Actin Filament Branching and Behavior Under Mechanical Constraints

Actin Filament Branching and Behavior Under Mechanical Constraints
Author: Viviana Ioana Risca
Publisher:
Total Pages: 187
Release: 2012
Genre:
ISBN:

Mechanical cues affect a number of important biological processes in metazoan cells, such as migration, proliferation, and differentiation. Many of these processes are mediated by the cytoskeleton, an intracellular network of protein filaments that provides mechanical rigidity to the cell and drives cellular shape change. In particular, actin, a very highly conserved and abundant cytoskeletal protein, forms filaments that, when organized by a large and diverse group of actin-binding and regulatory proteins, self-assemble into dynamic and mechanically complex networks. The actin filament itself is polymorphic, with a structure and a set of mechanical properties that are modulated by the binding of regulatory proteins. Both the structure and the mechanical properties of actin filaments play an important role in determining the mechanical properties, architecture, and dynamics of the subcellular structure that result from self-assembly. We sought to investigate an important unanswered question: how do mechanical constraints help regulate the assembly of an actin network? This dissertation focuses on branched actin networks, which play a key force-generating role in the formation of membrane protrusions, in endocytosis, and in several types of intracellular motility. These networks are nucleated by the Arp2/3 complex and display adaptive behavior in response to compressive forces. They consist of Y-shaped branches formed by a pre-existing filament, the Arp2/3 complex bound to its side, and a new actin filament nucleated by the Arp2/3 complex. To investigate how the architecture of these networks is shaped by mechanical constraints, such as compressive forces arising from the resistance of cellular membranes to deformation, we devised a methodology for mechanically constraining single actin filaments while new branches are nucleated from their sides by the Arp2/3 complex. Branch nucleation on individual filaments was imaged with two-color fluorescence microscopy using a protocol that distinguishes constrained mother filaments from freshly nucleated daughter filaments. Combining this two-color assay with quantitative analysis of filament curvature, we show that filamentous actin serves in a mechanosensitive capacity itself, by biasing the location of actin branch nucleation in response to filament bending. We observed preferential branch formation by the Arp2/3 complex on the convex face of the curved filament. At radii of curvature of 1 micrometer, we observed approximately twice as many branches on the convex face as on the concave face. In the cellular context, where actin filaments tend to make a ~35 degree angle with the normal to the membrane, this observation suggests that compressive forces that bend actin filament tips away from the membrane would result in an enhancement of branching nucleated on the membrane-facing convex face of each filament. This effect constitutes a novel mechanism by which branched actin networks may be oriented toward membranes, as observed in vivo. Furthermore, in the context of a limited branching zone near the membrane, which is expected from the known biochemistry of the process, orientation of new branches toward the membrane also leads to an increase in network density in response to force, which has been documented in experiments with motility of bacteria in cytoplasmic extract. To explain the biased nucleation of branches on curved actin filaments, we propose a fluctuation gating model in which filament binding or branch nucleation by Arp2/3 occur only when a sufficiently large, transient, local curvature fluctuation causes a favorable conformational change in the filament. Using Monte Carlo simulations of a discretized worm-like chain model of the actin filament immobilized on a surface like the filaments in the constrained branching assay, we show that the fluctuation gating model can quantitatively account for our experimental data. Expanding the scope of the simulations beyond the in vitro experiment, we hypothesize that the curvature fluctuations of filaments in the cell may be modulated by the architecture of the actin network to which they belong. To test this hypothesis, we computationally explore how three types of mechanical constraints - buckling or bending of a filament end by a hard wall, bundling of filaments by a crosslinking protein, and uniaxial tension applied to a single filament - affect local curvature fluctuations. We find that bending of simulated filaments by a hard wall can significantly alter curvature fluctuations, the magnitude of which can be approximately calculated by the simple geometry of filament bending at the barrier. On the other hand, crosslinking of simulated actin filaments with crosslinking elements of physiologically relevant stiffness has surprisingly little effect on the small-scale local curvature fluctuations. Similarly, enclosure of a simulated filament bundle in a tube does not significantly affect curvature of filaments on the nanometer scale. Tension, however, in the range of 100 pN, does have a marked effect on curvature fluctuations in our simulations, suggesting that any interactions of actin-binding proteins with actin filaments that depend on bending fluctuations may be modulated by tension. This has been observed in several recent experiments, suggesting that the effects of tension on the biochemical interactions regulating actin network assembly and disassembly warrant further study. Overall, the results presented here demonstrate how filament curvature can alter the interaction of cytoskeletal filaments with regulatory proteins, suggesting that direct mechanotransduction by actin may serve as a general mechanism for organizing the cytoskeleton in response to force.

