Gijsje H Koenderink

AMOLF · Biological Soft Matter

Septins are cytoskeletal proteins conserved from algae and protists to mammals. A unique feature of septins is their presence as heteromeric complexes that polymerize into filaments in solution and on lipid membranes. Although animal septins associate extensively with actin-based structures in cells, whether septins organize as filaments in cells a...

Septins, a family of GTP-binding proteins assembling into higher order structures, interface with the membrane, actin filaments and microtubules, which positions them as important regulators of cytoarchitecture. Septin 9 (Sept9), which is frequently overexpressed in tumors and mutated in hereditary neuralgic amyotrophy (HNA), mediates the binding o...

Septin GTP-binding proteins contribute essential biological functions that range from the establishment of cell polarity to animal tissue morphogenesis. Human septins in cells form hetero-octameric septin complexes containing the ubiquitously expressed SEPT9. Despite the established role of SEPT9 in mammalian development and human pathophysiology,...

Microtubule-dependent organization of membranous organelles occurs through motor-based pulling and by coupling microtubule dynamics to membrane remodeling. For example, tubules of endoplasmic reticulum (ER) can be extended by kinesin- and dynein-mediated transport and through the association with the tips of dynamic microtubules. The binding betwee...

Microtubule-dependent organization of membrane organelles, such as the endoplasmic reticulum, occurs through motor-based pulling and by coupling polymer dynamics to membrane remodeling. Membrane binding to dynamic microtubule ends involves transient interactions, but how such interactions can lead to membrane deformation is unclear. Here, we recons...

Cells and tissues have the remarkable ability to actively generate the forces required to change their shape. This active mechanical behavior is largely mediated by the actin cytoskeleton, a crosslinked network of actin filaments that is contracted by myosin motors. Experiments and active gel theories have established that the length scale over whi...

Bundles of polymer filaments are responsible for the rich and unique mechanical behaviors of many biomaterials, including cells and extracellular matrices. In fibrin biopolymers, whose nonlinear elastic properties are crucial for normal blood clotting, protofibrils self-assemble and bundle to form networks of semiflexible fibers. Here we show that...

In living cells, lipid membranes and biopolymers determine each other's conformation in a delicate force balance. Cellular polymers such as actin filaments are strongly confined by the plasma membrane in cell protrusions such as lamellipodia and filopodia. Conversely, protrusion formation is facilitated by actin-driven membrane deformation and thes...

Nonequilibrium systems that are driven or drive themselves towards a critical point have been studied for almost three decades. Here we present a minimalist example of such a system, motivated by experiments on collapsing active elastic networks. Our model of an unstable elastic network exhibits a collapse towards a critical point from any macrosco...

Disordered fibrous networks are ubiquitous in nature as major structural components of living cells and tissues. The mechanical stability of networks generally depends on the degree of connectivity: only when the average number of connections between nodes exceeds the isostatic threshold are networks stable (Maxwell, J. C., Philosophical Magazine 2...

The actin-myosin cytoskeleton allows cells to move, change shape, and exert forces. These fascinating functions involve active contraction of cross-linked networks of actin filaments by myosin II motor proteins. Unlike muscle cells, where actin and myosin form ordered bundles that contract homogeneously, nonmuscle cells have a variety of more disor...

Cells actively sense and process mechanical information that is provided by the extracellular environment to make decisions about growth, motility and differentiation. It is important to understand the underlying mechanisms given that deregulation of the mechanical properties of the extracellular matrix (ECM) is implicated in various diseases, such...

Type 2 diabetes mellitus is characterized by the pathological deposition of fibrillized protein, known as amyloids. It is thought that oligomers and/or amyloid fibrils formed from human islet amyloid polypeptide (hIAPP or amylin) cause cell death by membrane damage. The molecular structure of hIAPP amyloid fibrils is dominated by β-sheet structure,...

Filamentous biopolymer networks in cells and tissues are routinely imaged by confocal microscopy. Image analysis methods enable quantitative study of the properties of these curvilinear networks. However, software tools to quantify the geometry and topology of these often dense 3D networks and to localize network junctions are scarce. To fill this...

