Morphological Transitions of a Photoswitchable Aramid Amphiphile Nanostructure.

Self-assembly of small amphiphilic molecules in water can lead to nanostructures of varying geometries with pristine internal molecular organization. Here we introduce a photoswitchable aramid amphiphile (AA), designed to exhibit extensive hydrogen bonding and robust mechanical properties upon self-assembly, while containing a vinylnitrile group for photoinduced cis-trans isomerization. We demonstrate spontaneous self-assembly of the vinylnitrile-containing AA in water to form nanoribbons. Upon UV irradiation, trans-to-cis isomerizations occur concomitantly with a morphological transition from nanoribbons to nanotubes. The nanotube structure persists in water for over six months, stabilized by strong and collective intermolecular interactions. We demonstrate that the nanoribbon-to-nanotube transition is reversible upon heating and that switching between states can be achieved repeatedly. Finally, we use electron microscopy to capture the transition and propose mechanisms for nanoribbon-to-nanotube rearrangement and vice versa. The stability and switchability of photoresponsive AA nanostructures make them viable for a range of future applications.

Inverse Correlation between Amyloid Stiffness and Size.

We reveal that the axial stiffness of amyloid fibrils is inversely correlated with their cross-sectional area. Because amyloid fibrils' stiffness is determined by hydrogen bond (H-bond) density with a linear correlation, our finding implies that amyloid fibrils with larger radial sizes are generally softer and have lower density H-bond networks. In silico calculations show that the stiffness-size relationship of amyloid fibrils is, indeed, driven by the packing densities of residues and H-bonds. Our results suggest that polypeptide chains which form amyloid fibrils with narrow cross sections can optimize packing densities in the fibrillar core structure, in contrast to those forming wide amyloid fibrils. Consequently, the density of residues and H-bonds that contribute to mechanical stability is higher in amyloid fibrils with narrow cross sections. This size dependence of nanomechanics appears to be a global property of amyloid fibrils, just like the well-known cross-ß sheet topology.

Mapping the Broad Structural and Mechanical Properties of Amyloid Fibrils.

Amyloids are fibrillar nanostructures of proteins that are assembled in several physiological processes in human cells (e.g., hormone storage) but also during the course of infectious (prion) and noninfectious (nonprion) diseases such as Creutzfeldt-Jakob and Alzheimer's diseases, respectively. How the amyloid state, a state accessible to all proteins and peptides, can be exploited for functional purposes but also have detrimental effects remains to be determined. Here, we measure the nanomechanical properties of different amyloids and link them to features found in their structure models. Specifically, we use shape fluctuation analysis and sonication-induced scission in combination with full-atom molecular dynamics simulations to reveal that the amyloid fibrils of the mammalian prion protein PrP are mechanically unstable, most likely due to a very low hydrogen bond density in the fibril structure. Interestingly, amyloid fibrils formed by HET-s, a fungal protein that can confer functional prion behavior, have a much higher Young's modulus and tensile strength than those of PrP, i.e., they are much stiffer and stronger due to a tighter packing in the fibril structure. By contrast, amyloids of the proteins RIP1/RIP3 that have been shown to be of functional use in human cells are significantly stiffer than PrP fibrils but have comparable tensile strength. Our study demonstrates that amyloids are biomaterials with a broad range of nanomechanical properties, and we provide further support for the strong link between nanomechanics and ß-sheet characteristics in the amyloid core.

Changes in Structural-Mechanical Properties and Degradability of Collagen during Aging-associated Modifications.

