Aram Davtyan ◽  
Aleksander E. P. Durumeric ◽  
Glen M. Hocky ◽  
Anthony C. Schramm ◽  
...  
Keyword(s):  
Actin Filament ◽  
Actin Filaments ◽  
Atp Hydrolysis ◽  
Molecular System ◽  
Experimental Studies ◽  
Monomer Concentration ◽  
Growth Dynamics ◽  
Coarse Grained ◽  
Subtle Change ◽  
Internal States

ABSTRACTActin filaments continually assemble and disassemble within a cell. Assembled filaments “age” as a bound nucleotide ATP within each actin subunit quickly hydrolyzes, followed by a slower release of the phosphate Pi, leaving behind a bound ADP. This subtle change in nucleotide state of actin subunits affects filament rigidity as well as its interactions with binding partners. We present here a systematic multiscale ultra-coarse-graining (UCG) approach that provides a computationally efficient way to simulate a long actin filament undergoing ATP hydrolysis and phosphate release reactions, while systematically taking into account available atomistic details. The slower conformational changes and their dependence on the chemical reactions are simulated with the UCG model by assigning internal states to the coarse-grained sites. Each state is represented by a unique potential surface of a local heterogeneous elastic network. Internal states undergo stochastic transitions that are coupled to conformations of the underlying molecular system. The UCG model reproduces mechanical properties of the filament and allows us to study whether fluctuations in actin subunits produce cooperative aging in the filament. Our model predicts that nucleotide state of neighboring subunit significantly modulates the reaction kinetics, implying cooperativity in ATP hydrolysis and Pi release. We further systematically coarse-grain the system into a Markov state model that incorporates assembly and disassembly, facilitating a direct comparison with previously published models. We find that cooperativity in ATP hydrolysis and Pi release significantly affects the filament growth dynamics only near the critical G-actin monomer concentration, while both cooperative and random mechanisms show similar growth dynamics far from the critical concentration. In contrast, filament composition in terms of the bound nucleotide distribution varies significantly at all monomer concentrations studied. These results provide new insights into the cooperative nature of ATP hydrolysis and Pi release and the implications it has for actin filament properties, providing novel predictions for future experimental studies.

scholarly journals Modeling myosin Va liposome transport through actin filament networks reveals a percolation threshold that modulates transport properties

2021 ◽  
Author(s):  
Sam Walcott ◽  
David M Warshaw
Keyword(s):  
Phase Transition ◽  
Actin Filament ◽  
Actin Filaments ◽  
Three Dimensional ◽  
Fold Increase ◽  
Coarse Grained ◽  
Actin Network ◽  
Cargo Delivery ◽  
Myosin Va ◽  
Filament Networks

Myosin Va (myoVa) motors transport membrane-bound cargo through three-dimensional, intracellular actin filament networks. We developed a coarse-grained, in silico model to predict how actin filament density (3-800 filaments) within a randomly oriented actin network affects fluid-like liposome (350nm vs. 1,750nm) transport by myoVa motors. 5,000 simulated liposomes transported within each network adopted one of three states: transport, tug of war, or diffusion. Diffusion due to liposome detachment from actin rarely occurred given at least 10 motors on the liposome surface. However, with increased actin density, liposomes transitioned from primarily directed transport on single actin filaments to an apparent random walk, resulting from a mixture of transport and tug of wars as the probability of encountering additional actin filaments increased. This phase transition arises from a percolation phase transition at a critical number of accessible actin filaments, Nc. Nc, is a geometric property of the actin network that depends only on the position and polarity of the actin filaments and the liposome diameter, as evidenced by a five-fold increase in liposome diameter resulting in a five-fold decrease in Nc. Thus, in cells, actin network density and cargo size may be regulated to match cargo delivery to the cell's physiological demands.

scholarly journals Modeling myosin Va liposome transport through actin filament networks reveals a percolation threshold that modulates transport properties

