Biology subjects

Pollard, T. D.

Publications and source records attributed to Pollard, T. D..

At least 19 recordsLinked to original sources

bioRxiv2026

Physical Confinement Modulates the Rate-Limiting Transition in the Release of Phosphate from Actin Filaments

The nucleotide state and rates of transitions between states regulate the dynamics of ATPases. Slow inorganic phosphate (Pi) release following ATP hydrolysis is often rate-limiting and associated with key conformational changes. Actin filaments offer a unique opportunity to understand the fundamentals of Pi release, because identical subunits at filament ends and the interior release Pi at markedly different rates. The molecular origin of this difference is debated, so we employed extensive all-atom molecular dynamics simulations to characterize Pi release from different subunits within an actin filament. The calculated dissociation rates of Pi from ADP-Mg2+ in the active site correlate with experimentally measured Pi release rates and scale inversely with the numbers of water molecules in the cavity surrounding the {gamma}-phosphate. Simulations show that egress of Pi through the protein channels, including through the N111-R177 backdoor, is not rate-limiting and, importantly, that subunits at the filament ends use alternative egress pathways. TeaserMolecular dynamics simulations show that dissociation of phosphate from Mg2+ limits release from all parts of actin filaments

biophysics↗

bioRxiv2025

Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example

Cryo-electron microscopy (cryo-EM) structures of multi-protein complexes such as actin filaments help explain the mechanisms of assembly and interactions with partner proteins. Yet, rapid cooling during freezing may not preserve the conformations at physiological temperature. All-atom molecular dynamics simulations starting with cryo-EM reconstructions can provide additional insights. For example, at 310 K the states of ADP-actin filaments consistent with higher entropy favor partly twisted subunits and smaller rotations along short-pitch helix than the cryo-EM reconstructions, while cryogenic temperatures favor flattened conformations. In the active site, the positions of Q137 and the catalytic water 1 and activating water 2 optimal for in line attack on the {gamma}-phosphate of ATP are very rare at 310 K, explaining in part the slow rate of ATP hydrolysis in filaments. This favorable arrangement of the waters is not observed in simulations of actin monomers. At 310 K subunits in ADP-Pi-actin filaments have their backdoor gates open 60% of the time for phosphate release, a conformation not observed by cryo-EM. Rare fluctuations open binding sites for cofilin and phalloidin. The twisted conformations of pointed end subunits and interactions of the D-loop of the penultimate subunit explain the slow association of new subunits. The terminal subunit at the barbed end is tethered to its neighbor along the long-pitch helix but transiently dissociates from its lateral neighbor. These effects of subfreezing temperatures on actin filaments are surely not an isolated example, so MD simulations of structures of other frozen proteins will be informative. Significance statementFunctionally important properties of proteins are tightly linked to their conformations at physiological temperatures. While cryo-EM reconstructions and crystal structure of frozen proteins provide a molecular resolution of protein structures, they might differ from the conformations at physiological temperature. Using the actin filament as a case study, we find cryo-EM reconstructed structures correspond to low entropy conformations that differ from the ensemble of structures in molecular dynamics simulations at 310 K. The fluctuations of subunit dihedral angles, short-pitch rotations and some side chains explain functionally important properties of actin filaments, including the slow rates of ATP hydrolysis and phosphate release as well as the slow binding of the protein cofilin and cyclic peptide phalloidin.