Actin-based Motility

Actin-based Motility
Author: Marie-France Carlier
Publisher: Springer Science & Business Media
Total Pages: 434
Release: 2010-09-23
Genre: Medical
ISBN: 904819301X

Since the discovery of actin by Straub in the 1950’s and the pioneering work of Oosawa on actin self-assembly in helical laments in the 1960’s, many books and conference proceedings have been published. As one of the most essential p- teins in life, essential for movement in organisms rangingfrom bacteria to higher eukaryotes, it is no surprise that actin has fascinated generations of scientists from many different elds. Actin can be considered as a “living treasure” of biology; the kinetics and thermodynamics of self-assembly, the dissipative nature of actin po- merization, the molecular interactions of monomeric and polymerized actin with regulators, the mechanical properties of actin gels, and more recently the force p- ducing motile and morphogenetic processes organized by the actin nanomachine in response to signaling, are all milestones in actin research. Discoveries that directly derive from and provide deeper insight into the fundamental properties of actin are constantly being made, making actin an ever appealing research molecule. At the same time, the explosion in new technologies and techniques in biological sciences has served to attract researchers from an expanding number of disciplines, to study actin. This book presents the latest developments of these new multiscale approaches of force and movement powered by self-assembly processes, with the hope to opening our perspectives on the many areas of actin-based motility research.

Actin Filaments and Networks Under Force

Actin Filaments and Networks Under Force
Author: Evan Bo Wang
Publisher:
Total Pages: 93
Release: 2014
Genre:
ISBN:

Rich understanding of a complex system can often emerge from simple but carefully constructed models. With an appropriate model, we can ask questions about how tuning the parameters of the model or modifying the constraints of the system changes the system behavior. My research involves applying such an approach to actin, an essential biopolymer in the cell. In this work, we explore how forces affect actin at the filament and network length scales. In the first part, we investigate how different forces modulate the interaction between actin filaments and actin-binding proteins. One such protein complex, Arp2/3, can cause filaments to form branches. Experiments indicate that branches preferentially form on the convex side of bent filaments. Using a coarse-grained model discretized at the monomer pair level, we show that binding is dependent upon a high local curvature fluctuation of the filament. The results indicate that actin can sense and respond to mechanical environmental cues to regulate the binding of Arp2/3. We further believe such a picture can serve as a useful framework for studying the effects of force on the binding and function of other proteins. In a follow-up project, we derive analytical expressions for the nanoscale curvature distribution of a worm-like chain and membrane as a function of applied tension. These expressions can be used to understand the force dependence of protein binding on actin filaments and membranes within a biological context. In the second part, we focus on actin network elasticity. Specifically, we explore how actin networks respond to large external forces. However, the theoretical toolkit for such a task is incomplete. First we develop a constant-stress framework to apply large forces on soft but strongly nonlinear materials. Additionally, we create a toy model of a soft elastic solid with a nonlinear elastic response on which we test our constant-stress method. Finally, we utilize the constant-stress method and a coarse-grained model for short, semiflexible chains to explore actin network elasticity under compression. We consistently observe stress softening under compression, which we analyze from a single filament perspective and using normal mode analysis.

Cell Movements

Cell Movements
Author: Dennis Bray
Publisher: Garland Science
Total Pages: 396
Release: 2001
Genre: Cells
ISBN: 9780815332824

This book vividly describes how complex and integrated movements can arise from the properties and behaviors of biological molecules. It provides a uniquely integrated account in which the latest findings from biophysics and molecular biology are put into the context of living cells. This second edition is updated throughout with recent advances in the field and has a completely revised and redrawn art program. The text is suitable for advanced undergraduates, graduate students, and for professionals wishing for an overview of this field.

The Mechanoregulation of the Actin Cytoskeleton

The Mechanoregulation of the Actin Cytoskeleton
Author: Pamela Jreij
Publisher:
Total Pages: 112
Release: 2016
Genre:
ISBN:

The actin cytoskeleton is essential for maintaining mechanical integrity of cells and tissues and for providing structural support during dynamic processes including migration, endocytosis and cytokinesis. From a molecular perspective, it consists of (1) actin monomers polymerized in double helical filamentous structures and (2) an ensemble of regulatory proteins that regulate shape and function of actin structures. From a mechanics perspective, the cytoskeleton is a dynamic entity that can generate force while being subject to various load perturbations. Though molecular understanding of actin networks is extensive, our understanding of how molecular signaling is converted to force output and how force input feeds back into molecular activity remains limited. The goal of this dissertation is to investigate how the interplay between molecular and mechanical attributes of the actin cytoskeleton results in desired cellular activity and physiological phenotypes. We first focus on the leading edge of migrating cells where nucleation of branched actin structures is involved in membrane protrusion. In chapter 2, we investigate the effect of the biochemical composition of these structures on the observed dynamic properties of network growth. To do so, we reconstitute branched actin network assembly using a minimal set of essential proteins (i.e. nucleation promoting factors, ARP2/3 and capping proteins) and evaluate their role over a broad range of concentrations. We find that in the absence of opposing force, changes in the nanomolar range of soluble protein concentration significantly modulates architectural and kinetic properties of nucleating actin structures. In cells, branched actin networks do not just transmit forces in the form of protrusion but also resists opposing load imposed by the membrane and other physical barriers. In chapter 3, we use atomic force microscopy to study the impact of external force on the biochemical composition and mechanical properties of reconstituted branched actin structures. Interestingly, we find that mechanical loading alters network density and composition, which in turn modulates its bulk mechanical properties and renders it stiffer, more powerful and efficient. Central to assembly and function of actin networks is the activity of actin binding proteins. We next extend our investigation to ask whether forces on actin filaments can influence actin binding protein (ABP) localization and activity in the cytoskeleton. Despite sharing the same cytoplasm, ABPs in cells spatially segregate and differentially regulate actin structures. In the context of the leading edge of migrating cells, cofilin binds and severs filaments in the lamellipodia, whereas tropomyosin is secluded as it binds and stabilizes filaments in the lamellum. In chapter 4, we hypothesize that these proteins are mechanosensitive and show that cofilin preferentially binds to network structures subject to compression whereas tropomyosin favors relaxed structures. Lastly, in chapter 5, we explore the sensitivity of calponin homology domain-containing proteins to the mechanical state of actin filaments. We focus our study on wild type and mutated versions of the utrophin actin binding domain, which is used as a universal actin marker. Using a multiscale biophysical approach, we show that mutant utrophin can selectively bind highly stressed actin filaments in vitro and in cells. We use this mutant to develop a ratiometric actin mechanosensor for mapping physiological forces in-vivo which provides a new tool for exploring mechanoregulation of cellular processes. Overall, the findings in this dissertation provide direct evidence for the importance of mechanical perturbations in regulating structure and function of the actin cytoskeleton.

The Actin Cytoskeleton

The Actin Cytoskeleton
Author: Brigitte M. Jockusch
Publisher: Springer
Total Pages: 356
Release: 2017-01-03
Genre: Medical
ISBN: 3319463713

Actin is one of the most abundant proteins and ubiquitously expressed in all eukaryotes. In recent years, the analysis of structure and function of such complexes has shed new light on actin's role in cellular and tissue morphogenesis, locomotion and various forms of intracellular motility, but also on its role in nuclear processes like chromatin architecture and transcription. Progress in understanding these different physiological phenomena, but also in unravelling the basis of actin-based pathophysiological processes has been made by combining video microscopy, molecular biology, genetics and biochemistry. Thus, the current research on actin, as ongoing in many international laboratories, is a "hot spot" in basic and translational research in life sciences. In this book on "The Actin Cytoskeleton", twelve internationally renowned authors present specific chapters that cover their recent work concerned with the various roles of actin mentioned above. This comprehensive volume is therefore an attractive handbook for teachers and students in many fields of medicine and pharmacology.

Using Mathematics to Understand Biological Complexity

Using Mathematics to Understand Biological Complexity
Author: Rebecca Segal
Publisher: Springer Nature
Total Pages: 221
Release: 2020-12-29
Genre: Mathematics
ISBN: 3030571297

This volume tackles a variety of biological and medical questions using mathematical models to understand complex system dynamics. Working in collaborative teams of six, each with a senior research mentor, researchers developed new mathematical models to address questions in a range of application areas. Topics include retinal degeneration, biopolymer dynamics, the topological structure of DNA, ensemble analysis, multidrug-resistant organisms, tumor growth modeling, and geospatial modeling of malaria. The work is the result of newly formed collaborative groups begun during the Collaborative Workshop for Women in Mathematical Biology hosted by the Institute of Pure and Applied Mathematics at UCLA in June 2019. Previous workshops in this series have occurred at IMA, NIMBioS, and MBI.

Handbook of Imaging in Biological Mechanics

Handbook of Imaging in Biological Mechanics
Author: Corey P. Neu
Publisher: CRC Press
Total Pages: 579
Release: 2014-10-24
Genre: Medical
ISBN: 1466588144

Emerging imaging techniques have opened new fronts to investigate tissues, cells, and proteins. Transformative technologies such as microCT scans, super-resolution microscopy, fluorescence-based tools, and other methods now allow us to study the mechanics of cancer, dissect the origins of cellular force regulation, and examine biological specimens