2021 ◽  
Author(s):  
S. Walcott ◽  
D. M. Warshaw
Keyword(s):  
Phase Transition ◽  
Actin Filament ◽  
Actin Filaments ◽  
Three Dimensional ◽  
Fold Increase ◽  
Coarse Grained ◽  
Actin Network ◽  
Transport Distance ◽  
Myosin Va ◽  
Filament Networks

Myosin Va (myoVa) motors transport membrane-bound cargo through three-dimensional, intracellular actin filament networks. We developed a coarse-grained, in silico model to predict how actin filament density (3-800 filaments) within a randomly oriented actin network affects fluid-like liposome (350nm vs. 1,750nm) transport by myoVa motors. 5,000 simulated liposomes transported within each network adopted one of three states: transport, tug of war, or diffusion. Diffusion due to liposome detachment from actin rarely occurred given at least 10 motors on the liposome surface. However, with increased actin density, liposomes transitioned from primarily directed transport on single actin filaments to an apparent random walk, resulting from a mixture of transport and tug of wars as the probability of encountering additional actin filaments increased. This phase transition arises from a percolation phase transition at a critical number of accessible actin filaments, Nc. Nc is a geometric property of the actin network that depends only on the position and polarity of the actin filaments, transport distance, and the liposome diameter, as evidenced by a five-fold increase in liposome diameter resulting in a five-fold decrease in Nc. Thus, in cells, actin network density and cargo size may be regulated to match cargo delivery to the cell's physiological demands. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text]

scholarly journals Mathematical Modeling of Endocytic Actin Patch Kinetics in Fission Yeast: Disassembly Requires Release of Actin Filament Fragments

2010 ◽  
Vol 21 (16) ◽  
pp. 2905-2915 ◽  
Author(s):  
Julien Berro ◽  
Vladimir Sirotkin ◽  
Thomas D. Pollard
Keyword(s):  
Fission Yeast ◽  
Actin Filament ◽  
Actin Filaments ◽  
Atp Hydrolysis ◽  
Alternative Mechanism ◽  
Rapid Loss ◽  
Capping Protein ◽  
Actin Patch ◽  
Over Time

We used the dendritic nucleation hypothesis to formulate a mathematical model of the assembly and disassembly of actin filaments at sites of clathrin-mediated endocytosis in fission yeast. We used the wave of active WASp recruitment at the site of the patch formation to drive assembly reactions after activation of Arp2/3 complex. Capping terminated actin filament elongation. Aging of the filaments by ATP hydrolysis and γ-phosphate dissociation allowed actin filament severing by cofilin. The model could simulate the assembly and disassembly of actin and other actin patch proteins using measured cytoplasmic concentrations of the proteins. However, to account quantitatively for the numbers of proteins measured over time in the accompanying article ( Sirotkin et al., 2010 , MBoC 21: 2894–2904), two reactions must be faster in cells than in vitro. Conditions inside the cell allow capping protein to bind to the barbed ends of actin filaments and Arp2/3 complex to bind to the sides of filaments faster than the purified proteins in vitro. Simulations also show that depolymerization from pointed ends cannot account for rapid loss of actin filaments from patches in 10 s. An alternative mechanism consistent with the data is that severing produces short fragments that diffuse away from the patch.

scholarly journals Gating Mechanisms during Actin Filament Elongation by Formins

2018 ◽  
Author(s):  
Fikret Aydin ◽  
Naomi Courtemanche ◽  
Thomas D. Pollard ◽  
Gregory A. Voth
Keyword(s):  
Molecular Dynamics ◽  
Actin Filament ◽  
Actin Filaments ◽  
Coarse Grained ◽  
Gating Mechanisms ◽  
Helical Twist ◽  
Two Factors ◽  
Time Average ◽  
Coarse Grained Simulations ◽  
Dynamics Simulations