biophysics↗

bioRxiv2023

Mechanism of Phosphate Release from Actin Filaments

After ATP-actin monomers assemble filaments, the ATPs {gamma}-phosphate is hydrolyzed within seconds and dissociates over minutes. We used all-atom molecular dynamics simulations to sample the release of phosphate from filaments and study residues that gate release. Dissociation of phosphate from Mg2+ is rate limiting and associated with an energy barrier of 20 kcal/mol, consistent with experimental rates of phosphate release. Phosphate then diffuses in an internal cavity toward a gate formed by R177 suggested in prior computational studies and cryo-EM structures. The gate is closed when R177 hydrogen bonds with N111 and is open when R177 forms a salt bridge with D179. Most of the time interactions of R177 with other residues occludes the phosphate release pathway. Machine learning analysis reveals that the occluding interactions fluctuate rapidly, underscoring the secondary role of backdoor gate opening in Pi release, in contrast with the previous hypothesis that gate opening is the primary event. Significance StatementThe protein actin assembles into filaments that participate in muscle contraction and cellular movements. An ATP bound to the actin monomer is hydrolyzed rapidly during filament assembly, but the {gamma}-phosphate dissociates slowly from the filament. We identified phosphate dissociation from Mg2+ as the rate-limiting step in phosphate release from actin based on an energy barrier that aligns with the experimentally determined release rate. The release of phosphate from the protein requires opening a gate in the actin molecule formed by the interaction between sidechains of arginine 177 and asparagine 111. Surprisingly, simulations revealed other interactions of the sidechain of arginine 177 that occlude the release pathway most of the time but have not been observed in low-temperature cryo-EM structures.

biophysics↗

bioRxiv2023

Cryo-EM structures of both ends of the actin filament explain why the barbed end elongates faster than the pointed end

Actin filament ends are the sites of subunit addition during elongation and subunit loss during depolymerization. Prior work established the kinetics and thermodynamics of the assembly reactions at both ends but not the structural basis of their differences. Cryo-EM reconstructions of the barbed end at 3.1 [A] resolution and the pointed end at 3.5 [A] reveal distinct conformations at the two ends. These conformations explain why barbed ends elongate faster than pointed ends and why pointed ends rapidly dissociate the {gamma}-phosphate released from ATP hydrolysis during assembly. The D-loop of the penultimate subunit at the pointed end is folded onto the terminal subunit, precluding its binding incoming actin monomers, and gates on the phosphate release channels of both subunits are wide open. The samples were prepared with FH2 dimers from fission yeast formin Cdc12. The barbed end reconstruction has extra density that may be partial occupancy by the FH2 domains. Significance StatementCells depend cytoplasmic filaments assembled from the protein actin for their physical integrity, as tracks for myosin motor proteins and movements of the whole cell and internal organelles. Actin filaments elongate and shrink at their ends by adding or dissociating single actin molecules. We used cryo-electron microscopy to determine the structures of the two ends of actin filaments at 3.5 [A] resolution for the slowly growing pointed end and 3.1 [A] for the rapidly growing barbed end. These structures reveal why barbed ends grow faster than the pointed ends, why the rate at the pointed end is not diffusion-limited and why the pointed end has a low affinity for the {gamma}-phosphate released from bound ATP inside the filament.

biochemistry↗

bioRxiv2022

Interaction of the Proline-Rich Domain of Fission Yeast WASp (Ws1p1) with Actin Filaments

BackgroundThe Wiskott-Aldrich Syndrome protein (WASp) family of proteins plays a crucial role in the activation of the Arp2/3 (actin-related protein 2/3) complex to promote the branching of actin filaments. The proline-rich domain (PRD) of WASp is known to contribute to branching nucleation but was overlooked, until experiments showed that the PRD of budding yeast Las17 can bind actin filaments (1). MethodsWe purified recombinant proline-rich domains from fission yeast S. pombe Wsp1 and budding yeast S. cerevisiae Las17 to test in biochemical assays of actin binding and polymerization. ResultsThe PRD of the S. pombe Wsp1 binds actin filaments with micromolar affinity. The PRDs of both Wsp1 and Las17 slowed the rate of actin filament elongation by Mg-ATP-actin monomers by half and slowed the spontaneous polymerization of Mg-ATP-actin monomers modestly. ConclusionThe affinity of PRDs of WASp-family proteins for actin filaments is high enough to contribute to the reported stimulation of actin filament branching by Arp2/3 complex.

biochemistry↗

bioRxiv2021

Counting actin in contractile rings reveals novel contributions of cofilin and type II myosins to fission yeast cytokinesis

