Depolymerization Dynamics Research Articles

Bacteria face trade-offs in the decomposition of complex biopolymers.

Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system's complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.

Actin Filament Barbed-End Depolymerization by Combined Action of Profilin, Cofilin, and Twinfilin

Cellular actin dynamics results from the collective action of hundreds of regulatory proteins, majority of which target actin filaments at their barbed ends. Three key actin binding proteins—profilin, cofilin, and twinfilin—individually depolymerize filament barbed ends. Notwithstanding recent leaps in our understanding of their individual action, how they collectively regulate filament dynamics remains an open question. In the absence of direct and simultaneous visualization of these proteins at barbed ends, gaining mechanistic insights has been challenging. We have here investigated multicomponent dynamics of profilin, cofilin, and twinfilin using a hybrid approach that combines high-throughput single filament experiments with theory. We discovered that while twinfilin competes with profilin, it promotes binding of cofilin to filament sides. Interestingly, contrary to previous expectations, we found that profilin and cofilin can simultaneously bind the same filament barbed end, resulting in its accelerated depolymerization. Our study reveals that pairwise interactions can effectively capture depolymerization dynamics in simultaneous presence of all three proteins. We thus believe that our approach of employing a theory-experiment dialog can potentially help decipher multicomponent regulation of actin dynamics. Published by the American Physical Society 2024

Impact of Copolymer Architecture on Demicellization and Cargo Release via Head-to-Tail Depolymerization of Hydrophobic Blocks or Branches.

Utilizing molecular dynamics simulations, we explored the demicellization and cargo release dynamics of linear and miktoarm copolymers, featuring one, two, and three hydrophobic blocks or branches, each capable of head-to-tail depolymerization. Our findings revealed that, under stoichiometric trigger molecule concentrations, miktoarms with three branches exhibited consistently faster depolymerization rates than those with two branches and linear copolymers. Conversely, at constant trigger molecule concentrations, the depolymerization rates of copolymers exhibited more complex behaviors influenced by two opposing factors: the excess of trigger molecules, which increased with a decrease in the number of hydrophobic branches or blocks, and simultaneous head-to-tail depolymerization, which intensified with an increasing number of branches. Our study elucidates the intricate interplay between copolymer architecture, trigger molecule concentrations, and depolymerization dynamics, providing valuable insights for the rational design of amphiphilic copolymers with tunable demicellization and cargo release properties.

A model of microtubule depolymerization by kinesin-8 motor proteins.

The dimeric kinesin-8 motors have the biological function of depolymerizing microtubules (MTs) from the plus end. However, the molecular mechanism of the depolymerization promoted by the kinesin-8 motors is still undetermined. Here, a model is proposed for the MT depolymerization by the kinesin-8 motors. Based on the model, the dynamics of depolymerization in the presence of the single motor at the MT plus end under no load and under load on the motor is studied theoretically. The dynamics of depolymerization in the presence of multiple motors at the MT plus end is also analyzed. The theoretical results explain well the available experimental data. The studies can also be applicable to other families of kinesin motors such as kinesin-13 mitotic centromere-associated kinesin motors that have the ability to depolymerize MTs.

Modeling cellular adhesion.

Cellular adhesion strength, described by the fraction of cells that detach from a surface for a range of applied shear stresses, is predictive of cancer cell migration in 2D and 3D environments and the overall metastatic potential of these cells. Simply stated, cell adhesion strength depends on the balance between cell-surface bond formation and breakage rates. This has been previously modeled as such using the concentration of adhesion proteins such as integrins, the cell-surface interaction area, and a shear force dependent bond breakage rate between the surface ligands and adhesion proteins. However, we have shown that changes in intracellular myosin motor activity, actin stress fibers and force responsive focal adhesion complex proteins can also influence cell adhesion strength and alter cell migration behavior. Using a computational model, we explore how various intracellular factors beyond the concentration of adhesion proteins, govern cell adhesion strengths as measured by shear flow analysis. Overall, our model focuses on 5 key cytoskeletal aspects and their impact on cellular adhesion because of their apparent relevance from previous studies. These include: average number of stress fibers per cell (dictated by f-actin and myosin concentrations), available integrins per stress fiber (dictated by integrin concentration and actin branching), likelihood of bound paxillin, active myosin motors (dictated by myosin light chain phosphorylation), and finally actin polymerization and depolymerization dynamics (governed by time between depolymerization and repolymerization events). The model is further used as a predictive tool in order to determine the particular intracellular factors differentiating cancer strains. The goal of this research is to unravel biomechanical and consequently biochemical differences between cytoskeletal elements of highly metastatic and non-metastatic cancer cells.