We develop a percolation model motivated by recent experimental studies of gels with active network remodeling by molecular motors. This remodeling was found to lead to a critical state reminiscent of random percolation (RP), but with a cluster distribution inconsistent with RP. Our model not only can account for these experiments, but also exhibit...

When we cut ourselves, our body's immediate response is to stop the bleeding by repairing the damage to the wall of the blood vessel_forming a “blood clot”. This is physically carried out by forming a network of semiflexible fibrin fibers, which bind together red blood cells and platelets, thus effectively plugging the hole that results from the in...

While semi-flexible polymers and fibres are an important class of material due to their rich mechanical properties, it remains unclear how these properties relate to the microscopic conformation of the polymers. Actin filaments constitute an ideal model polymer system due to their micron-sized length and relatively high stiffness that allow imaging...

To power dynamic processes in cells, the actin and microtubule cytoskeletons organize into complex structures. Although it is known that cytoskeletal coordination is vital for cell function, the mechanisms by which cross-linking proteins coordinate actin and microtubule activities remain poorly understood. In particular, it is unknown how the disti...

Background Factor XIII (FXIII)-induced cross-linking has long been associated with the ability of fibrin blood clots to resist mechanical deformation, but how FXIII can directly modulate clot stiffness is unknown.Objectives and Methods We hypothesized that FXIII affects the self-assembly of the fibrin fibers by altering the lateral association betw...

We theoretically and experimentally study nematic liquid crystal equilibria within shallow rectangular wells. We model the wells within a two-dimensional Oseen-Frank framework, with strong tangent anchoring, and obtain explicit analytic expressions for the director fields and energies of the 'diagonal' and 'rotated' solutions reported in the litera...

Living cells constitute an extraordinary state of matter since they are inherently out of thermal equilibrium due to internal metabolic processes. Indeed, measurements of particle motion in the cytoplasm of animal cells have revealed clear signatures of nonthermal fluctuations superposed on passive thermal motion. However, it has been difficult to...

The transport of organelles and proteins is of vital importance for living cells. Besides passive transport by diffusion, active transport by molecular motors hopping over the cytoskeleton is crucial for the survival of cells. We study in vitro the movement of molecular motors over microtubule network. With Totally Internal Reflection Microscopy (T...

Interactions between microtubules and actin filaments (F-actin) are essential for eukaryotic cell migration, polarization, growth, and division. Although the importance of these interactions has been long recognized, the inherent complexity of the cell interior hampers a detailed mechanistic study of how these two cytoskeletal systems influence eac...

Animal cell cytokinesis requires a contractile ring of crosslinked actin filaments and myosin motors. How contractile rings form and are stabilized in dividing cells remains unclear. We address this problem by focusing on septins, highly conserved proteins in eukaryotes whose precise contribution to cytokinesis remains elusive. We use the cleavage...

The finite size of cells poses severe spatial constraints on the network of semiflexible filaments called the cytoskeleton, a main determinant of cell shape. At the same time, the high packing density of cytoskeletal filaments poses mutual packing constraints. Here we investigate the competition between excluded volume interactions in the bulk and...

We report analytical and numerical modelling of active elastic networks, motivated by experiments on crosslinked actin networks contracted by myosin motors. Within a broad range of parameters, the motor-driven collapse of active elastic networks leads to a critical state. We show that this state is qualitatively different from that of the random pe...

Nearly all proteins and peptides have the ability to self-assemble into amyloids when they are denatured. These highly ordered nanofibrils exhibit superior mechanical properties, which are relatively insensitive to their protein amino acid sequence. This makes them attractive candidates for applications in materials science and food industry. Howev...

During wound healing and angiogenesis, fibrin serves as a provisional extracellular matrix. We use a model system of fibroblasts embedded in fibrin gels to study how cell-mediated contraction may influence the macroscopic mechanical properties of their extracellular matrix during such processes. We demonstrate by macroscopic shear rheology that the...

Significance Animal cells continuously move, divide, and transmit forces by actively reorganizing their internal scaffold or cytoskeleton. Molecular motors pull actin filaments together and generate contraction of the cytoskeleton underneath the cell membrane. We address the detailed mechanism of contraction by using a minimal in vitro assay: a lip...