Cytokinesis by animals, fungi and amoebas depends on actomyosin contractile rings, which are stabilized by continuous turnover of actin filaments. Remarkably little is known about the amount of polymerized actin in contractile rings, so we used low concentration of GFP-Lifeact to count total polymerized actin molecules in the contractile rings of live fission yeast cells. Contractile rings of wild-type cells accumulated polymerized actin molecules at 4,900/min to a peak number of [~]198,000 followed by a loss of actin at 5,400/min throughout ring constriction. In adf1-M3 mutant cells with cofilin that severs actin filaments poorly, contractile rings accumulated polymerized actin at twice the normal rate and eventually had almost two-fold more actin along with a proportional increase in type II myosins Myo2, Myp2 and formin Cdc12. Although 30% of adf1-M3 mutant cells failed to constrict their rings fully, the rest lost actin from the rings at the wild-type rates. Mutations of type II myosins Myo2 and Myp2 reduced contractile ring actin filaments by half and slowed the rate of actin loss from the rings.

cell biology↗

bioRxiv2021

A model of actin-driven endocytosis explains differences of endocytic motility in budding and fission yeast

A comparative study (Sun et al., eLife, 2019) showed that the abundance of proteins at sites of endocytosis in fission and budding yeast is more similar in the two species than previously thought, yet membrane invaginations in fission yeast elongate two-fold faster and are nearly twice as long as in budding yeast. Here we use a three-dimensional model of a motile endocytic invagination (Nickaeen et al., MBoC, 2019) to investigate factors affecting elongation of the invaginations. We found that differences in turgor pressure in the two yeast species can largely explain the paradoxical differences observed experimentally in endocytic motility.

cell biology↗

bioRxiv2021

The number of cytokinesis nodes in mitotic fission yeast scales with cell volume

Cytokinesis nodes are assemblies of stoichiometric ratios of proteins associated with the plasma membrane, which serve as precursors for the contractile ring during cytokinesis by fission yeast. The total number of nodes is uncertain, because of the limitations of the methods used previously. Here we used the [~]140 nm resolution of Airyscan confocal microscopy to resolve a large population of small, unitary cytokinesis nodes in 3D reconstructions of whole fission yeast cells. Wild-type fission yeast cells make about 200 unitary cytokinesis nodes early in mitosis. Most, but not all of these nodes condense into a contractile ring. The number of cytokinesis nodes scales with cell size in four strains tested, although wide rga4{Delta} mutant cells form somewhat fewer cytokinesis nodes than expected from the overall trend. The surface density of Pom1 kinase on the plasma membrane around the equators of cells is similar with a wide range of node numbers, so Pom1 does not control cytokinesis node number. However, varying protein concentrations with the nmt1 promoter showed that the numbers of nodes increase above a baseline of about 200 with the total cellular concentration of either kinase Pom1 or Cdr2.

cell biology↗

bioRxiv2021

Myosins generate contractile force and maintain organization in the cytokinetic contractile ring

During cytokinesis cells assemble an actomyosin contractile ring whose tension constricts and divides cells, but the ring tension was rarely measured. Actomyosin force generation is well understood for the regular sarcomeric architecture of striated muscle, but recent super-resolution studies of fission yeast contractile rings revealed organizational building blocks that are not sarcomeres but irregularly positioned plasma membrane-anchored protein complexes called nodes. Here we measured contractile ring tensions in fission yeast protoplast cells. The myosin II isoforms Myo2 and Myp2 generated the tension, with a ~2-fold greater contribution from Myo2. Simulations of a molecularly detailed ring model revealed a sliding node mechanism for tension, where nodes hosting tense actin filaments were pulled bidirectionally around the ring. Myo2 and Myp2 chaperoned self-assembling components into the ring organization, and anchored the ring against bridging instabilities. Thus, beyond force production, Myo2 and Myp2 are the principal organizers, bundlers and anchors of the contractile ring.

cell biology↗

bioRxiv2020

Cryo-electron microscopy structures of pyrene-labeled ADP-Pi- and ADP-actin filaments