During aging, changes occur in the collagen network that contribute to various pathological phenotypes in the skeletal, vascular, and pulmonary systems. The aim of this study was to investigate the consequences of age-related modifications on the mechanical stability and in vitro proteolytic degradation of type I collagen. Analyzing mouse tail and bovine bone collagen, we found that collagen at both fibril and fiber levels varies in rigidity and Young's modulus due to different physiological changes, which correlate with changes in cathepsin K (CatK)-mediated degradation. A decreased susceptibility to CatK-mediated hydrolysis of fibrillar collagen was observed following mineralization and advanced glycation end product-associated modification. However, aging of bone increased CatK-mediated osteoclastic resorption by ∼27%, and negligible resorption was observed when osteoclasts were cultured on mineral-deficient bone. We observed significant differences in the excavations generated by osteoclasts and C-terminal telopeptide release during bone resorption under distinct conditions. Our data indicate that modification of collagen compromises its biomechanical integrity and affects CatK-mediated degradation both in bone and tissue, thus contributing to our understanding of extracellular matrix aging.

The prion protein ligand, stress-inducible phosphoprotein 1, regulates amyloid-ß oligomer toxicity.

In Alzheimer's disease (AD), soluble amyloid-ß oligomers (AßOs) trigger neurotoxic signaling, at least partially, via the cellular prion protein (PrP(C)). However, it is unknown whether other ligands of PrP(C) can regulate this potentially toxic interaction. Stress-inducible phosphoprotein 1 (STI1), an Hsp90 cochaperone secreted by astrocytes, binds to PrP(C) in the vicinity of the AßO binding site to protect neurons against toxic stimuli. Here, we investigated a potential role of STI1 in AßO toxicity. We confirmed the specific binding of AßOs and STI1 to the PrP and showed that STI1 efficiently inhibited AßO binding to PrP in vitro (IC50 of ∼70 nm) and also decreased AßO binding to cultured mouse primary hippocampal neurons. Treatment with STI1 prevented AßO-induced synaptic loss and neuronal death in mouse cultured neurons and long-term potentiation inhibition in mouse hippocampal slices. Interestingly, STI1-haploinsufficient neurons were more sensitive to AßO-induced cell death and could be rescued by treatment with recombinant STI1. Noteworthy, both AßO binding to PrP(C) and PrP(C)-dependent AßO toxicity were inhibited by TPR2A, the PrP(C)-interacting domain of STI1. Additionally, PrP(C)-STI1 engagement activated α7 nicotinic acetylcholine receptors, which participated in neuroprotection against AßO-induced toxicity. We found an age-dependent upregulation of cortical STI1 in the APPswe/PS1dE9 mouse model of AD and in the brains of AD-affected individuals, suggesting a compensatory response. Our findings reveal a previously unrecognized role of the PrP(C) ligand STI1 in protecting neurons in AD and suggest a novel pathway that may help to offset AßO-induced toxicity.

Effects of cysteine proteases on the structural and mechanical properties of collagen fibers.

Excessive cathepsin K (catK)-mediated turnover of fibrillar type I and II collagens in bone and cartilage leads to osteoporosis and osteoarthritis. However, little is known about how catK degrades compact collagen macromolecules. The present study is aimed to explore the structural and mechanical consequences of collagen fiber degradation by catK. Mouse tail type I collagen fibers were incubated with either catK or non-collagenase cathepsins. Methods used include scanning electron microscopy, protein electrophoresis, atomic force microscopy, and tensile strength testing. Our study revealed evidence of proteoglycan network degradation, followed by the progressive disassembly of macroscopic collagen fibers into primary structural elements by catK. Proteolytically released GAGs are involved in the generation of collagenolytically active catK-GAG complexes as shown by AFM. In addition to their structural disintegration, a decrease in the tensile properties of fibers was observed due to the action of catK. The Young's moduli of untreated collagen fibers versus catK-treated fibers in dehydrated conditions were 3.2 ± 0.68 GPa and 1.9 ± 0.65 GPa, respectively. In contrast, cathepsin L, V, B, and S revealed no collagenase activity, except the disruption of proteoglycan-GAG interfibrillar bridges, which slightly decreased the tensile strength of fibers.

Mechanically tightening a protein slipknot into a trefoil knot.