ABSTRACTFormins play an important role in the polymerization of unbranched actin filaments, and particular formins slow elongation by 5-95%. We studied the interactions between actin and the FH2 domains of formins Cdc12, Bni1 and mDia1 to understand the factors underlying their different rates of polymerization. All-atom molecular dynamics simulations revealed two factors that influence actin filament elongation and correlate with the rates of elongation. First, FH2 domains can sterically block the addition of new actin subunits. Second, FH2 domains flatten the helical twist of the terminal actin subunits, making the end less favorable for subunit addition. Coarse-grained simulations over longer time scales support these conclusions. The simulations show that filaments spend time in states that either allow or block elongation. The rate of elongation is a time-average of the degree to which the formin compromises subunit addition rather than the formin-actin complex literally being in ‘open’ or ‘closed’ states.

scholarly journals Twinfilin bypasses assembly conditions and actin filament aging to drive barbed end depolymerization

2020 ◽  
Vol 220 (1) ◽  
Author(s):  
Shashank Shekhar ◽  
Gregory J. Hoeprich ◽  
Jeff Gelles ◽  
Bruce L. Goode
Keyword(s):  
Actin Filament ◽  
Actin Filaments ◽  
Atp Hydrolysis ◽  
Tirf Microscopy ◽  
Actin Networks ◽  
Rapid Elongation ◽  
In Cells

Cellular actin networks grow by ATP-actin addition at filament barbed ends and have long been presumed to depolymerize at their pointed ends, primarily after filaments undergo “aging” (ATP hydrolysis and Pi release). The cytosol contains high levels of actin monomers, which favors assembly over disassembly, and barbed ends are enriched in ADP-Pi actin. For these reasons, the potential for a barbed end depolymerization mechanism in cells has received little attention. Here, using microfluidics-assisted TIRF microscopy, we show that mouse twinfilin, a member of the ADF-homology family, induces depolymerization of ADP-Pi barbed ends even under assembly-promoting conditions. Indeed, we observe in single reactions containing micromolar concentrations of actin monomers the simultaneous rapid elongation of formin-bound barbed ends and twinfilin-induced depolymerization of free barbed ends. The data show that twinfilin catalyzes dissociation of subunits from ADP-Pi barbed ends and thereby bypasses filament aging prerequisites to disassemble newly polymerized actin filaments.

scholarly journals Actin filaments undergo limited subunit exchange in physiological salt conditions.

1982 ◽  
Vol 94 (2) ◽  
pp. 316-324 ◽  
Author(s):  
J D Pardee ◽  
P A Simpson ◽  
L Stryer ◽  
J A Spudich
Keyword(s):  
Skeletal Muscle ◽  
Energy Transfer ◽  
Actin Filament ◽  
Actin Filaments ◽  
Atp Hydrolysis ◽  
Fluorescence Energy Transfer ◽  
Subunit Exchange ◽  
Filament Assembly ◽  
Fluorescence Energy ◽  
Energy Acceptor

The exchange of actin filament subunits for unpolymerized actin or for subunits in other filaments has been quantitated by three experimental techniques: fluorescence energy transfer, incorporation of 35S-labeled actin monomers into unlabeled actin filaments, and exchange of [14C]ATP with filament-bound ADP. In the fluorescence energy transfer experiments, actin labeled with 5-(iodoacetamidoethyl)aminonaphthalene-1-sulfonic acid (IAENS) served as the fluorescent energy donor, and actin labeled with either fluorescein-5-isothiocyanate (FITC) or fluorescein-5-maleimide (FM) served as the energy acceptor. Fluorescent-labeled actins from Dictyostelium amoebae and rabbit skeletal muscle were very similar to their unlabeled counterparts with respect to critical actin concentration for filament assembly, assembly rate, ATP hydrolysis upon assembly, and steady-state ATPase. As evidenced by two different types of fluorescence energy transfer experiments, less than 5% of the actin filament subunits exchanged under a variety of buffer conditions at actin concentrations greater than 0.5 mg/ml. At all actin concentrations limited exchange to a plateau level occurred with a half-time of about 20 min. Nearly identical results were obtained when exchange was quantitated by incorporation of 35S-labeled Dictyostelium actin monomers into unlabeled muscle actin or Dictyostelium actin filaments. Furthermore, the proportion of filament-bound ADP which exchanged with [14C]-ATP was nearly the same as actin subunit exchange measured by fluorescence energy transfer and 35S-labeled actin incorporation. These experiments demonstrate that under approximately physiologic ionic conditions only a small percentage of subunits in highly purified skeletal muscle or Dictyostelium F-actin participate in exchange.