We report high resolution cryo-electron microscopy structures of actin filaments with N-1-pyrene conjugated to cysteine 374 and either ADP (3.2 [A]) or ADP-phosphate (3.0 [A]) in the active site. Polymerization buries pyrene in a hydrophobic cavity between subunits along the long-pitch helix with only minor differences in conformation compared with native actin filaments. These structures explain how polymerization increases the fluorescence 20-fold, how myosin and cofilin binding to filaments reduces the fluorescence and how profilin binding to actin monomers increases the fluorescence.

biochemistry↗

bioRxiv2020

Structural basis for polarized elongation of actin filaments

Actin filaments elongate and shorten much faster at their barbed end than their pointed end, but the molecular basis of this difference has not been understood. We use all-atom molecular dynamics simulations to investigate the properties of subunits at both ends of the filament. The terminal subunits tend towards conformations that resemble actin monomers in solution, while contacts with neighboring subunits progressively flatten the conformation of internal subunits. At the barbed end the terminal subunit is loosely tethered by its DNase-1 loop to the third subunit, because its monomer-like conformation precludes stabilizing contacts with the penultimate subunit. The motions of the terminal subunit make the partially flattened penultimate subunit accessible for binding monomers. At the pointed end, unique contacts between the penultimate and terminal subunits are consistent with existing cryo-EM maps, limit binding to incoming monomers, and flatten the terminal subunit, which likely promotes ATP hydrolysis and rapid phosphate release. These structures explain the distinct polymerization kinetics of the two ends. Significance StatementEukaryotic cells utilize actin filaments to move, change shape, divide, and transport cargo. Decades of experiments have established that actin filaments elongate and shorten significantly faster from one end than the other, but the underlying mechanism for this asymmetry has not been explained. We used molecular dynamics simulations to investigate the structures of the actin filament ends in the ATP, ADP plus{gamma} -phosphate, and ADP nucleotide states. We characterize the structures of actin subunits at both ends of the filament, explain the mechanisms leading to these differences, and connect the divergent structural properties of the two ends to their distinct polymerization rate constants.

biophysics↗

bioRxiv2020

Optimizing imaging conditions for photoconvertible protein mEos3.2 in live and fixed cells

Photoconvertible fluorescent proteins (PCFPs) are widely used in super-resolution microscopy and studies of cellular dynamics. However, our understanding of their photophysics is still limited, hampering their quantitative application. For example, we do not know the optimal sample preparation methods or imaging conditions to count protein molecules fused to PCFPs by single-molecule localization microscopy in live and fixed cells. We also do not know how the behavior of PCFPs in live cells compares with fixed cells. Therefore, we investigated how formaldehyde fixation influences the photophysical properties of the popular green-to-red PCFP mEos3.2 in fission yeast cells under a wide range of imaging conditions. We estimated photophysical parameters by fitting a 3-state model of photoconversion and photobleaching to the time course of fluorescence signal per yeast cell expressing mEos3.2. We discovered that formaldehyde fixation makes the fluorescence signal, photoconversion rate and photobleaching rate of mEos3.2 sensitive to the buffer conditions by permeabilizing the yeast cell membrane. Under some imaging conditions, the time-integrated mEos3.2 signal per yeast cell is similar in live cells and fixed cells imaged in buffer at pH 8.5 with 1 mM DTT, indicating that light chemical fixation does not destroy mEos3.2 molecules. We also discovered that some red-state mEos3.2 molecules entered an intermediate dark state that is converted back to the red fluorescent state by 561-nm illumination. Our findings provide a guide to compare quantitatively conditions for imaging and counting of mEos3.2-tagged molecules in yeast cells. Our imaging assay and mathematical model are easy to implement and provide a simple quantitative approach to measure the time-integrated signal and the photoconversion and photobleaching rates of fluorescent proteins in cells. STATEMENT OF SIGNIFICANCEMaking quantitative measurements with single-molecule localization microscopy (SMLM) has been impeded by limited understanding of the photophysics of the fluorophores, which is very sensitive to the sample preparation and imaging conditions. We characterized the photophysics of the green-to-red photoconvertible fluorescent protein mEos3.2, which is widely used in SMLM. We combined quantitative fluorescence microscopy and mathematical modeling to measure the fluorescence signal and rate constants for photoconversion and photobleaching of mEos3.2 in live and fixed cells under a wide range of illumination intensities. Our findings provide a guide to compare conditions for imaging and counting mEos3.2-tagged proteins in cells. The presented approach is generally applicable to characterize other fluorescent proteins or dyes in cells.

