Folding Instability Research Articles

Intracellular spatially-targeted chemical chaperones increase native state stability of mutant SOD1 barrel.

Amyotrophic lateral sclerosis (ALS) is a progressive neurological disorder with currently no cure. Central to the cellular dysfunction associated with this fatal proteinopathy is the accumulation of unfolded/misfolded superoxide dismutase 1 (SOD1) in various subcellular locations. The molecular mechanism driving the formation of SOD1 aggregates is not fully understood but numerous studies suggest that aberrant aggregation escalates with folding instability of mutant apoSOD1. Recent advances on combining organelle-targeting therapies with the anti-aggregation capacity of chemical chaperones have successfully reduce the subcellular load of misfolded/aggregated SOD1 as well as their downstream anomalous cellular processes at low concentrations (micromolar range). Nevertheless, if such local aggregate reduction directly correlates with increased folding stability remains to be explored. To fill this gap, we synthesized and tested here the effect of 9 ER-, mitochondria- and lysosome-targeted chemical chaperones on the folding stability of truncated monomeric SOD1 (SOD1bar) mutants directed to those organelles. We found that compound ER-15 specifically increased the native state stability of ER-SOD1bar-A4V, while scaffold compound FDA-approved 4-phenylbutyric acid (PBA) decreased it. Furthermore, our results suggested that ER15 mechanism of action is distinct from that of PBA, opening new therapeutic perspectives of this novel chemical chaperone on ALS treatment.

Pinning of graphene for conformal wrinkling over a soft corrugated substrate through prestretch-release process

The adhesion of a 2D material to a substrate is facilitated by the van der Waals (vdW) interactions, which is significantly influenced by the roughness and wettability of the substrate. It is challenging to achieve good as well as conformal adhesion of mechanically exfoliated 2D materials to a hydrophobic soft substrate like polydimethylsiloxane (PDMS). In addition, the mechanical folding instabilities are inevitably observed in 2D elastic nanosheets over a smooth PDMS substrate under higher compressions in a prestretch-release process. However, the manipulation of the soft substrate’s surface roughness may provide an essential degree of freedom for tailoring the conformation level and topography of the 2D elastic nanosheets. Herein, we propose a technique to improve the interfacial adhesion of the graphene membrane to a periodically trenched PDMS substrate by suppressing the mechanical folding instabilities in a prestretch-release process. The conformal wrinkling of the graphene membrane, as confirmed through atomic force microscopy (AFM) imaging, is found to result from its pinning into the trenches via snap-through transition. We also show the impact of the substrate’s topography on the buckling behavior of the graphene membrane under the stress loading-unloading cycle by surface-engineering of the PDMS substrate using ion beam irradiation. This study offers fundamental as well as practical insights into the adhesion mechanics of the 2D elastic nanosheets over the corrugated soft substrates under the prestretch-release process. The wrinkled topography of the membrane could be harnessed for flexible, conformal, and tunable electronic devices.

Liquid crystal defect structures with Möbius strip topology

Topological solitons commonly appear as energy-minimizing field configurations, but examples of stable, spatially localized objects with coexisting solitonic structures and singular defects are rare. Here we use a nonpolar chiral liquid crystal system to show how twist domain walls can co-self-assemble with vortices to form spatially localized topological objects with spontaneous folding. These soliton–vortex assemblies, which we call ‘möbiusons’, have a topology of the molecular alignment field resembling that of the Möbius strip’s surface and package localized field excitations into folded structures within a confinement-frustrated uniform far-field background. Upon supplying energy in the form of electric pulses, möbiusons with different overall symmetries of structure exhibit folding-dependent rotational and translational motions, as well as topological cargo-carrying abilities that can be controlled by tuning the amplitude and frequency of the applied fields. We demonstrate on-demand transformations between various möbiusons and show examples of encoding information by manipulating folds in such structures. A model based on the energetics of solitons and vortices provides insights into the origins of the folding instability, whereas minimization of the Landau–de Gennes free energy closely reproduces details of their internal structure. Our findings may provide a route towards topology-enabled light-steering designs.

Epistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability

The Q80K polymorphism in the NS3-4A protease of the hepatitis C virus is associated with treatment failure of direct-acting antiviral agents. This polymorphism is highly prevalent in genotype 1a infections and stably transmitted between hosts. Here, we investigated the underlying molecular mechanisms of evolutionarily conserved coevolving amino acids in NS3-Q80K and revealed potential implications of epistatic interactions in immune escape and variants persistence. Using purified protein, we characterized the impact of epistatic amino acid substitutions on the physicochemical properties and peptide cleavage kinetics of the NS3-Q80K protease. We found that Q80K destabilized the protease protein fold (p < 0.0001). Although NS3-Q80K showed reduced peptide substrate turnover (p < 0.0002), replicative fitness in an H77S.3 cell culture model of infection was not significantly inferior to the WT virus. Epistatic substitutions at residues 91 and 174 in NS3-Q80K stabilized the protein fold (p < 0.0001) and leveraged the WT protease stability. However, changes in protease stability inversely correlated with enzymatic activity. In infectious cell culture, these secondary substitutions were not associated with a gain of replicative fitness in NS3-Q80K variants. Using molecular dynamics, we observed that the total number of residue contacts in NS3-Q80K mutants correlated with protein folding stability. Changes in the number of contacts reflected the compensatory effect on protein folding instability by epistatic substitutions. In summary, epistatic substitutions in NS3-Q80K contribute to viral fitness by mechanisms not directly related to RNA replication. By compensating for protein-folding instability, epistatic interactions likely protect NS3-Q80K variants from immune cell recognition.

The Force Cone Method Applied to Explain Hidden Whirls in Tribology.

In tribologically loaded materials, folding instabilities and vortices lead to the formation of complex internal structures. This is true for geological as well as nanoscopic contacts. Classically, these structures have been described by Kelvin–Helmholtz instabilities or shear localization. We here introduce an alternative explanation based on an intuitive approach referred to as the force cone method. It is considered how whirls are situated near forces acting on a free surface of an elastic or elastoplastic solid. The force cone results are supplemented by finite element simulations. Depending on the direction of the acting force, one or two whirls are predicted by the simplified force cone method. In 3D, there is always a ring shaped whirl present. These modelling findings were tested in simple model experiments. The results qualitatively match the predictions and whirl formation was found. The force cone method and the experiments may seem trivial, but they are an ideal tool to intuitively understand the presence of whirls within a solid under a tribological load. The position of these whirls was found at the predicted places and the force cone method allows a direct approach to understand the complex processes in the otherwise buried interfaces of tribologically loaded materials.

Material-Dependent Evolution of Mechanical Folding Instabilities in Two-Dimensional Atomic Membranes.

Inducing and controlling three-dimensional deformations in monolayer two-dimensional materials is important for applications from stretchable electronics to origami nanoelectromechanical systems. For these applications, it is critical to understand how the properties of different materials influence the morphologies of two-dimensional atomic membranes under mechanical loading. Here, we systematically investigate the evolution of mechanical folding instabilities in uniaxially compressed monolayer graphene and MoS2 on a soft polydimethylsiloxane substrate. We examine the morphology of the compressed membranes using atomic force microscopy for compression from 0 to 33%. We find the membranes display roughly evenly spaced folds and observe two distinct stress release mechanisms under increasing compression. At low compression, the membranes delaminate to generate new folds. At higher compression, the membranes slip over the surface to enlarge existing folds. We observe a material-dependent transition between these two behaviors at a critical fold spacing of 1000 ± 250 nm for graphene and 550 ± 20 nm for MoS2. We establish a simple shear-lag model which attributes the transition to a competition between static friction and adhesion and gives the maximum interfacial static friction on polydimethylsiloxane of 3.8 ± 0.8 MPa for graphene and 7.7 ± 2.5 MPa for MoS2. Furthermore, in graphene, we observe an additional transition from standing folds to fallen folds at 8.5 ± 2.3 nm fold height. These results provide a framework to control the nanoscale fold structure of monolayer atomic membranes, which is a critical step in deterministically designing stretchable or foldable nanosystems based on two-dimensional materials.

A Novel Cycs Missense Mutation in the α-Helix of the Cycs C-Terminal Domain Causes Non-Syndromic Thrombocytopenia

