Conformation of Fibronectin Fibrils Varies: Discrete Globular Domains of Type III Repeats Detected

Emerging Trends in Information-Driven Engineering of Complex Biological Systems

Synthetic biological systems are used for a myriad of applications, including tissue engineered constructs for in vivo use and microengineered devices for in vitro testing. Recent advances in engineering complex biological systems have been fueled by opportunities arising from the combination of bioinspired materials with biological and computational tools. Driven by the availability of large datasets in the "omics" era of biology, the design of the next generation of tissue equivalents will have to integrate information from single-cell behavior to whole organ architecture. Herein, recent trends in combining multiscale processes to enable the design of the next generation of biomaterials are discussed. Any successful microprocessing pipeline must be able to integrate hierarchical sets of information to capture key aspects of functional tissue equivalents. Micro- and biofabrication techniques that facilitate hierarchical control as well as emerging polymer candidates used in these technologies are also reviewed.

3D mapping of native extracellular matrix reveals cellular responses to the microenvironment

Cells and extracellular matrix (ECM) are mutually interdependent: cells guide self-assembly of ECM precursors, and the resulting ECM architecture supports and instructs cells. Though bidirectional signaling between ECM and cells is fundamental to cell biology, it is challenging to gain high-resolution structural information on cellular responses to the matrix microenvironment. Here we used cryo-scanning transmission electron tomography (CSTET) to reveal the nanometer- to micron-scale organization of major fibroblast ECM components in a native-like context, while simultaneously visualizing internal cell ultrastructure including organelles and cytoskeleton. In addition to extending current models for collagen VI fibril organization, three-dimensional views of thick cell regions and surrounding matrix showed how ECM networks impact the structures and dynamics of intracellular organelles and how cells remodel ECM. Collagen VI and fibronectin were seen to distribute in fundamentally different ways in the cell microenvironment and perform distinct roles in supporting and interacting with cells. This work demonstrates that CSTET provides a new perspective for the study of ECM in cell biology, highlighting labeled extracellular elements against a backdrop of unlabeled but morphologically identifiable cellular features with nanometer resolution detail.

The Molecular Dance of Fibronectin: Conformational Flexibility Leads to Functional Versatility

Fibronectin, a large multimodular protein and one of the major fibrillar components of the extracellular matrix, has been the subject of study for many decades and plays critical roles in embryonic development and tissue homeostasis. Moreover, fibronectin has been implicated in the pathology of many diseases, including cancer, and abnormal depositions of fibronectin have been identified in a number of amyloid and nonamyloid lesions. The ability of fibronectin to carry all these diverse functionalities depends on interactions with a large number of molecules, including adhesive and signaling cell surface receptors, other components of the extracellular matrix, and growth factors and cytokines. The regulation and integration of such large number of interactions depends on the modular architecture of fibronectin, which allows a large number of conformations, exposing or destroying different binding sites. In this Review, we summarize the current knowledge regarding the conformational flexibility of fibronectin, with an emphasis on how it regulates the ability of fibronectin to interact with various signaling molecules and cell-surface receptors and to form supramolecular assemblies and fibrillar structures.

Shear-dependent fibrillogenesis of fibronectin: Impact of platelet integrins and actin cytoskeleton

Soluble plasma fibronectin (Fn) with its inactive compact structure requires unfolding to assemble into active fibrils, which play a role in hemostasis and thrombosis. Fn fibril assembly involves Fn binding to cell receptors, biomechanical coupling of Fn to the cytoskeleton by integrins, exposure of self-assembly sites via contractile cell forces, and elongation of fibrils by Fn polymerization. In this report, we investigated the effect of platelet integrins and actin cytoskeleton on conformational changes of Fn induced by shear. Plasma Fn, in the presence or absence of washed platelets, was exposed to dynamic shear simulating venous or arterial flow conditions. Platelet integrins (αIIbβ3, αvβ3, and α5β1) were blocked by inhibitory antibodies to determine their contribution to shear-induced Fn fibrillogenesis. To examine the role of platelet cytoskeleton in Fn fibrillogenesis induced by shear, platelets were preincubated with cytoskeleton drugs, i. e jasplakinolide to stabilize actin or cytochalasin D to inhibit actin polymerization. Microscopic analyses demonstrated that flow and resulting shear stress over a broad range of physiological and pathological rates (50-5000 s^-1) could induce conformational changes of plasma Fn. In addition, the formation of Fn fibrils is modulated by platelet integrins. In this respect, β3 integrins play a dominant role in terms of Fn fibrillogenesis induced by shear. Disruption of the actin polymerization markedly diminished Fn unfolding and assembly. These observations lead to the conclusion that Fn-integrin β3-cytoskeleton interaction is crucial for the assembly of plasma Fn matrix under flow conditions.