Giant unilamellar vesicles or GUVs are systems of choice as biomimetic models of cellular membranes. Although a variety of procedures exist for making single walled vesicles of tens of microns in size, the range of lipid compositions that can be used to grow GUVs by the conventional methods is quite limited, and many of the available methods involv...

Collagen fibrils form extracellular networks that regulate cell functions and provide mechanical strength to tissues. Collagen fibrillogenesis is an entropy-driven process promoted by warming and reversed by cooling. Here, we investigate the influence of noncovalent interactions mediated by the collagen triple helix on fibril stability. We measure...

CRYAB (αB-crystallin) is expressed in many tissues and yet the R120G mutation in CRYAB causes tissue-specific pathologies, namely cardiomyopathy and cataract. Here, we present evidence to demonstrate that there is a specific functional interaction of CRYAB with desmin intermediate filaments that predisposes myocytes to disease caused by the R120G m...

Biomechanical properties of healthy and degenerated nucleus pulposus (NP) are thought to be important for future regenerative strategies for intervertebral disc (IVD) repair. However, which properties are pivotal as design criteria when developing NP replacement materials is ill understood. Therefore, we determined and compared segmental biomechani...

Many proteins of diverse sequence, structure and function self-assemble into morphologically similar fibrillar aggregates known as amyloids. Amyloids are remarkable polymers in several respects. First of all, amyloids can be formed from proteins with very different amino acid sequences; the common denominator is that the individual proteins constit...

Nanotechnology is a multidisciplinary field that covers a vast and diverse array of devices and machines derived from engineering, physics, materials science, chemistry and biology. These devices have found applications in biomedical sciences, such as targeted drug delivery, bio-imaging, sensing and diagnosis of pathologies at early stages. In thes...

Living systems often exhibit internal driving: active, molecular processes drive nonequilibrium phenomena such as metabolism or migration. Active gels constitute a fascinating class of internally driven matter, where molecular motors exert localized stresses inside polymer networks. There is evidence that network crosslinking is required to allow m...

Self-organized contractile arrays of actin filaments and myosin motors drive cell division, migration, and tissue morphogenesis. Biophysical studies have provided detailed mechanistic insights into the mechanisms of force production by individual motor molecule. However, it is not well understood how motors and actin filaments collectively self-org...

The cytoskeleton is a fascinating material, where myosin pulling forces drive actin networks out of equilibrium. Recent studies have found that network response to motor activity is governed by connectivity: weakly connected networks give rise to ordered patterns and dynamic clusters, whereas well connected networks are elastic and propagate tensio...

Nearly all proteins and peptides have the ability to self-assemble into amyloid fibrils when they are denatured. These highly ordered nanofibrils exhibit superior mechanical properties, and are therefore attractive candidates for applications in materials science and food industry. The flipside of the remarkable stability is their accumulation in t...

The cytoskeleton of eukaryotic cells provides mechanical support and governs intracellular transport. These functions rely on the complex mechanical properties of networks of semiflexible protein filaments. Recent theoretical interest has focused on mesoscopic properties of such networks and especially on the effect of local, non-affine bending def...

Vasodilator-stimulated phosphoprotein (Ena/VASP) is an actin binding protein, important for actin dynamics in motile cells and developing organisms. Though VASP's main activity is the promotion of barbed end growth, it has an F-actin binding site and can form tetramers, and so could additionally play a role in actin crosslinking and bundling in the...

Motor proteins actively contract the actin cytoskeleton of cells and thereby give rise to nonequilibrium fluctuations as well as changes in the architecture of the cytoskeleton. Here, we show, by video microrheology of a reconstituted cytoskeleton, that motors generate time-dependent nonequilibrium fluctuations, which evolve as the network is remod...

The nonlinear elastic properties of fibrin networks are crucial for normal blood clotting. Here, we show that the extraordinary strain-stiffening response of fibrin clots reflects the hierarchical architecture of the fibrin fibers, which are bundles of wormlike protofibrils. We measure the rheology of networks of unbundled protofibrils, and find ex...

The formation of amyloid fibrils is a self-assembly process of peptides or proteins. The superior mechanical properties of these fibrils make them interesting for materials science but constitute a problem in amyloid-related diseases. Amyloid structures tend to be polymorphic, and their structure depends on growth conditions. To understand and cont...