biophysics↗

bioRxiv2019

Astral Microtubules Regulate Formation of the Cytokinetic Cleavage Furrow in Fission Yeast

Microtubules of the mitotic spindle direct cytokinesis in metazoans but this has not been documented in fungi. We report evidence that astral microtubules help coordinate cytokinetic furrow formation in fission yeast. The temperature-sensitive cps1-191 strain (Liu et al., 1999) with a D277N substitution in {beta}-glucan synthase 1 (Cps1/Bgs1) was reported to arrest with an unconstricted contractile ring. We discovered that contractile rings in cps1-191 cells do constrict slowly and that an S338N mutation in the mto2 gene is required with the bgs1D277N mutation to reproduce the cps1-191 phenotype. Complexes of Mto2 and Mto1 with {gamma}-tubulin regulate microtubule assembly. Deletion of Mto1 along with the bgs1D277N mutation also gives the cps1-191 phenotype, which is not observed in mto2S338N or mto1{Delta} cells expressing bgs1+. Both mto2S338N and mto1{Delta} cells nucleate fewer astral microtubules than normal and have higher levels of Rho1-GTP at the division site than wild-type cells. We report multiple conditions that sensitize mto1{Delta} and mto2S338N cells to furrow ingression phenotypes. SummaryDundon and Pollard show that compromising the Mto1 or Mto2 regulators of the fission yeast {gamma}-tubulin complex reduces or eliminates astral microtubules, exaggerates the effects of a D277N substitution in {beta}-glucan synthase 1 (Cps1/Bgs1) on the rate of cytokinetic furrow formation, and increases Rho1-GTP at the cleavage site.

cell biology↗

bioRxiv2019

Simulation of the mechanics of actin assembly during endocytosis in yeast

We formulated a spatially resolved model to estimate forces exerted by a polymerizing actin meshwork on an invagination of the plasma membrane during endocytosis in yeast cells. The model is a continuous approximation tightly constrained by experimental data. Simulations of the model produce forces that can overcome resistance of turgor pressure in yeast cells. Strong forces emerge due to the high density of polymerized actin in the vicinity of the invagination and because of entanglement of the meshwork due to its dendritic structure and crosslinking. The model predicts forces orthogonal to the invagination that would result in a flask shape that diminishes the net force due to turgor pressure. Simulations of the model with either two rings of nucleation promoting factors as in fission yeast or a single ring of nucleation promoting factors as in budding yeast produce enough force to elongate the invagination against the turgor pressure.

cell biology↗

bioRxiv2018

Phosphorylation of Arp2 is not essential for Arp2/3 complex activity in fission yeast

LeClaire et al. presented evidence that phosphorylation of three sites on the Arp2 subunit activates Arp2/3 complex to nucleate actin filaments. We mutated the homologous residues of Arp2 (Y198, T233 and T234) in the fission yeast genome to amino acids that preclude or mimic phosphorylation. Arp2/3 complex is essential for the viability of fission yeast, yet strains unable to phosphorylate these sites grew normally. Y198F/T233A/T234A Arp2 was only nonfunctional if GFP-tagged, as observed by LeClaire et al. in Drosophila cells. Replacing both T233 and T234 with aspartic acid was lethal, suggesting that phosphorylation might be inhibitory. Nevertheless, blocking phosphorylation at these sites had the same effect as mimicking it: slowing assembly of endocytic actin patches. Mass spectrometry revealed phosphorylation at a fourth conserved Arp2 residue, Y218, but both blocking and mimicking phosphorylation of Y218 only slowed actin patch assembly slightly. Therefore, phosphorylation of Y198, T233, T234 and Y218 is not required for the activity of fission yeast Arp2/3 complex.\n\nSummaryPrevious research concluded that phosphorylation at three sites on Arp2 is necessary to activate Arp2/3 complex. Epstein et al. make genomic substitutions blocking or mimicking phosphorylation to demonstrate that phosphorylation of these three sites does not regulate Arp2/3 complex in fission yeast.