Stretch-dependent changes in molecular conformation in fibronectin nanofibers

Fibronectin (FN) is an extracellular matrix (ECM) glycoprotein that plays an important role in a wide range of biological processes including embryonic development, wound healing, and fibrosis. Recent evidence has demonstrated that FN is mechanosensitive, where the application of force induces conformational changes within the FN molecule to expose otherwise cryptic binding domains. However, it has proven technically challenging to dynamically monitor how the nanostructure of FN fibers changes as a result of force-induced extension, due in part to the inherent complexity of FN networks within tissue and cell-generated extracellular matrix (ECM). This has limited our understanding of FN matrix mechanobiology and the complex bi-directional signaling between cells and the ECM, and de novo FN fiber fabrication strategies have only partially addressed this. Towards addressing this need, we have developed a modified surface-initiated assembly (SIA) technique to engineer FN nanofibers that we can uniaxially stretch to >7-fold extensions and subsequently immobilize them in the stretched state for high resolution atomic force microscopy (AFM) imaging. Using this approach, we analyzed how the nanostructure of FN molecules within the nanofibers changed with stretch. In fully contracted FN nanofibers, we observed large, densely packed, isotropically-oriented nodules. With intermediate extension, uniaxially-aligned fibrillar regions developed and nodules became progressively smaller. At high extension, the nanostructure consisted of highly aligned fibrils with small nodules in a beads-on-a-string arrangement. In summary, we have established a methodology to uniaxially stretch FN fibers and monitor changes in nanostructure using AFM. Our results provide new insight into how FN fiber extension can affect the morphology of the constituent FN molecules.

Studying early stages of fibronectin fibrillogenesis in living cells by atomic force microscopy

Time-lapse atomic force microscopy imaging is used to visualize the initial stages of fibronectin fibrillogenesis directly in living cells with high resolution. This approach provides new structural and mechanistic details, such as a stepwise extension mechanism and an accelerating effect of extracellular Mn²⁺ on early FN fibrillogenesis.

Fibronectin (FN) is an extracellular matrix protein that can be assembled by cells into large fibrillar networks, but the dynamics of FN remodeling and the transition through intermediate fibrillar stages are incompletely understood. Here we used a combination of fluorescence microscopy and time-lapse atomic force microscopy (AFM) to visualize initial stages of FN fibrillogenesis in living fibroblasts at high resolution. Initial FN nanofibrils form within <5 min of cell–matrix contact and subsequently extend at a rate of 0.25 μm/min at sites of cell membrane retraction. FN nanofibrils display a complex linear array of globular features spaced at varying distances, indicating the coexistence of different conformational states within the fibril. In some cases, initial fibrils extended in discrete increments of ∼800 nm during a series of cyclical membrane retractions, indicating a stepwise fibrillar extension mechanism. In presence of Mn²⁺, a known activator of integrin adhesion to FN, fibrillogenesis was accelerated almost threefold to 0.68 μm/min and fibrillar dimensions were increased, underlining the importance of integrin activation for early FN fibrillogenesis. FN fibrillogenesis visualized by time-lapse AFM thus provides new structural and mechanistic insight into initial steps of cell-driven FN fibrillogenesis.