Competitive binding of independent extension and retraction motors explains the quantitative dynamics of type IV pili

Type IV pili (TFP) function through cycles of extension and retraction. The coordination of these cycles remains mysterious due to a lack of quantitative measurements of multiple features of TFP dynamics. Here, we fluorescently label TFP in the pathogen Pseudomonas aeruginosa and track full extension and retraction cycles of individual filaments. Polymerization and depolymerization dynamics are stochastic; TFP are made at random times and extend, pause, and retract for random lengths of time. TFP can also pause for extended periods between two extension or two retraction events in both wild-type cells and a slowly retracting PilT mutant. We developed a biophysical model based on the stochastic binding of two dedicated extension and retraction motors to the same pilus machine that predicts the observed features of the data with no free parameters. We show that only a model in which both motors stochastically bind and unbind to the pilus machine independent of the piliation state of the machine quantitatively explains the experimentally observed pilus production rate. In experimental support of this model, we show that the abundance of the retraction motor dictates the pilus production rate and that PilT is bound to pilus machines even in their unpiliated state. Together, the strong quantitative agreement of our model with a variety of experiments suggests that the entire repetitive cycle of pilus extension and retraction is coordinated by the competition of stochastic motor binding to the pilus machine, and that the retraction motor is the major throttle for pilus production.

Tubulin Maytansine Site Binding Ligands and their Applications as MTAs and ADCs for Cancer Therapy.

Microtubule Targeting Agents (MTAs) represent the most successful anticancer drugs for cancer chemotherapy. Through interfering with the tubulin polymerization and depolymerization dynamics, MTAs influence intracellular transport and cell signal pathways, inhibit cell mitosis and cell proliferation, and induce cell apoptosis and death. The tubulin maytansine site binding agents are natural or nature-derived products that represent one type of the MTAs that inhibit tubulin polymerization and exhibit potent antitumor activity both in vitro and in vivo. They are used as Antibody-Drug Conjugates (ADCs) in cancer chemotherapy. Using SciFinder® as a tool, the publications about maytansine, its derivatives, maytansine binding site, maytansine site binding agents and their applications as MTAs for cancer therapy were surveyed with an exclusion on those published as patents. The latest progresses in clinical trials were obtained from the clinical trial web. This article presents an introduction about MTAs, maytansine, maytansine binding site and its ligands, the applications of these ligands as MTAs and ADCs in cancer therapy. The maytansine site binding agents are powerful MTAs for cancer chemotherapy. The maytansine site ligands-based ADCs are used in clinic or under clinical trials as cancer targeted therapy to improve their selectivity and to reduce their side effects. Further improvements in the delivery efficiency of the ADCs will benefit the patients in cancer targeted therapy.

On the Role of Interacting Particles and Limited Resources in the Regulation of Lattice Length Dynamics

Motivated by the significant effect of particle–particle interactions on the driven stochastic transport system, we examine how interacting particles control the lattice polymerization and depolymerization dynamics under the restricted supply of involved resources. We carried out a theoretical analysis based on the simple mean-field and cluster mean-field theory to predict the fundamental role of interactions on the steady-state length dynamics. It has been detected that there is a strong correlation between the lattice length dynamics and the concentration of the total number of lattice sites in the reservoir. For lower and higher values of available resources, depolymerization and polymerization process dominates the lattice dynamics, respectively, while for intermediate values of resources we observe a competition between polymerization and depolymerization kinetics. Further, it is examined that for a specific range of interaction energy E, the system remains in low density phase, on the contrary, for its significantly higher value, the system transits to high-density phase. In contrast to the high density phase, it is observed that in low density phase, lattice length decreases with an increase in interaction strength. Finally, the theoretical outcomes are validated with extensive Monte Carlo simulations.

Computational analysis of filament polymerization dynamics in cytoskeletal networks.

The polymerization-depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material.

