scholarly journals Coarse-grained simulations of actomyosin rings point to a nodeless model involving both unipolar and bipolar myosins

2017 ◽  
Author(s):  
Lam T. Nguyen ◽  
Matthew T. Swulius ◽  
Samya Aich ◽  
Mithilesh Mishra ◽  
Grant J. Jensen
Keyword(s):  
Experimental Data ◽  
Cell Division ◽  
Fluorescence Microscopy ◽  
Actin Filaments ◽  
Coarse Grained ◽  
Eukaryotic Cells ◽  
Ring Assembly ◽  
Assembly Result ◽  
Coarse Grained Simulations ◽  
Electron Cryotomography

AbstractCytokinesis in most eukaryotic cells is orchestrated by a contractile actomyosin ring. While many of the proteins involved are known, the mechanism of constriction remains unclear. Informed by existing literature and new 3D molecular details from electron cryotomography, here we develop 3D coarse-grained models of actin filaments, unipolar and bipolar myosins, actin crosslinkers, and membranes and simulate their nteractions. Exploring a matrix of possible actomyosin configurations suggested that node-based architectures ike those presently described for ring assembly result in membrane puckers not seen in EM images of real cells. Instead, the model that best matches data from fluorescence microscopy, electron cryotomography, and biochemical experiments is one in which actin filaments transmit force to the membrane through evenly-distributed, membrane-attached, unipolar myosins, with bipolar myosins in the ring driving contraction. While at this point this model is only favored (not proven), the work highlights the power of coarse-grained biophysical simulations to compare complex mechanistic hypotheses.Significance StatementIn most eukaryotes, a ring of actin and myosin drives cell division, but how the elements of the ring are arranged and constrict remain unclear. Here we use 3D coarse-grained simulations to explore various possibilities. Our simulations suggest that if actomyosin is arranged in nodes (as suggested by a popular model of ring assembly), the membrane distorts in ways not seen experimentally. Instead, actin and myosin are more ikely uniformly distributed around the ring. In the model that best fits experimental data, ring tension is generated by interactions between bipolar myosins and actin, and transmitted to the membrane via unipolar myosins. Technologically the study highlights how coarse-grained simulations can test specific mechanistic hypotheses by comparing their predicted outcomes to experimental results.

scholarly journals Coarse-grained simulations of actomyosin rings point to a nodeless model involving both unipolar and bipolar myosins

2018 ◽  
Vol 29 (11) ◽  
pp. 1318-1331 ◽  
Author(s):  
Lam T. Nguyen ◽  
Matthew T. Swulius ◽  
Samya Aich ◽  
Mithilesh Mishra ◽  
Grant J. Jensen
Keyword(s):  
Cell Wall ◽  
Actin Filaments ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Eukaryotic Cells ◽  
Ring Assembly ◽  
Assembly Result ◽  
Microscope Images ◽  
Coarse Grained Simulations ◽  
Electron Cryotomography

Cytokinesis in many eukaryotic cells is orchestrated by a contractile actomyosin ring. While many of the proteins involved are known, the mechanism of constriction remains unclear. Informed by the existing literature and new three-dimensional (3D) molecular details from electron cryotomography, here we develop 3D coarse-grained models of actin filaments, unipolar and bipolar myosins, actin cross-linkers, and membranes and simulate their interactions. Assuming that local force on the membrane results in inward growth of the cell wall, we explored a matrix of possible actomyosin configurations and found that node-based architectures like those presently described for ring assembly result in membrane puckers not seen in electron microscope images of real cells. Instead, the model that best matches data from fluorescence microscopy, electron cryotomography, and biochemical experiments is one in which actin filaments transmit force to the membrane through evenly distributed, membrane-attached, unipolar myosins, with bipolar myosins in the ring driving contraction. While at this point this model is only favored (not proven), the work highlights the power of coarse-grained biophysical simulations to compare complex mechanistic hypotheses.

scholarly journals A Model of the Open Pore MscL Based on Experimental Data and Restrained Coarse Grained Simulations

2012 ◽  
Vol 102 (3) ◽  
pp. 121a-122a
Author(s):  
Evelyne Deplazes ◽  
Dylan Jayatilaka ◽  
Martti Louhivuori ◽  
Siewert-Jan Marrink ◽  
Ben Corry
Keyword(s):  
Experimental Data ◽  
Coarse Grained ◽  
Coarse Grained Simulations

scholarly journals The formins Cdc12 and For3 cooperate during contractile ring assembly in cytokinesis

2013 ◽  
Vol 203 (1) ◽  
pp. 101-114 ◽  
Author(s):  
Valerie C. Coffman ◽  
Jennifer A. Sees ◽  
David R. Kovar ◽  
Jian-Qiu Wu
Keyword(s):  
Fluorescence Microscopy ◽  
Fission Yeast ◽  
Actin Filaments ◽  
De Novo ◽  
Ring Formation ◽  
Actin Assembly ◽  
Contractile Ring ◽  
Synthetic Lethal ◽  
Division Site ◽  
Ring Assembly

Both de novo–assembled actin filaments at the division site and existing filaments recruited by directional cortical transport contribute to contractile ring formation during cytokinesis. However, it is unknown which source is more important. Here, we show that fission yeast formin For3 is responsible for node condensation into clumps in the absence of formin Cdc12. For3 localization at the division site depended on the F-BAR protein Cdc15, and for3 deletion was synthetic lethal with mutations that cause defects in contractile ring formation. For3 became essential in cells expressing N-terminal truncations of Cdc12, which were more active in actin assembly but depended on actin filaments for localization to the division site. In tetrad fluorescence microscopy, double mutants of for3 deletion and cdc12 truncations were severely defective in contractile ring assembly and constriction, although cortical transport of actin filaments was normal. Together, these data indicate that different formins cooperate in cytokinesis and that de novo actin assembly at the division site is predominant for contractile ring formation.