Studying early stages of fibronectin fibrillogenesis in living cells by atomic force microscopy

Fibronectin (FN) is an extracellular matrix protein that can be assembled by cells into large fibrillar networks, but the dynamics of FN remodeling and the transition through intermediate fibrillar stages are incompletely understood. Here we used a combination of fluorescence microscopy and time-lapse atomic force microscopy (AFM) to visualize initial stages of FN fibrillogenesis in living fibroblasts at high resolution. Initial FN nanofibrils form within <5 min of cell–matrix contact and subsequently extend at a rate of 0.25 μm/min at sites of cell membrane retraction. FN nanofibrils display a complex linear array of globular features spaced at varying distances, indicating the coexistence of different conformational states within the fibril. In some cases, initial fibrils extended in discrete increments of ∼800 nm during a series of cyclical membrane retractions, indicating a stepwise fibrillar extension mechanism. In presence of Mn2+, a known activator of integrin adhesion to FN, fibrillogenesis was accelerated almost threefold to 0.68 μm/min and fibrillar dimensions were increased, underlining the importance of integrin activation for early FN fibrillogenesis. FN fibrillogenesis visualized by time-lapse AFM thus provides new structural and mechanistic insight into initial steps of cell-driven FN fibrillogenesis.

Molecular architecture of native fibronectin fibrils

Fibronectin fibrils within the extracellular matrix play central roles in physiological and pathological processes, yet many structural details about their hierarchical and molecular assembly remain unknown. Here we combine site-specific protein labelling with single-molecule localization by stepwise photobleaching or direct stochastic optical reconstruction microscopy (dSTORM), and determine the relative positions of various labelled sites within native matrix fibrils. Single end-labelled fibronectin molecules in fibrils display an average end-to-end distance of ∼133 nm. Sampling of site-specific antibody epitopes along the thinnest fibrils (protofibrils) shows periodic punctate label patterns with ∼95 nm repeats and alternating N- and C-terminal regions. These measurements suggest an antiparallel 30–40 nm overlap between N-termini, suggesting that the first five type I modules bind type III modules of the adjacent molecule. Thicker fibres show random bundling of protofibrils without a well-defined line-up. This super-resolution microscopy approach can be applied to other fibrillar protein assemblies of unknown structure.

Fibronectin fibres are an important component of the extracellular matrix, supporting cell adhesion, growth and migration. Here the authors combine site-specific protein labelling with single-molecule localization microscopy to provide detailed insights into the molecular organization of native fibronectin fibrils.

The ultrastructure of fibronectin fibers pulled from a protein monolayer at the air-liquid interface and the mechanism of the sheet-to-fiber transition

Fibronectin is a globular protein that circulates in the blood and undergoes fibrillogenesis if stretched or under other partially denaturing conditions, even in the absence of cells. Stretch assays made by pulling fibers from droplets of solutions containing high concentrations of fibronectin have previously been introduced in mechanobiology, particularly to ask how bacteria and cells exploit the stretching of fibronectin fibers within extracellular matrix to mechano-regulate its chemical display. Our electron microscopy analysis of their ultrastructure now reveals that the manually pulled fibronectin fibers are composed of densely packed lamellar spirals, whose interlamellar distances are dictated by ion-tunable electrostatic interactions. Our findings suggest that fibrillogenesis proceeds via an irreversible sheet-to-fiber transition as the fibronectin sheet formed at the air-liquid interface of the droplet is pulled off by a sharp tip. This far from equilibrium process is driven by the externally applied force, interfacial surface tension, shear-induced fibronectin self-association, and capillary force-induced buffer drainage. The ultrastructural characterization is then contrasted with previous FRET studies that characterized the molecular strain within these manually pulled fibers. Particularly relevant for stretch-dependent binding studies is the finding that the interior fiber surfaces are accessible to nanoparticles smaller than 10 nm. In summary, our study discovers the underpinning mechanism by which highly hierarchically structured fibers can be generated with unique mechanical and mechano-chemical properties, a concept that might be extended to other bio- or biomimetic polymers.

A fluorophore-tagged RGD peptide to control endothelial cell adhesion to micropatterned surfaces

The long-term patency rates of vascular grafts and stents are limited by the lack of surface endothelialisation of the implanted materials. We have previously reported that GRGDS and WQPPRARI peptide micropatterns increase the endothelialisation of prosthetic materials in vitro. To investigate the mechanisms by which the peptide micropatterns affect endothelial cell adhesion and proliferation, a TAMRA fluorophore-tagged RGD peptide was designed. Live cell imaging revealed that the micropatterned surfaces led to directional cell spreading dependent on the location of the RGD-TAMRA spots. Focal adhesions formed within 3 h on the micropatterned surfaces near RGD-TAMRA spot edges, as expected for cell regions experiencing high tension. Similar levels of focal adhesion kinase phosphorylation were observed after 3 h on the micropatterned surfaces and on surfaces treated with RGD-TAMRA alone, suggesting that partial RGD surface coverage is sufficient to elicit integrin signaling. Lastly, endothelial cell expansion was achieved in serum-free conditions on gelatin-coated, RGD-TAMRA treated or micropatterned surfaces. These results show that these peptide micropatterns mainly impacted cell adhesion kinetics rather than cell proliferation. This insight will be useful for the optimization of micropatterning strategies to improve vascular biomaterials.