scholarly journals Gating mechanisms during actin filament elongation by formins

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Fikret Aydin ◽  
Naomi Courtemanche ◽  
Thomas D Pollard ◽  
Gregory A Voth
Keyword(s):  
Molecular Dynamics ◽  
Actin Filament ◽  
Actin Filaments ◽  
Coarse Grained ◽  
Gating Mechanisms ◽  
Helical Twist ◽  
Two Factors ◽  
Time Average ◽  
Coarse Grained Simulations ◽  
Dynamics Simulations

Formins play an important role in the polymerization of unbranched actin filaments, and particular formins slow elongation by 5–95%. We studied the interactions between actin and the FH2 domains of formins Cdc12, Bni1 and mDia1 to understand the factors underlying their different rates of polymerization. All-atom molecular dynamics simulations revealed two factors that influence actin filament elongation and correlate with the rates of elongation. First, FH2 domains can sterically block the addition of new actin subunits. Second, FH2 domains flatten the helical twist of the terminal actin subunits, making the end less favorable for subunit addition. Coarse-grained simulations over longer time scales support these conclusions. The simulations show that filaments spend time in states that either allow or block elongation. The rate of elongation is a time-average of the degree to which the formin compromises subunit addition rather than the formin-actin complex literally being in ‘open’ or ‘closed’ states.

Microbiological substantiation of application of phytopreparations in treatment of inflammatory periodontal diseases

2019 ◽  
Vol 24 (3) ◽  
pp. 196-202 ◽  
Author(s):  
S. A. Abdurakhmanova ◽  
G. S. Runova ◽  
M. S. Podporin ◽  
E. V. Tsareva ◽  
E. V. Ippolitov ◽  
...  
Keyword(s):  
Tooth Loss ◽  
Periodontal Diseases ◽  
Adult Population ◽  
Experimental Studies ◽  
Herbal Medicines ◽  
Growth Dynamics ◽  
Integrated Approach ◽  
Bacterial Populations ◽  
Streptococcus Constellatus ◽  
Urgent Task

Relevance: Inflammatory-destructive periodontal diseases are the most complicated and became the main cause of tooth loss in adult population. Herbal medicines have a variety of pharmacological properties, so the development and introduction of new forms for the treatment of inflammatory periodontal diseases is an urgent task today.Purpose – experimental evaluation of effectiveness of the use of herbal medicines “Tonzinal” and “CM-1” in relation to the priority periodontal pathogenes.Materials and methods: in experimental studies, the basis for the experiment was the system for the cultivation of microorganisms in real time – the Revers-Spinner RTS-1 bioreactor. With the priority strains of periodontitis pathogens, the study of the growth dynamics of the culture was carried out in several parallels.Results: herbal medicines “CM-1” and “Tonsinal” has a multilateral therapeutic effect, exerting a diverse influence on the key stages of development of such bacterial populations as Aggregatibacter actinomycetemcomitans, Streptococcus constellatus, Candida albicans.Conclusion: tan integrated approach in the treatment of patients with inflammatory periodontal diseases is promising and will contribute to a more prolonged remission and increase the effectiveness of treatment. 

scholarly journals Specification of Actin Filament Function and Molecular Composition by Tropomyosin Isoforms

2003 ◽  
Vol 14 (3) ◽  
pp. 1002-1016 ◽  
Author(s):  
Nicole S. Bryce ◽  
Galina Schevzov ◽  
Vicki Ferguson ◽  
Justin M. Percival ◽  
Jim J.-C. Lin ◽  
...  
Keyword(s):  
Cell Size ◽  
Functional Properties ◽  
Actin Filament ◽  
Actin Filaments ◽  
Myosin Ii ◽  
Molecular Composition ◽  
Cellular Migration ◽  
Stress Fibers ◽  
Human Homologue ◽  
Tropomyosin Isoforms