The knotted/slipknotted polypeptide chain is one of the most surprising topological features found in certain proteins. Understanding how knotted/slipknotted proteins overcome the topological difficulty during the folding process has become a challenging problem. By stretching a knotted/slipknotted protein, it is possible to untie or tighten a knotted polypeptide and even convert a slipknot to a true knot. Here, we use single molecule force spectroscopy as well as steered molecular dynamics (SMD) simulations to investigate how the slipknotted protein AFV3-109 is transformed into a tightened trefoil knot by applied pulling force. Our results show that by pulling the N-terminus and the threaded loop of AFV3-109, the protein can be unfolded via multiple pathways and the slipknot can be transformed into a tightened trefoil knot involving ∼13 amino acid residues as the polypeptide chain is apparently shortened by ∼4.7 nm. The SMD simulation results are largely consistent with our experimental findings, providing a plausible and detailed molecular mechanism of mechanical unfolding and knot tightening of AFV3-109. These simulations reveal that interactions between shearing ß-strands on the threaded and knotting loops provide high mechanical resistance during mechanical unfolding.

Construction and characterization of kilobasepair densely labeled peptide-DNA.

Directed assembly of biocompatible materials benefits from modular building blocks in which structural organization is independent of introduced functional modifications. For soft materials, such modifications have been limited. Here, long DNA is successfully functionalized with dense decoration by peptides. Following introduction of alkyne-modified nucleotides into kilobasepair DNA, measurements of persistence length show that DNA mechanics are unaltered by the dense incorporation of alkynes (∼1 alkyne/2 bp) and after click-chemistry attachment of a tunable density of peptides. Proteolytic cleavage of densely tethered peptides (∼1 peptide/3 bp) demonstrates addressability of the functional groups, showing that this accessible approach to creating hybrid structures can maintain orthogonality between backbone mechanics and overlaid function. The synthesis and characterization of these hybrid constructs establishes the groundwork for their implementation in future applications, such as building blocks in modular approaches to a range of problems in synthetic biology.

Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes.

Because of their pervasiveness in eukaryotic genomes and their unique properties, understanding the role that ID (intrinsically disordered) regions in proteins play in the interactome is essential for gaining a better understanding of the network. Especially critical in determining this role is their ability to bind more than one partner using the same region. Studies have revealed that proteins containing ID regions tend to take a central role in protein interaction networks; specifically, they act as hubs, interacting with multiple different partners across time and space, allowing for the co-ordination of many cellular activities. There appear to be three different modules within ID regions responsible for their functionally promiscuous behaviour: MoRFs (molecular recognition features), SLiMs (small linear motifs) and LCRs (low complexity regions). These regions allow for functionality such as engaging in the formation of dynamic heteromeric structures which can serve to increase local activity of an enzyme or store a collection of functionally related molecules for later use. However, the use of promiscuity does not come without a cost: a number of diseases that have been associated with ID-containing proteins seem to be caused by undesirable interactions occurring upon altered expression of the ID-containing protein.

Dynamically Mapping the Topography and Stiffness of the Leading Edge of Migrating Cells Using AFM in Fast-QI Mode.

Cell migration profoundly influences cellular function, often resulting in adverse effects in various pathologies including cancer metastasis. Directly assessing and quantifying the nanoscale dynamics of living cell structure and mechanics has remained a challenge. At the forefront of cell movement, the flat actin modules─the lamellipodium and the lamellum─interact to propel cell migration. The lamellipodium extends from the lamellum and undergoes rapid changes within seconds, making measurement of its stiffness a persistent hurdle. In this study, we introduce the fast-quantitative imaging (fast-QI) mode, demonstrating its capability to simultaneously map both the lamellipodium and the lamellum with enhanced spatiotemporal resolution compared with the classic quantitative imaging (QI) mode. Specifically, our findings reveal nanoscale stiffness gradients in the lamellipodium at the leading edge, where it appears to be slightly thinner and significantly softer than the lamellum. Additionally, we illustrate the fast-QI mode's accuracy in generating maps of height and effective stiffness through a streamlined and efficient processing of force-distance curves. These results underscore the potential of the fast-QI mode for investigating the role of motile cell structures in mechanosensing.