Fibers with integrated mechanochemical switches: minimalistic design principles derived from fibronectin

Inspired by molecular mechanisms that cells exploit to sense mechanical forces and convert them into biochemical signals, chemists dream of designing mechanochemical switches integrated into materials. Using the adhesion protein fibronectin, whose multiple repeats essentially display distinct molecular recognition motifs, we derived a computational model to explain how minimalistic designs of repeats translate into the mechanical characteristics of their fibrillar assemblies. The hierarchy of repeat-unfolding within fibrils is controlled not only by their relative mechanical stabilities, as found for single molecules, but also by the strength of cryptic interactions between adjacent molecules that become activated by stretching. The force-induced exposure of cryptic sites furthermore regulates the nonlinearity of stress-strain curves, the strain at which such fibers break, and the refolding kinetics and fraction of misfolded repeats. Gaining such computational insights at the mesoscale is important because translating protein-based concepts into novel polymer designs has proven difficult.

Using molecular mechanics to predict bulk material properties of fibronectin fibers

The structural proteins of the extracellular matrix (ECM) form fibers with finely tuned mechanical properties matched to the time scales of cell traction forces. Several proteins such as fibronectin (Fn) and fibrin undergo molecular conformational changes that extend the proteins and are believed to be a major contributor to the extensibility of bulk fibers. The dynamics of these conformational changes have been thoroughly explored since the advent of single molecule force spectroscopy and molecular dynamics simulations but remarkably, these data have not been rigorously applied to the understanding of the time dependent mechanics of bulk ECM fibers. Using measurements of protein density within fibers, we have examined the influence of dynamic molecular conformational changes and the intermolecular arrangement of Fn within fibers on the bulk mechanical properties of Fn fibers. Fibers were simulated as molecular strands with architectures that promote either equal or disparate molecular loading under conditions of constant extension rate. Measurements of protein concentration within micron scale fibers using deep ultraviolet transmission microscopy allowed the simulations to be scaled appropriately for comparison to in vitro measurements of fiber mechanics as well as providing estimates of fiber porosity and water content, suggesting Fn fibers are approximately 75% solute. Comparing the properties predicted by single molecule measurements to in vitro measurements of Fn fibers showed that domain unfolding is sufficient to predict the high extensibility and nonlinear stiffness of Fn fibers with surprising accuracy, with disparately loaded fibers providing the best fit to experiment. This work shows the promise of this microstructural modeling approach for understanding Fn fiber properties, which is generally applicable to other ECM fibers, and could be further expanded to tissue scale by incorporating these simulated fibers into three dimensional network models.

There is growing awareness of the role of mechanical properties within biological tissues. Cells both generate force and are sensitive to applied forces, however nuanced sensitivity to externally applied forces also extends outside the cell to the fibrous structural proteins of the extracellular matrix. It has been shown that stretching these proteins under force can change their biochemical properties in a way that impacts tissue function. In this work we were able, for the first time, to measure the concentration of protein within fibronectin extracellular matrix fibers. This key measurement then enabled us to evaluate a model that links mechanical properties of fibers directly to molecular structural changes that form the physical basis for force sensitivity. The model was found to be predictive of fiber mechanical properties without fitting. This combination of modeling and experiment also offers insights into molecular forces, as well as estimates of fiber hydration and porosity.