Depolymerization dynamics study of poly-alpha-methylstyrene

Polymers are macromolecus composed of repeated monomer subunits, which construct the fabulous world of DNA, protein, cellulose, rubber, plastic, etc. and possess crucial positions in fields like life science, chemistry industry and material preparation with special demands. However, the performance of polymer would decay because of the influence of environment effects and even be depolymerized. While under particular scenarios, such a decomposition process might be valuable. Poly-alpha-methylstyrene (PAMS) is the substrate materials for preparing glow discharge polymer (GDP) shell which coats the fuel target for inertial confinement fusion. The key step for its involvement is to depolymerize into single molecules under high temperature so that it can escape through the space among GDP molecules which has deposited on it, and then leaves only the GDP shell. Besides of this special application, the atomic level understanding of depolymerization processes is also at the key position to modulate other reactions involving polymer materials. Here, through molecular dynamic simulation based on density functional tight-binding methods containing dispersion correction (DFTB-D), we demonstrate the typical dissociation of sequential poly-alpha- methylstyrene (PAMS) tetramer fragments with unsaturation on both ends, on the C- end and on the CH2- end, respectively. DFTB method we used here is an approximation based on the second order expansion of the density functional theory (DFT) total energy with respect to charge density variation relative to a chosen reference density. It promotes the efficiency of DFT method around two to three orders meanwhile remains acceptable precision for electronic structure calculation and large-scale quantum dynamic simulations. The reliability of the method has been admitted in massive researches, especially those on carbon-based molecules and organic systems. Our results show, with the temperature of 500 and 600 K, the dissociation of PAMS fragments is implemented by depolymerization processes, where monomers separate from one of the unsaturated ends one by one, and rising temperature could reasonably accelerate the reaction. Further simulations of a longer hexamer PAMS fragment under 600 K indicates the length effect won’t cause qualitative influence on the depolymerization process. The electronic structures of these three fragments indicate both the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) are localized at the bond-breaking unsaturated ends, which supports the prediction of dynamic simulations for reaction sits. Furthermore, the DFTB-D electronic structure calculations following the C—C bond breaking steps at different possible sites along the backbone chain also show the preference of the reaction to unsaturated end sites, from the view of potential energy surface. Spin distribution analysis also reflects the energy curves respect to the different depolymerization processes are closely related to the spin-polarized electronic structures of corresponding products. These results give a representative atomic-level prospect about the decomposition process of sequential PAMS under high temperature with detailed interpretation on the reaction sit preference and order, which may be informative for preparation of relative device. Besides, we hope this theoretical study could offer a fundamental reference for understanding the mechanism of decomposition for polymer materials beyond PAMS and spread across the wonderful microscopic world.

Bacterial Cell Division: A Swirling Ring to Rule Them All?

FtsZ, a tubulin homologue and the major constituent of the bacterial Z ring, hasbeen shown to assemble into curved filament bundles, which exhibit GTP-hydrolysis-dependent turnover. Surprisingly, the presence of its membrane adaptor FtsA renders this turnover directional, inducing treadmilling and collective circular motion of filaments invitro.

Mechanics of severing for large microtubule complexes revealed by coarse-grained simulations

We investigate the mechanical behavior of microtubule (MT) protofilaments under the action of bending forces, ramped up linearly in time, to provide insight into the severing of MTs by microtubule associated proteins (MAPs). We used the self-organized polymer model which employs a coarse-grained description of the protein chain and ran Brownian dynamics simulations accelerated on graphics processing units that allow us to follow the dynamics of a MT system on experimental timescales. Our study focused on the role played in the MT depolymerization dynamics by the inter-tubulin contacts a protofilament experiences when embedded in the MT lattice, and the number of binding sites of MAPs on MTs. We found that proteins inducing breaking of MTs must have at least three attachment points on any tubulin dimer from an isolated protofilament. In contrast, two points of contact would suffice when dimers are located in an intact MT lattice, in accord with experimental findings on MT severing proteins. Our results show that confinement of a protofilament in the MT lattice leads to a drastic reduction in the energy required for the removal of tubulin dimers, due to the drastic reduction in entropy. We further showed that there are differences in the energetic requirements based on the location of the dimer to be removed by severing. Comparing the energy of tubulin dimers removal revealed by our simulations with the amount of energy resulting from one ATP hydrolysis, which is the source of energy for all MAPs, we provided strong evidence for the experimental finding that severing proteins do not bind uniformly along the MT wall.

Dynamics and Regulation of RecA Polymerization and De-Polymerization on Double-Stranded DNA

The RecA filament formed on double-stranded (ds) DNA is proposed to be a functional state analogous to that generated during the process of DNA strand exchange. RecA polymerization and de-polymerization on dsDNA is governed by multiple physiological factors. However, a comprehensive understanding of how these factors regulate the processes of polymerization and de-polymerization of RecA filament on dsDNA is still evolving. Here, we investigate the effects of temperature, pH, tensile force, and DNA ends (in particular ssDNA overhang) on the polymerization and de-polymerization dynamics of the E. coli RecA filament at a single-molecule level. Our results identified the optimal conditions that permitted spontaneous RecA nucleation and polymerization, as well as conditions that could maintain the stability of a preformed RecA filament. Further examination at a nano-meter spatial resolution, by stretching short DNA constructs, revealed a striking dynamic RecA polymerization and de-polymerization induced saw-tooth pattern in DNA extension fluctuation. In addition, we show that RecA does not polymerize on S-DNA, a recently identified novel base-paired elongated DNA structure that was previously proposed to be a possible binding substrate for RecA. Overall, our studies have helped to resolve several previous single-molecule studies that reported contradictory and inconsistent results on RecA nucleation, polymerization and stability. Furthermore, our findings also provide insights into the regulatory mechanisms of RecA filament formation and stability in vivo.