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 A multiscale computational study of the conformation of the full-length intrinsically disordered protein MeCP2

2021 ◽  
Author(s):  
Cecilia Chavez-Garcia ◽  
Jerome Henin ◽  
Mikko Karttunen
Keyword(s):  
Experimental Data ◽  
Computational Study ◽  
Intrinsically Disordered Protein ◽  
Full Length ◽  
Conformational Space ◽  
Coarse Grained ◽  
Conformational Ensemble ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Coarse Grained Simulations

The malfunction of the Methyl CpG binding protein 2 (MeCP2) is associated to the Rett syndrome, one of the most common causes of cognitive impairment in females. MeCP2 is an intrinsically disordered protein (IDP), making its experimental characterization a challenge. There is currently no structure available for the full-length MeCP2 in any of the databases, and only the structure of its MBD domain has been solved. We used this structure to build a full-length model of MeCP2 by completing the rest of the protein via ab initio modelling. Using a combination of all-atom and coarse-grained simulations, we characterized its structure and dynamics as well as the conformational space sampled by the ID and TRD domains in the absence of the rest of the protein. The present work is the first computational study of the full-length protein. Two main conformations were sampled in the coarse-grained simulations: a globular structure similar to the one observed in the all-atom force field and a two-globule conformation. Our all-atom model is in good agreement with the available experimental data, predicting amino acid W104 to be buried, amino acids R111 and R133 to be solvent accessible, and having 4.1% of α-helix content, compared to the 4% found experimentally. Finally, we compared the model predicted by AlphaFold to our Modeller model. The model was not stable in water and underwent further folding. Together, these simulations provide a detailed (if perhaps incomplete) conformational ensemble of the full-length MeCP2, which is compatible with experimental data and can be the basis of further studies, e.g., on mutants of the protein or its interactions with its biological partners.

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.

Confocal microscopy of the cytoskeleton in living plant cells following microinjection of fluorescent probes

1993 ◽  
Vol 51 ◽  
pp. 130-131
Author(s):  
Ann Cleary
Keyword(s):  
Cell Division ◽  
Fluorescent Probes ◽  
Actin Filaments ◽  
Intracellular Transport ◽  
Cell Structure ◽  
Plant Cells ◽  
Cell Plate ◽  
Cell Cortex ◽  
Living Plant ◽  
Rhodamine Phalloidin

Microinjection of fluorescent probes into living plant cells reveals new aspects of cell structure and function. Microtubules and actin filaments are dynamic components of the cytoskeleton and are involved in cell growth, division and intracellular transport. To date, cytoskeletal probes used in microinjection studies have included rhodamine-phalloidin for labelling actin filaments and fluorescently labelled animal tubulin for incorporation into microtubules. From a recent study of Tradescantia stamen hair cells it appears that actin may have a role in defining the plane of cell division. Unlike microtubules, actin is present in the cell cortex and delimits the division site throughout mitosis. Herein, I shall describe actin, its arrangement and putative role in cell plate placement, in another material, living cells of Tradescantia leaf epidermis.The epidermis is peeled from the abaxial surface of young leaves usually without disruption to cytoplasmic streaming or cell division. The peel is stuck to the base of a well slide using 0.1% polyethylenimine and bathed in a solution of 1% mannitol +/− 1 mM probenecid.

Grand-Reaction Method for Simulations of Ionization Equilibria and Ion Partitioning in a Broad Range of pH and Ionic Strength

2019 ◽  
Author(s):  
Jonas Landsgesell ◽  
Oleg Rud ◽  
Pascal Hebbeker ◽  
Raju Lunkad ◽  
Peter Košovan ◽  
...  
Keyword(s):  
Mean Field ◽  
Coarse Grained ◽  
Reactive System ◽  
Acid Base ◽  
Buffer Solution ◽  
Reaction Method ◽  
Ionization Equilibria ◽  
Coarse Grained Simulations ◽  
Ph Range ◽  
Weak Polyelectrolytes

We introduce the grand-reaction method for coarse-grained simulations of acid-base equilibria in a system coupled to a reservoir at a given pH and concentration of added salt. It can be viewed as an extension of the constant-pH method and the reaction ensemble, combining explicit simulations of reactions within the system, and grand-canonical exchange of particles with the reservoir. Unlike the previously introduced methods, the grand-reaction method is applicable to acid-base equilibria in the whole pH range because it avoids known artifacts. However, the method is more general, and can be used for simulations of any reactive system coupled to a reservoir of a known composition. To demonstrate the advantages of the grand-reaction method, we simulated a model system: A solution of weak polyelectrolytes in equilibrium with a buffer solution. By carefully accounting for the exchange of all constituents, the method ensures that all chemical potentials are equal in the system and in the multi-component reservoir. Thus, the grand-reaction method is able to predict non-monotonic swelling of weak polyelectrolytes as a function of pH, that has been known from mean-field predictions and from experiments but has never been observed in coarse-grained simulations. Finally, we outline possible extensions and further generalizations of the method, and provide a set of guidelines to enable safe usage of the method by a broad community of users.<br><br>

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