The specific functions of greater than 40 vertebrate nonmuscle tropomyosins (Tms) are poorly understood. In this article we have tested the ability of two Tm isoforms, TmBr3 and the human homologue of Tm5 (hTM5NM1), to regulate actin filament function. We found that these Tms can differentially alter actin filament organization, cell size, and shape. hTm5NM1was able to recruit myosin II into stress fibers, which resulted in decreased lamellipodia and cellular migration. In contrast, TmBr3 transfection induced lamellipodial formation, increased cellular migration, and reduced stress fibers. Based on coimmunoprecipitation and colocalization studies, TmBr3 appeared to be associated with actin-depolymerizing factor/cofilin (ADF)-bound actin filaments. Additionally, the Tms can specifically regulate the incorporation of other Tms into actin filaments, suggesting that selective dimerization may also be involved in the control of actin filament organization. We conclude that Tm isoforms can be used to specify the functional properties and molecular composition of actin filaments and that spatial segregation of isoforms may lead to localized specialization of actin filament function.

scholarly journals Stimulus-response uncoupling in the neutrophil. Adenosine A2-receptor occupancy inhibits the sustained, but not the early, events of stimulus transduction in human neutrophils by a mechanism independent of actin-filament formation

1992 ◽  
Vol 281 (3) ◽  
pp. 631-635 ◽  
Author(s):  
B N Cronstein ◽  
K A Haines
Keyword(s):  
Actin Filament ◽  
Adenosine Receptor ◽  
Actin Filaments ◽  
Cytochalasin B ◽  
Receptor Occupancy ◽  
Neutrophil Activation ◽  
Filament Formation ◽  
Stimulus Response ◽  
Adenosine A2 Receptor ◽  
A2 Receptors

Generation of superoxide anion (O2-) in response to occupancy of neutrophil chemoattractant receptors requires both early events (‘triggering’) and sustained signals (‘activation’). We have previously demonstrated that occupancy of adenosine A2 receptors inhibits O2- generation by neutrophils. In parallel, adenosine-receptor occupancy promotes association of bound N-formylmethionyl-leucyl-phenylalanine (fMLP) receptors with the cytoskeleton, a process associated with termination of neutrophil activation (stimulus-response uncoupling). We undertook this study to determine whether inhibition of neutrophil function by adenosine-receptor occupancy requires intact actin filaments and to examine the effect of adenosine-receptor occupancy on the stimulated generation of intracellular signals involved in neutrophil triggering and activation. Occupancy of adenosine A2 receptors by 5′-N-ethylcarboxamidoadenosine (NECA, 1 microM) significantly increased (130 +/- 1% of control, P less than 0.001, n = 3) association of [3H]fMLP with cytoskeletal preparations. Cytochalasin B (5 micrograms/ml), an agent which disrupts actin filaments, completely blocked association of [3H]fMLP with cytoskeletal preparations, as previously reported. However, NECA markedly increased association of [3H]fMLP with the cytoskeleton even in the presence of cytochalasin B (P less than 0.0002). Moreover, NECA did not significantly affect either the early (30s) or the late (5 min) formation of actin filaments after stimulation by chemoattractant (fMLP, 0.1-100 nM). Cytochalasin B markedly inhibited actin-filament formation by stimulated neutrophils, and NECA did not reverse the effect of cytochalasin B on actin-filament formation. Adenosine-receptor occupancy did not affect the rapid peak in diacylglycerol generation (less than or equal to 15 s) from either [3H]arachidonate- or [14C]glycerol-labelled phospholipid pools. However, as would be predicted if occupancy of the adenosine receptor was a signal for early termination of cell activation, NECA (1 microM) markedly diminished the slow sustained generation of diacylglycerol. These results suggest that adenosine-A2-receptor occupancy does not affect triggering of the neutrophil, but that occupancy of adenosine receptors is an early signal for the termination of neutrophil activation, i.e. the ‘premature’ finish of signal transduction. Moreover, these data indicate that at least two pathways are available for increasing the association of ligated chemoattractant receptors with the cytoskeleton of neutrophils: F-actin-dependent and -independent.

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