Mechanical Characterization of Murine Oocytes by Atomic Force Microscopy.

The quality of murine and human oocytes correlates to their mechanical properties, which are tightly regulated to reach the blastocyst stage after fertilization. Oocytes are nonadherent spherical cells with a diameter over 80 µm. Their mechanical properties have been studied in our lab and others using the micropipette aspiration technique, particularly to obtain the oocyte cortical tension. Micropipette aspiration is affordable but has a low throughput and induces cell-scale deformation. Here we present a step-by-step protocol to characterize the mechanical properties of oocytes using atomic force microscopy (AFM), which is minimally invasive and has a much higher throughput. We used electron microscopy grids to immobilize oocytes. This allowed us to obtain local and reproducible measurements of the cortical tension of murine oocytes during their meiotic divisions. Cortical tension values obtained by AFM are in agreement with the ones previously obtained by micropipette aspiration. Our protocol could help characterize the biophysical properties of oocytes or other types of large nonadherent samples in fundamental and medical research.

Biomechanical Characterization of Retinal Pigment Epitheliums Derived from hPSCs Using Atomic Force Microscopy.

The retinal pigment epithelium (RPE), a multifunctional cell monolayer located at the back of the eye, plays a crucial role in the survival and homeostasis of photoreceptors. Dysfunction or death of RPE cells leads to retinal degeneration and subsequent vision loss, such as in Age-related macular degeneration and some forms of Retinitis Pigmentosa. Therefore, regenerative medicine that aims to replace RPE cells by new cells obtained from the differentiation of human pluripotent stem cells, is the focus of intensive research. However, despite their critical interest in therapy, there is a lack of biomechanical RPE surface description. Such biomechanical properties are tightly related to their functions. Herein, we used atomic force microscopy (AFM) to analyze both the structural and mechanical properties of RPEs obtained from four cell lines and at different stages of epithelial formation. To characterize epitheliums, we used apical markers in immunofluorescence and showed the increase of transepithelial resistance, as well as the ability to secrete cytokines with an apico-basal polarity. Then, we used AFM to scan the apical surface of living or fixed RPE cells. We show that RPE monolayers underwent softening of apical cell center as well as stiffening of cell borders over epithelial formation. We also observed apical protrusions that depend on actin network, suggesting the formation of microvilli at the surface of RPE epitheliums. These RPE cell characteristics are essential for their functions into the retina and AFM studies may improve the characterization of the RPE epithelium suitable for cell therapy.

Using Adhesive Micropatterns and AFM to Assess Cancer Cell Morphology and Mechanics.

The mechanical properties of living cells reflect their physiological and pathological state. In particular, cancer cells undergo cytoskeletal modifications that typically make them softer than healthy cells, a property that could be used as a diagnostic tool. However, this is challenging because cells are complex structures displaying a broad range of morphologies when cultured in standard 2D culture dishes. Here, we use adhesive micropatterns to impose the cell geometry and thus standardize the mechanics and morphologies of cancer cells, which we measure by atomic force microscopy (AFM), mechanical nanomapping, and membrane nanotube pulling. We show that micropatterning cancer cells leads to distinct morphological and mechanical changes for different cell lines. Micropatterns did not systematically lower the variability in cell elastic modulus distribution. These effects emerge from a variable cell spreading rate associated with differences in the organization of the cytoskeleton, thus providing detailed insights into the structure-mechanics relationship of cancer cells cultured on micropatterns. Combining AFM with micropatterns reveals new mechanical and morphological observables applicable to cancer cells and possibly other cell types.