Cells use actin filaments to define and maintain their shape and to exert forces on the surrounding tissue. Accessory proteins like crosslinkers and motors organize these filaments into functional structures. However, physical effects also influence filament organization: steric interactions impose packing constraints at high filament density and s...

Alginate is frequently studied as a scaffold for intervertebral disc (IVD) repair, since it closely mimics mechanical and cell-adhesive properties of the nucleus pulposus (NP) of the IVD. The aim of this study was to assess the relation between alginate concentration and scaffold stiffness and find preparation conditions where the viscoelastic beha...

Howard Stone and co-workers have proposed that lipid bilayers can also control their surface area passively when attached to elastic substrates. They show that stretching of bilayer-adhered polymeric substrates leads to the spontaneous uptake of vesicles, whereas compression causes reversible expulsion of membrane tube. In their approach, this unit...

We demonstrate that cytoskeletal actin-myosin networks can be encapsulated with high efficiency in giant liposomes by hydration of lipids in an agarose hydrogel. The liposomes have cell-sized diameters of 10-20 μm and a uniform actin content. We show by measurements of membrane fluorescence intensity and bending rigidity that the majority of liposo...

Collagen fibrils are the main structural element of connective tissues. In many tissues, these fibrils contain two fibrillar collagens (types I and V) in a ratio that changes during tissue development, regeneration, and various diseases. Here we investigate the influence of collagen composition on the structure and rheology of networks of purified...

In cells, many vital processes involve myosin-driven motility that actively remodels the actin cytoskeleton and changes cell shape. Here we study how the collective action of myosin motors organizes actin filaments into contractile structures in a simplified model system devoid of biochemical regulation. We show that this self-organization occurs t...

We measure the elastic properties of composite cytoskeletal networks consisting of cross-linked actin filaments and microtubules. We show that even a small concentration of microtubules leads to dramatic and qualitative changes in the non-linear elastic properties of the actin filament networks. Specifically, we find that microtubules promote non-l...

Networks of the cytoskeletal biopolymer actin cross-linked by the compliant protein filamin form soft gels that stiffen dramatically under shear stress. We demonstrate that the elasticity of these networks shows a strong dependence on the mean length of the actin polymers, unlike networks with small, rigid cross-links. This behavior is in agreement...

Fibrin gels are responsible for the mechanical strength of blood clots, which are among the most resilient protein materials in nature. Here we investigate the physical origin of this mechanical behavior by performing rheology measurements on reconstituted fibrin gels. We find that increasing levels of shear strain induce a succession of distinct e...

We describe an active polymer network in which processive molecular motors control network elasticity. This system consists of actin filaments cross-linked by filamin A (FLNa) and contracted by bipolar filaments of muscle myosin II. The myosin motors stiffen the network by more than two orders of magnitude by pulling on actin filaments anchored in...

All substances exhibit constant random motion at the microscopic scale. This is a direct consequence of thermal agitation, and leads to diffusion of molecules and small particles in a liquid. In addition to this nondirected motion, living cells also use active transport mechanisms, such as motor activity and polymerization forces that depend on lin...

Lumbar discectomy is an effective therapy for neurological decompression in patients suffering from sciatica due to a herniated nucleus pulposus (NP). However, high numbers of patients suffering from persisting postoperative low back pain have resulted in many strategies targeting the regeneration of the NP. For successful regeneration, the stiffne...

Networks of the biopolymer actin, cross-linked by the compliant protein filamin, form soft gels. They can, however, withstand large shear stresses due to their pronounced nonlinear elastic behavior. The nonlinear elasticity can be controlled by varying the number of cross-links per actin filament. We propose and test a model of rigid filaments deco...

We present techniques based on optical trapping of micron-sized particles as probes and detecting their motion with sub-nanometer accuracy at 100 kHz bandwidth that can measure viscoelastic properties of biomaterials and cells on micrometer scales.

Random motion within the cytoplasm gives rise to molecular diffusion; this motion is essential to many biological processes. However, in addition to thermal Brownian motion, the cytoplasm also undergoes constant agitation caused by the activity of molecular motors and other nonequilibrium cellular processes. Here, we discuss recent work that sugges...

