The advantages of microfluidics to study actin biochemistry and biomechanics

Dynamic clamping induces rotation-to-beating transition of pinned filaments in gliding assays

We used numerical simulations to investigate how properties of motor proteins control the dynamical behaviour of driven flexible filaments. A filament on top of a patch of anchored motor proteins is pinned at one end, a setup referred to as a spiral gliding assay. There exists a variety of motor proteins with different properties. We found that when these properties are changed, this system generally can show three different regimes: (i) fluctuation, where the filament undergoes random fluctuations because the motors are unable to bend it, (ii) rotation, in which the filament bends and then moves continuously in one direction, and (iii) beating, where the filament rotation direction changes over time. We found that the transition between fluctuation and rotation occurs when motors exert a force sufficient to buckle the filament. The threshold force coincides with the second buckling mode of a filament undergoing a continuously distributed load. Moreover, we showed that when motors near the pinning point work close to their stall force, they cause dynamic clamping, leading to the beating regime. Rather than being imposed by experimental conditions, this clamping is transient and results from the coupling between filament mechanics and the collective behaviour of motors.

Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton

In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the actin cytoskeleton.

Regulation of branched versus linear Arp2/3-generated actin filaments

Activation of the Arp2/3 complex by VCA-motif-bearing actin nucleation-promoting factors results in the formation of "daughter" actin filaments branching off the sides of pre-existing "mother" filaments. Alternatively, when stimulated by SPIN90, Arp2/3 directly nucleates "linear" actin filaments. Uncovering the similarities and differences between these two mechanisms is fundamental to understanding how actin cytoskeleton dynamics are regulated. Here, analysis of individual filaments reveals that, unexpectedly, the VCA motifs of WASP, N-WASP, and WASH destabilize existing branches, as well as SPIN90-Arp2/3 at linear filament ends. Furthermore, branch stabilizer cortactin and destabilizer GMF each have a similar impact on SPIN90-activated Arp2/3. However, unlike branch junctions, SPIN90-Arp2/3 at the ends of linear filaments is not destabilized by piconewton forces and does not become less stable with time. It thus appears that linear and branched Arp2/3-generated filaments respond similarly to the regulatory proteins we have tested, albeit with some differences, but significantly differ in their responses to aging and mechanical stress. These kinetic differences likely reflect the small conformational differences recently reported between Arp2/3 in branch junctions and linear filaments and suggest that their turnover in cells may be differently regulated.

Structural basis of rapid actin dynamics in the evolutionarily divergent Leishmania parasite

Actin polymerization generates forces for cellular processes throughout the eukaryotic kingdom, but our understanding of the 'ancient' actin turnover machineries is limited. We show that, despite > 1 billion years of evolution, pathogenic Leishmania major parasite and mammalian actins share the same overall fold and co-polymerize with each other. Interestingly, Leishmania harbors a simple actin-regulatory machinery that lacks cofilin 'cofactors', which accelerate filament disassembly in higher eukaryotes. By applying single-filament biochemistry we discovered that, compared to mammalian proteins, Leishmania actin filaments depolymerize more rapidly from both ends, and are severed > 100-fold more efficiently by cofilin. Our high-resolution cryo-EM structures of Leishmania ADP-, ADP-Pi- and cofilin-actin filaments identify specific features at actin subunit interfaces and cofilin-actin interactions that explain the unusually rapid dynamics of parasite actin filaments. Our findings reveal how divergent parasites achieve rapid actin dynamics using a remarkably simple set of actin-binding proteins, and elucidate evolution of the actin cytoskeleton.

Recent Advances and Emerging Challenges in the Molecular Modeling of Mechanobiological Processes

Many biological processes result from the effect of mechanical forces on macromolecular structures and on their interactions. In particular, the cell shape, motion, and differentiation directly depend on mechanical stimuli from the extracellular matrix or from neighboring cells. The development of experimental techniques that can measure and characterize the tiny forces acting at the cellular scale and down to the single-molecule, biomolecular level has enabled access to unprecedented details about the involved mechanisms. However, because the experimental observables often do not provide a direct atomistic picture of the corresponding phenomena, particle-based simulations performed at various scales are instrumental in complementing these experiments and in providing a molecular interpretation. Here, we will review the recent key achievements in the field, and we will highlight and discuss the many technical challenges these simulations are facing, as well as suggest future directions for improvement.

Formins

Actin is one of the most abundant proteins in eukaryotes. Discovered in muscle and described as far back as 1887, actin was first purified in 1942. It plays myriad roles in essentially every eukaryotic cell. Actin is central to development, muscle contraction, and cell motility, and it also functions in the nucleus, to name a spectrum of examples. The flexibility of actin function stems from two factors: firstly, it is dynamic, transitioning between monomer and filament, and, secondly, there are hundreds of actin-binding proteins that build and organize specific actin-based structures. Of prime importance are actin nucleators - proteins that stimulate de novo formation of actin filaments. There are three known classes of actin nucleators: the Arp2/3 complex, formins, and tandem WASP homology 2 (WH2) nucleators. Each class nucleates by a distinct mechanism that contributes to the organization of the larger structure being built. Evidence shows that the Arp2/3 complex produces branched actin filaments, remaining bound at the branch point, while formins create linear actin filaments, remaining bound at the growing end. Here, we focus on the formin family of actin nucleators.

Actin filament oxidation by MICAL1 suppresses protections from cofilin-induced disassembly

Proteins of the ADF/cofilin family play a central role in the disassembly of actin filaments, and their activity must be tightly regulated in cells. Recently, the oxidation of actin filaments by the enzyme MICAL1 was found to amplify the severing action of cofilin through unclear mechanisms. Using single filament experiments in vitro, we found that actin filament oxidation by MICAL1 increases, by several orders of magnitude, both cofilin binding and severing rates, explaining the dramatic synergy between oxidation and cofilin for filament disassembly. Remarkably, we found that actin oxidation bypasses the need for cofilin activation by dephosphorylation. Indeed, non-activated, phosphomimetic S3D-cofilin binds and severs oxidized actin filaments rapidly, in conditions where non-oxidized filaments are unaffected. Finally, tropomyosin Tpm1.8 loses its ability to protect filaments from cofilin severing activity when actin is oxidized by MICAL1. Together, our results show that MICAL1-induced oxidation of actin filaments suppresses their physiological protection from the action of cofilin. We propose that, in cells, direct post-translational modification of actin filaments by oxidation is a way to trigger their disassembly.