Structure and functional impact of glycosaminoglycan modification of HSulf-2 endosulfatase revealed by atomic force microscopy and mass spectrometry.

The human sulfatase HSulf-2 is one of only two known endosulfatases that play a decisive role in modulating the binding properties of heparan sulfate proteoglycans on the cell surface and in the extracellular matrix. Recently, HSulf-2 was shown to exhibit an unusual post-translational modification consisting of a sulfated glycosaminoglycan chain. This study describes the structural characterization of this glycosaminoglycan (GAG) and provides new data on its impact on the catalytic properties of HSulf-2. The unrevealed nature of this GAG chain is identified as a chondroitin/dermatan sulfate (CS/DS) mixed chain, as shown by mass spectrometry combined with NMR analysis. It consists primarily of 6-O and 4-O monosulfated disaccharide units, with a slight predominance of the 4-O-sulfation. Using atomic force microscopy, we show that this unique post-translational modification dramatically impacts the enzyme hydrodynamic volume. We identified human hyaluronidase-4 as a secreted hydrolase that can digest HSulf-2 GAG chain. We also showed that HSulf-2 is able to efficiently 6-O-desulfate antithrombin III binding pentasaccharide motif, and that this activity was enhanced upon removal of the GAG chain. Finally, we identified five N-glycosylation sites on the protein and showed that, although required, reduced N-glycosylation profiles were sufficient to sustain HSulf-2 integrity.

The molecular mechanism underlying mechanical anisotropy of the protein GB1.

Mechanical responses of elastic proteins are crucial for their biological function and nanotechnological use. Loading direction has been identified as one key determinant for the mechanical responses of proteins. However, it is not clear how a change in pulling direction changes the mechanical unfolding mechanism of the protein. Here, we combine protein engineering, single-molecule force spectroscopy, and steered molecular dynamics simulations to systematically investigate the mechanical response of a small globular protein GB1. Force versus extension profiles from both experiments and simulations reveal marked mechanical anisotropy of GB1. Using native contact analysis, we relate the mechanically robust shearing geometry with concurrent rupture of native contacts. This clearly contrasts the sequential rupture observed in simulations for the mechanically labile peeling geometry. Moreover, we identify multiple distinct mechanical unfolding pathways in two loading directions. Implications of such diverse unfolding mechanisms are discussed. Our results may also provide some insights for designing elastomeric proteins with tailored mechanical properties.

Long-time scale fluctuations of human prion protein determined by restrained MD simulations.

Cellular prion protein (PrP(C)) has the ability to trigger transmissible lethal diseases after in vivo maturation into a toxic amyloidogenic misfolded form (PrP(Sc)). Here, we use hydrogen exchange protection factors in restrained molecular dynamics simulations to characterize long-time scale fluctuations in human PrP(C). We find that the regions of residues 138-141 and 183-192 form new ß-strands in several exchange-competent structures. Moreover, these structural changes are associated with the disruption of native contacts that when tethered prevent fibril formation. Our findings illustrate the structural plasticity of PrP(C) and are valuable for understanding the conversion of PrP(C) to PrP(Sc).

Domain-selective thermal decomposition within supramolecular nanoribbons.

Self-assembly of small molecules in water provides a powerful route to nanostructures with pristine molecular organization and small dimensions (<10 nm). Such assemblies represent emerging high surface area nanomaterials, customizable for biomedical and energy applications. However, to exploit self-assembly, the constituent molecules must be sufficiently amphiphilic and satisfy prescribed packing criteria, dramatically limiting the range of surface chemistries achievable. Here, we design supramolecular nanoribbons that contain: (1) inert and stable internal domains, and (2) sacrificial surface groups that are thermally labile, and we demonstrate complete thermal decomposition of the nanoribbon surfaces. After heating, the remainder of each constituent molecule is kinetically trapped, nanoribbon morphology and internal organization are maintained, and the nanoribbons are fully hydrophobic. This approach represents a pathway to form nanostructures that circumvent amphiphilicity and packing parameter constraints and generates structures that are not achievable by self-assembly alone, nor top-down approaches, broadening the utility of molecular nanomaterials for new targets.