We have directly observed short-time stress propagation in viscoelastic fluids using two optically trapped particles and a fast interferometric particle-tracking technique. We have done this both by recording correlations in the thermal motion of the particles and by measuring the response of one particle to the actively oscillated second particle....

Cells actively produce contractile forces for a variety of processes including cytokinesis and motility. Contractility is known to rely on myosin II motors which convert chemical energy from ATP hydrolysis into forces on actin filaments. However, the basic physical principles of cell contractility remain poorly understood. We reconstitute contracti...

Biological activity gives rise to nonequilibrium fluctuations in the cytoplasm of cells; however, there are few methods to directly measure these fluctuations. Using a reconstituted actin cytoskeleton, we show that the bending dynamics of embedded microtubules can be used to probe local stress fluctuations. We add myosin motors that drive the netwo...

Microtubules are filamentous protein biopolymers found in eukaryotic cells. They form networks that guide active intracellular transport and support the overall cell structure. Microtubules are very rigid polymers, with persistence lengths as large as a millimeter. As such, they constitute an example of rodlike polymers, whose mechanical and rheolo...

Microscope images of fluctuating biopolymers contain a wealth of information about their underlying mechanics and dynamics. However, successful extraction of this information requires precise localization of filament position and shape from thousands of noisy images. Here, we present careful measurements of the bending dynamics of filamentous (F-)a...

We image semiflexible polymer networks under shear at the micrometer scale. By tracking embedded probe particles, we determine the local strain field, and directly measure its uniformity, or degree of affineness, on scales of 2-100 microm. The degree of nonaffine strain depends upon the polymer length and cross-link density, consistent with theoret...

We explore the non-linear shearing behavior of composite actin and microtubule networks. Large bending rigid microtubules are used as a probe of the deformation mode of cross-linked actin networks. For a sparsely cross-linked actin network that deforms non-affinely, adding microtubules can drive the system back to affine by suppressing local rearra...

To elucidate the dynamic and functional role of a cell within the tissue it belongs to, it is essential to understand its material properties. The cell is a viscoelastic material with highly unusual properties. Measurements of the mechanical behavior of cells are beginning to probe the contribution of constituent components to cell mechanics. Recon...

The Brownian motions of microscopic particles in viscous or viscoelastic fluids can be used to measure rheological properties. This is the basis of recently developed one- and two-particle microrheology techniques. For increased temporal and spatial resolution, some microrheology techniques employ optical traps, which introduce additional forces on...

Semiflexible polymers are of great biological importance in determining the mechanical properties of cells. We have used optical tweezers to trap pairs of micron-sized silica spheres in solutions of semiflexible polymers, and laser interferometry to detect their thermal motions with high bandwidth. Frequency-dependent complex shear moduli were extr...

We measure the linear viscoelasticity of sterically entangled and chemically cross-linked networks of actin filaments over more than five decades of frequency. The high-frequency response reveals rich dynamics unique to semiflexible polymers, including a previously unobserved relaxation due to rapid axial tension propagation. For high molecular wei...

We probe the response of viscous and viscoelastic fluids on micrometer and microsecond length and time scales using two optically trapped beads. In this way we resolve the flow field, which exhibits clear effects of fluid inertia. Specifically, we resolve the short-time vortex flow and the corresponding evolution of this vortex, which propagates di...

We present a convenient and low-cost method to prepare milligram amounts of completely monodisperse DNA restriction fragments in a physico-chemical laboratory setting to study (in part II) the effect of limited flexibility on the concentration dependent sedimentation velocity. Four fragments of 200, 400, 800, and 1600 bp were designed to span a ran...

We report sedimentation velocity and equilibrium measurements performed with an analytical ultracentrifuge to elucidate the effects of limited flexibility on the transport properties of semiflexible, monodisperse, double-stranded, blunt-ended DNA restriction fragments. We study a homologous series of fragments with 400, 800, and 1600 base pairs (3...

The polymerization in a microemulsion, which provides a useful technique for the synthesis of very small fluorinated latex particles in the size range 17-50 nm, was described. The microemulsion was irradiated at room temperature for 8 h by an 8-W ultraviolet (UV) lightbulb to promote the radical polymerization. Dynamic light scattering (DLS) and tr...