Actin recruitment to the Chlamydia inclusion is spatiotemporally regulated by a mechanism that requires host and bacterial factors.

The ability to exit host cells at the end of their developmental growth is a critical step for the intracellular bacterium Chlamydia. One exit strategy, extrusion, is mediated by host signaling pathways involved with actin polymerization. Here, we show that actin is recruited to the chlamydial inclusion as a late event, occurring after 20 hours post-infection (hpi) and only within a subpopulation of cells. This event increases significantly in prevalence and extent from 20 to 68 hpi, and actin coats strongly correlated with extrusions. In contrast to what has been reported for other intracellular pathogens, actin nucleation on Chlamydia inclusions did not ‘flash’, but rather exhibited moderate depolymerization dynamics. By using small molecule agents to selectively disrupt host signaling pathways involved with actin nucleation, modulate actin polymerization dynamics and also to disable the synthesis and secretion of chlamydial proteins, we further show that host and bacterial proteins are required for actin coat formation. Transient disruption of either host or bacterial signaling pathways resulted in rapid loss of coats in all infected cells and a reduction in extrusion formation. Inhibition of Chlamydia type III secretion also resulted in rapid loss of actin association on inclusions, thus implicating chlamydial effector proteins(s) as being central factors for engaging with host actin nucleating factors, such as formins. In conclusion, our data illuminate the host and bacterial driven process by which a dense actin matrix is dynamically nucleated and maintained on the Chlamydia inclusion. This late stage event is not ubiquitous for all infected cells in a population, and escalates in prevalence and extent throughout the developmental cycle of Chlamydia, culminating with their exit from the host cell by extrusion. The initiation of actin recruitment by Chlamydia appears to be novel, and may serve as an upstream determinant of the extrusion mechanism.

History-Dependent Depolymerization of Actin Filaments

Depolymerizing cytoskeletal filaments are involved in cell division, cell motility, and other cellular functions. Understanding the dynamics of depolymerization is as important as understanding the dynamics of polymerization. We study nonequilibrium depolymerization of actin filaments using a simple two-state model. We show that the polymerization history influences the dynamics of depolymerization as well as the length fluctuations during depolymerization. We also simulate depolymerization under different experimentally feasible conditions. Under conditions of constant concentration, we show that the depolymerization happens in two regimes. Under the conditions of mass conservation, the depolymerization can have three regimes.

Depolymerization dynamics of individual filaments of bacterial cytoskeletal protein FtsZ

We report observation and analysis of the depolymerization filaments of the bacterial cytoskeletal protein FtsZ (filament temperature-sensitive Z) formed on a mica surface. At low concentration, proteins adsorbed on the surface polymerize forming curved filaments that close into rings that remain stable for some time before opening irreversibly and fully depolymerizing. The distribution of ring lifetimes (T) as a function of length (N), shows that the rate of ring aperture correlates with filament length. If this ring lifetime is expressed as a bond survival time, (T(b)≡NT), this correlation is abolished, indicating that these rupture events occur randomly and independently at each monomer interface. After rings open irreversibly, depolymerization of the remaining filaments is fast, but can be slowed down and followed using a nonhydrolyzing GTP analogue. The histogram of depolymerization velocities of individual filaments has an asymmetric distribution that can be fit with a computer model that assumes two rupture rates, a slow one similar to the one observed for ring aperture, affecting monomers in the central part of the filaments, and a faster one affecting monomers closer to the open ends. From the quantitative analysis, we conclude that the depolymerization rate is affected both by nucleotide hydrolysis rate and by its exchange along the filament, that all monomer interfaces are equally competent for hydrolysis, although depolymerization is faster at the open ends than in central filament regions, and that all monomer-monomer interactions, regardless of the nucleotide present, can adopt a curved configuration.