Surface-initiated assembly of protein nanofabrics

Cells and tissues are self-organized within an extracellular matrix (ECM) composed of multifunctional, nano- to micrometer scale protein fibrils. We have developed a cell-free, surface-initiated assembly technique to rebuild this ECM structure in vitro. The matrix proteins fibronectin, laminin, fibrinogen, collagen type I, and collagen type IV are micropatterned onto thermosensitive surfaces as 1 to 10 nm thick, micrometer to centimeter wide networks, and released as flexible, free-standing nanofabrics. Independent control of microstructure and protein composition enables us to engineer the mechanical and chemical anisotropy. Fibronectin nanofabrics are highly extensible (>4-fold) and serve as scaffolds for engineering synchronously contracting, cardiac muscle; demonstrating biofunctionality comparable to cell-generated ECM.

Periodic beaded-filament assembly of fibronectin on negatively charged surface

Fibronectin (FN) is an extracellular glycoprotein with critical roles in many fundamental biological processes. A hallmark of FN function is its characteristic assembly into filaments and fibers to form an insoluble matrix which functions as a scaffolding onto which cells attach, migrate, and deposit other matrix constituents. In this study, we have investigated the effects of differently charged and functionalized surfaces on FN conformations using atomic force microscopy. We demonstrate that a negatively charged polysulfonated surface promotes the formation of highly periodic, micrometer-long FN filaments having a "bead-on-a-string" structure with a bead periodicity of about 60 nm. Beaded filaments were observed when FN was adsorbed to polysulfonate surface in water; higher ionic strength allowed formation of filamentous structures but altered the regularity of the beads. FN did not form filaments when adsorbed onto the polysulfonate surface in the presence of soluble polysulfonates emphasizing the role of negatively charged, solid-phase elements on FN assembly. This charge-driven assembly likely derives from the negative surface promoting extension and opening of the protein, and we suggest a model where this assembly pattern is further stabilized by known self-assembly regions. Our results give insight into how FN fibrillogenesis might be promoted in vivo at cell surfaces by the negatively charged and sulfonated environment created by cell-surface, transmembrane proteoglycans.

Assay to mechanically tune and optically probe fibrillar fibronectin conformations from fully relaxed to breakage

In response to growing needs for quantitative biochemical and cellular assays that address whether the extracellular matrix (ECM) acts as a mechanochemical signal converter to co-regulate cellular mechanotransduction processes, a new assay is presented where plasma fibronectin fibers are manually deposited onto elastic sheets, while force-induced changes in protein conformation are monitored by fluorescence resonance energy transfer (FRET). Fully relaxed assay fibers can be stretched at least 5-6 fold, which involves Fn domain unfolding, before the fibers break. In native fibroblast ECM, this full range of stretch-regulated conformations coexists in every field of view confirming that the assay fibers are physiologically relevant model systems. Since alterations of protein function will directly correlate with their extension in response to force, the FRET vs. strain curves presented herein enable the mapping of fibronectin strain distributions in 2D and 3D cell cultures with high spatial resolution. Finally, cryptic sites for fibronectin's N-terminal 70-kD fragment were found to be exposed at relatively low strain, demonstrating the assay's potential to analyze stretch-regulated protein-protein interactions.

Force-induced unfolding of fibronectin in the extracellular matrix of living cells

Whether mechanically unfolded fibronectin (Fn) is present within native extracellular matrix fibrils is controversial. Fn extensibility under the influence of cell traction forces has been proposed to originate either from the force-induced lengthening of an initially compact, folded quaternary structure as is found in solution (quaternary structure model, where the dimeric arms of Fn cross each other), or from the force-induced unfolding of type III modules (unfolding model). Clarification of this issue is central to our understanding of the structural arrangement of Fn within fibrils, the mechanism of fibrillogenesis, and whether cryptic sites, which are exposed by partial protein unfolding, can be exposed by cell-derived force. In order to differentiate between these two models, two fluorescence resonance energy transfer schemes to label plasma Fn were applied, with sensitivity to either compact-to-extended conformation (arm separation) without loss of secondary structure or compact-to-unfolded conformation. Fluorescence resonance energy transfer studies revealed that a significant fraction of fibrillar Fn within a three-dimensional human fibroblast matrix is partially unfolded. Complete relaxation of Fn fibrils led to a refolding of Fn. The compactly folded quaternary structure with crossed Fn arms, however, was never detected within extracellular matrix fibrils. We conclude that the resting state of Fn fibrils does not contain Fn molecules with crossed-over arms, and that the several-fold extensibility of Fn fibrils involves the unfolding of type III modules. This could imply that Fn might play a significant role in mechanotransduction processes.