cell biology↗

bioRxiv2018

Gating Mechanisms during Actin Filament Elongation by Formins

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.

biophysics↗

bioRxiv2018

Mechanism of actin polymerization revealed by cryo-EM structures of actin filaments with three different bound nucleotides

We used electron cryo-micrographs to reconstruct actin filaments with bound AMPPNP ({beta},{gamma}-imidoadenosine 5-triphosphate, an ATP analog), ADP-Pi (ADP with inorganic phosphate) or ADP to resolutions of 3.4 [A], 3.4 [A] and 3.6 [A]. Subunits in the three filaments have nearly identical backbone conformations, so assembly rather than ATP hydrolysis or phosphate dissociation is responsible for their flattened conformation in filaments. Polymerization increases the rate of ATP hydrolysis by changing the conformations of the three ATP phosphates and the side chains of Gln137 and His161 in the active site. Flattening also promotes interactions along both the long-pitch and short-pitch helices. In particular, conformational changes in subdomain 3 open up favorable interactions with the DNase-I binding loop in subdomain 2 of the adjacent subunit. Subunits at the barbed end of the filament are likely to be in this favorable conformation, while monomers are not. This difference explains why filaments grow faster at the barbed end than the pointed end. Loss of hydrogen bonds after phosphate dissociation may account for the greater flexibility of ADP-actin filaments.\n\nSignificance StatementActin filaments comprise a major part of the cytoskeleton of eukaryotic cells and serve as tracks for myosin motor proteins. The filaments assemble from actin monomers with a bound ATP. After polymerization, actin rapidly hydrolyzes the bound ATP and slowly dissociates the {gamma}-phosphate. ADP-actin filaments then disassemble to recycle the subunits. Understanding how actin filaments assemble, disassemble and interact with numerous regulatory proteins depends on knowing the structure of the filament. High quality structures of ADP-actin filaments were available, but not of filaments with bound ATP- or with ADP and phosphate. We determined structures of actin filaments with bound AMPPNP (a slowly hydrolyzed ATP analog), ADP and phosphate and ADP by cryo-electron microscopy. These structures show how conformational changes during actin assembly promote ATP hydrolysis and faster growth at one end of the filament than the other.

biochemistry↗

bioRxiv2017

Conformational changes in Arp2/3 complex induced by ATP, WASp-VCA and actin filaments

We used fluorescence spectroscopy and electron microscopy to determine how binding of ATP, nucleation-promoting factors (NPF), actin monomers and actin filaments change the conformation of Arp2/3 complex during the process that nucleates an actin filament branch. We mutated subunits of Schizosaccharomyces pombe Arp2/3 complex for labeling with fluorescent dyes at either the C-termini of Arp2 and Arp3 or ArpC1 and ArpC3. We measured Forster resonance energy transfer (FRET) efficiency (ETeff) between the dyes in the presence of the various ligands. We also computed class averages from electron micrographs of negatively stained specimens. ATP binding made small conformational changes of the nucleotide binding clefts of the Arp subunits. WASp-VCA, WASp-CA, and WASp-actin-VCA changed the ETeff between the dyes on the Arp2 and Arp3 subunits much more than between dyes on ArpC1 and ArpC3. Ensemble FRET detected a different structural change that involves bringing ArpC1 and ArpC3 closer together when Arp2/3 complex bound actin filaments. Each of the ligands that activates Arp2/3 complex changes the structure in different ways, each leading progressively to fully activated Arp2/3 complex on the side of a filament.

biophysics↗