Self-assembly of aramid amphiphiles into ultra-stable nanoribbons and aligned nanoribbon threads.

Small-molecule self-assembly is an established route for producing high-surface-area nanostructures with readily customizable chemistries and precise molecular organization. However, these structures are fragile, exhibiting molecular exchange, migration and rearrangement-among other dynamic instabilities-and are prone to dissociation upon drying. Here we show a small-molecule platform, the aramid amphiphile, that overcomes these dynamic instabilities by incorporating a Kevlar-inspired domain into the molecular structure. Strong, anisotropic interactions between aramid amphiphiles suppress molecular exchange and elicit spontaneous self-assembly in water to form nanoribbons with lengths of up to 20 micrometres. Individual nanoribbons have a Young's modulus of 1.7 GPa and tensile strength of 1.9 GPa. We exploit this stability to extend small-molecule self-assembly to hierarchically ordered macroscopic materials outside of solvated environments. Through an aqueous shear alignment process, we organize aramid amphiphile nanoribbons into arbitrarily long, flexible threads that support 200 times their weight when dried. Tensile tests of the dry threads provide a benchmark for Young's moduli (between ~400 and 600 MPa) and extensibilities (between ~0.6 and 1.1%) that depend on the counterion chemistry. This bottom-up approach to macroscopic materials could benefit solid-state applications historically inaccessible by self-assembled nanomaterials.

Mechanical Anisotropy in GNNQQNY Amyloid Crystals.

Mapping the nanomechanical properties of amyloids can provide valuable insights into structure and assembly mechanisms of protein aggregates that underlie the development of various human diseases. Although it is well-known that amyloids exhibit an intrinsic stiffness comparable to that of silk (1-10 GPa), a detailed understanding of the directional dependence (anisotropy) of the stiffness of amyloids and how it relates to structural features in these protein aggregates is missing. Here we used steered molecular dynamics (SMD) simulations and amplitude modulation-frequency modulation (AM-FM) atomic force microscopy to measure the directional variation in stiffness of GNNQQNY amyloid crystals. We reveal that individual crystals display significant mechanical anisotropy and relate this anisotropy to subtle but mechanically important differences in interactions between interfaces that define the crystal architecture. Our results provide detailed insights into the structure-mechanics relationship of amyloid that may help in designing amyloid-based nanomaterials with tailored mechanical properties.

A Rational Structured Epitope Defines a Distinct Subclass of Toxic Amyloid-beta Oligomers.

Oligomers of amyloid-ß (AßO) are deemed key in synaptotoxicity and amyloid seeding of Alzheimer's disease (AD). However, the heterogeneous and dynamic nature of AßO and inadequate markers for AßO subtypes have stymied effective AßO identification and therapeutic targeting in vivo. We identified an AßO-subclass epitope defined by differential solvent orientation of the lysine 28 side chain in a constrained loop of serine-asparagine-lysine (cSNK), rarely displayed in molecular dynamics simulations of monomer and fibril ensembles. A mouse monoclonal antibody targeting AßOcSNK recognizes ∼50-60 kDa SDS-resistant soluble Aß assemblages in AD brain and prolongs the lag phase of Aß aggregation in vitro. Acute peripheral infusion of a murine IgG1 anti-AßOcSNK in two AD mouse models reduced soluble brain Aß aggregates by 20-30%. Chronic cSNK peptide immunization of APP/PS1 mice engendered an anti-AßOcSNK IgG1 response without epitope spreading to Aß monomers or fibrils and was accompanied by preservation of global PSD95 expression and improved cued fear memory. Our data indicate that the oligomer subtype AßOcSNK participates in synaptotoxicity and propagation of Aß aggregation in vitro and in vivo.