Domain Unfolding Plays a Role in Superfibronectin Formation

Superfibronectin (sFN) is a fibronectin (FN) aggregate that is formed by mixing FN with anastellin, a fragment of the first type III domain of FN. However, the mechanism of this aggregation has not been clear. In this study, we found that anastellin co-precipitated with FN in a ratio of approximately 4:1, anastellin:FN monomer. The primary binding site for anastellin was in the segment (III)1-3, which bound three molecules of anastellin and was able to form a precipitate without the rest of the FN molecule. Anastellin binding to (III)3 caused a conformational change in that domain that exposed a cryptic thermolysin-sensitive site. An additional anastellin binds to (III)11, where it enhances thermolysin digestion of (III)11. An engineered disulfide bond in (III)3 inhibited both aggregation and protease digestion, suggesting that the stability of (III)3 is a key factor in sFN formation. We propose a three-step model for sFN formation: 1) FN-III domains spontaneously unfold and refold; 2) anastellin binds to an unfolded domain, preventing its refolding and leaving it with exposed hydrophobic surfaces and beta-sheet edges; and 3) these exposed elements bind to similar exposed elements on other molecules, leading to aggregation. The model is consistent with our observation that the kinetics of aggregation are first order, with a reaction time of 500-700 s. Similar mechanisms may contribute to the assembly of the native FN matrix.

Dual labeling of the fibronectin matrix and actin cytoskeleton with green fluorescent protein variants

We have prepared 3T3 cells doubly labeled to visualize simultaneously the extracellular fibronectin (FN) matrix and intracellular actin cytoskeleton in living cell cultures. We used FN-yellow fluorescent protein (FN-yfp) for the FN matrix, and the actin-binding domain of moesin fused to cyan fluorescent protein (cfp-Moe) to stain actin. Actin filament bundles were clearly seen in the protruding lamellae of the cells. FN matrix assembly appeared to be initiated as small spots of FN at the ends of actin filament bundles. The spots then elongated along the actin filament bundle toward the cell center to form FN fibrils. The end of the fibril towards the cell edge appeared immobile, and probably attached to the substrate, whereas the end toward the cell center frequently showed movements, suggesting attachment to the cell. Combining our data with the observations of Pankov et al. we suggest that fibrils grow by stretching this mobile end toward the cell center while adding new FN molecules at the end and along the entire lenght. When the cell culture was treated with cytochalasin to disrupt the actin cytoskeleton, some fibrils contracted substantially, suggesting that the segment attached primarily to the cell surface is stretched.

Stimulation of integrin-mediated cell contractility by fibronectin polymerization

Ligation of integrins with extracellular matrix molecules induces the clustering of actin and actin-binding proteins to focal adhesions, which serves to mechanically couple the matrix with the cytoskeleton. During wound healing and development, matrix deposition and remodeling may impart additional tensile forces that modulate integrin-mediated cell functions, including cell migration and proliferation. We have utilized the ability of cells to contract floating collagen gels to determine the effect of fibronectin polymerization on mechanical tension generation by cells. Our data indicate that fibronectin polymerization promotes cell spreading in collagen gels and stimulates cell contractility by a Rho-dependent mechanism. Fibronectin-stimulated contractility was dependent on integrin ligation; however, integrin ligation by fibronectin fragments was not sufficient to induce either tension generation or cell spreading. Furthermore, treatment of cells with polyvalent RGD peptides or pre-polymerized fibronectin did not stimulate cell contractility. Fibronectin-induced contractility was blocked by agents that inhibit fibronectin polymerization, suggesting that the process of fibronectin polymerization is critical in triggering cytoskeletal tension generation. These data indicate that Rho-mediated cell contractility is regulated by the process of fibronectin polymerization and suggest a novel mechanism by which extracellular matrix fibronectin regulates cytoskeletal organization and cell function.

Fibronectin fibrillogenesis: a paradigm for extracellular matrix assembly

Fibronectin matrix assembly is a regulated stepwise process. In the past year, analyses of fibronectin domains, integrin and cytoskeletal contributions, and fibril architecture have provided new insights into assembly mechanisms and matrix control of cell functions. Like fibronectin, laminin polymerization is cell-mediated. Thus a common pathway for extracellular matrix assembly is emerging.