Crowding of Molecular Motors Determines Microtubule Depolymerization

The assembly and disassembly dynamics of microtubules (MTs) is tightly controlled by MT-associated proteins. Here, we investigate how plus-end-directed depolymerases of the kinesin-8 family regulate MT depolymerization dynamics. Using an individual-based model, we reproduce experimental findings. Moreover, crowding is identified as the key regulatory mechanism of depolymerization dynamics. Our analysis reveals two qualitatively distinct regimes. For motor densities above a particular threshold, a macroscopic traffic jam emerges at the plus-end and the MT dynamics become independent of the motor concentration. Below this threshold, microscopic traffic jams at the tip arise that cancel out the effect of the depolymerization kinetics such that the depolymerization speed is solely determined by the motor density. Because this density changes over the MT length, length-dependent regulation is possible. Remarkably, motor cooperativity affects only the end-residence time of depolymerases and not the depolymerization speed.

Kinesin-13 Regulates Flagellar, Interphase, and Mitotic Microtubule Dynamics in Giardia intestinalis

Microtubule depolymerization dynamics in the spindle are regulated by kinesin-13, a nonprocessive kinesin motor protein that depolymerizes microtubules at the plus and minus ends. Here we show that a single kinesin-13 homolog regulates flagellar length dynamics, as well as other interphase and mitotic dynamics in Giardia intestinalis, a widespread parasitic diplomonad protist. Both green fluorescent protein-tagged kinesin-13 and EB1 (a plus-end tracking protein) localize to the plus ends of mitotic and interphase microtubules, including a novel localization to the eight flagellar tips, cytoplasmic anterior axonemes, and the median body. The ectopic expression of a kinesin-13 (S280N) rigor mutant construct caused significant elongation of the eight flagella with significant decreases in the median body volume and resulted in mitotic defects. Notably, drugs that disrupt normal interphase and mitotic microtubule dynamics also affected flagellar length in Giardia. Our study extends recent work on interphase and mitotic kinesin-13 functioning in metazoans to include a role in regulating flagellar length dynamics. We suggest that kinesin-13 universally regulates both mitotic and interphase microtubule dynamics in diverse microbial eukaryotes and propose that axonemal microtubules are subject to the same regulation of microtubule dynamics as other dynamic microtubule arrays. Finally, the present study represents the first use of a dominant-negative strategy to disrupt normal protein function in Giardia and provides important insights into giardial microtubule dynamics with relevance to the development of antigiardial compounds that target critical functions of kinesins in the giardial life cycle.

Measuring Nanometer Scale Gradients in Spindle Microtubule Dynamics Using Model Convolution Microscopy

A computational model for the budding yeast mitotic spindle predicts a spatial gradient in tubulin turnover that is produced by kinetochore-attached microtubule (kMT) plus-end polymerization and depolymerization dynamics. However, kMTs in yeast are often much shorter than the resolution limit of the light microscope, making visualization of this gradient difficult. To overcome this limitation, we combined digital imaging of fluorescence redistribution after photobleaching (FRAP) with model convolution methods to compare computer simulations at nanometer scale resolution to microscopic data. We measured a gradient in microtubule dynamics in yeast spindles at approximately 65-nm spatial intervals. Tubulin turnover is greatest near kinetochores and lowest near the spindle poles. A beta-tubulin mutant with decreased plus-end dynamics preserves the spatial gradient in tubulin turnover at a slower time scale, increases average kinetochore microtubule length approximately 14%, and decreases tension at kinetochores. The beta-tubulin mutant cells have an increased frequency of chromosome loss, suggesting that the accuracy of chromosome segregation is linked to robust kMT plus-end dynamics.

A Mutation of β-Actin That Alters Depolymerization Dynamics Is Associated with Autosomal Dominant Developmental Malformations, Deafness, and Dystonia

Actin, one of the major filamentous cytoskeletal molecules, is involved in a variety of cellular functions. Whereas an association between muscle actin mutations and skeletal and cardiac myopathies has been well documented, reports of human disease arising from mutations of nonmuscle actin genes have been rare. We have identified a missense point mutation in the gene coding for beta -actin that results in an arginine-to-tryptophan substitution at position 183. The disease phenotype includes developmental midline malformations, sensory hearing loss, and a delayed-onset generalized dystonia syndrome in monozygotic twins. Cellular studies of a lymphoblastoid cell line obtained from an affected patient demonstrated morphological abnormalities of the actin cytoskeleton and altered actin depolymerization dynamics in response to latrunculin A, an actin monomer-sequestering drug. Resistance to latrunculin A was also observed in NIH 3T3 cells expressing the mutant actin. These findings suggest that mutations in nonmuscle actins may be associated with a broad spectrum of developmental malformations and/or neurological abnormalities such as dystonia.