We report a patient with thrombocytopenia from a Japanese family with hemophilia A spanning four generations. Various etiologies of thrombocytopenia, including genetic, immunological, and hematopoietic abnormalities, determine the prognosis for this disease. The CYCS gene (MIM123970) encodes cytochrome c, somatic, a small heme protein localized in the inner membrane of mitochondria. Cytochrome c is an electron carrier in the mitochondrial respiratory chain as well as a key initiator of apoptosis (Cell Death Differ. 2018;25(1):46-55). To date, only three families with CYCS missense variants have been reported: a large New Zealander family (p.Gly42Ser), an Italian family (p.Tyr49His), and a white/mixed British family (p.Ala52Val) (Nat Genet. 2008;40(4):387-9, Biochim Biophys Acta. 2014;1842(2):269-74, Haematologica. 2016;101(10):1170-1179). These patients were affected by an autosomal dominant phenotype characterized by low platelet count without extra-hematological findings. Moreover, these patients' peripheral blood cell morphologies, including platelet size, were all normal.In this study, we identified a novel heterozygous mutation in CYCS using whole exome sequencing. This variant (c.301_303del:p.Lys101del) is located in the α-helix of the cytochrome c (CYCS) C-terminal domain. In silico structural analysis suggested that this mutation results in protein folding instability. By the deletion mutation, the Ala102 position is considered to be replaced with the neighboring Thr103, which would impair the hydrophobic core and destabilize protein folding. All three reported missense mutations are clustered within the highly conserved Ω-loop (Biochim Biophys Acta. 2014;1842(2):269-74, Sci Rep. 2016, 27;6:30447, Biophys Chem. 2017;230:117-126). Previous structural analyses also showed that two mutations in the Ω-loop (p.Gly42Ser and p.Tyr49His) of CYCS disrupted hydrogen bonds (Sci Rep. 2016, 27;6:30447, Biophys Chem. 2017;230:117-126). Although in silico analysis suggested the significant structural impact of p.Lys101del, it is arguable that a one amino acid in-frame deletion outside the Ω-loop would have a mild or neutral effect. To verify the pathogenicity of this variant in the less characterized C-terminal region, we used the fission yeast Schizosaccharomyces pombe as a model system (Biosci Biotechnol Biochem. 2013;77(7):1548-55). Using the yeast model system, we clearly demonstrated that this one amino acid deletion (in-frame) resulted in significantly reduced cytochrome c protein expression and functional defects in the mitochondrial respiratory chain, indicating that the loss of function of cytochrome c underlies thrombocytopenia. Similar deleterious effects in terms of mitochondrial respiratory function were reported for two other pathogenic mutations, p.Gly42Ser and p.Tyr49His in CYCS (Biochim Biophys Acta. 2014;1842(2):269-74). The clinical features of known CYCS variants have been reported to be confined to mild or asymptomatic thrombocytopenia, as was observed for the patient in our study. Hence, we suggest that loss-of function variants in CYCS cause non-syndromic thrombocytopenia.In conclusion, our findings provide further support for CYCS mutations being causative for pure isolated thrombocytopenia. In a clinical setting, differential diagnosis of thrombocytopenia is important for evaluating the risk of developing hematological malignancies. Genetic testing complemented with the relevant functional studies should be considered part of appropriate patient care.The study protocol was approved by Institutional Review Boards of Yokohama City University School of Medicine and the Gunma University Graduate School of Medicine. Written informed consent was obtained from all participants. DisclosuresHanda:Takeda: Consultancy, Honoraria, Research Funding, Speakers Bureau; Celgene: Honoraria, Research Funding, Speakers Bureau.

Long-wavelength topography on Mercury is not from folding of the lithosphere

Previous work suggested that the lithosphere of Mercury could undergo folding in response to global contraction, and indeed observations from the MESSENGER mission revealed several regions where long-wavelength topography is present. Here, we test, via finite-element simulations that use a more realistic rheological model than that earlier work, lithospheric folding as a formation mechanism for long-wavelength topography on Mercury from interior secular cooling over the last 3.8 Gyr. This radial contraction has been estimated from geological observations to be less than 10 km, which translates into small amounts of horizontal shortening of < 0.3%. Under expected surface temperatures of ∼440 K, the development of even modest fold amplification in such low strain environments is untenable. The scenarios under which there is this positive fold amplification begin with a fully compensated crust, but amplifications are small (factors < 1.1). Under other, non-compensated scenarios (e.g., a constant thickness crust), the collapse to isostasy overwhelms any folding instability. In order to produce lithospheric fold amplitudes that match those observed on Mercury, unrealistically large amounts of horizontal shortening (in excess of 10%, corresponding to hundreds of kilometers of radius change) are required. Therefore, we find that lithospheric folding cannot produce the observed long-wavelength topography on Mercury, and conclude that this topography must be buoyantly supported.

A novel CYCS mutation in the α-helix of the CYCS C-terminal domain causes non-syndromic thrombocytopenia.

We report a patient with thrombocytopenia from a Japanese family with hemophilia A spanning four generations. Various etiologies of thrombocytopenia, including genetic, immunological, and hematopoietic abnormalities, determine the prognosis for this disease. In this study, we identified a novel heterozygous mutation in a gene encoding cytochrome c, somatic (CYCS, MIM123970) using whole exome sequencing. This variant (c.301_303del:p.Lys101del) is located in the α-helix of the cytochrome c (CYCS) C-terminal domain. In silico structural analysis suggested that this mutation results in protein folding instability. CYCS is one of the key factors regulating the intrinsic apoptotic pathway and the mitochondrial respiratory chain. Using the yeast model system, we clearly demonstrated that this one amino acid deletion (in-frame) resulted in significantly reduced cytochrome c protein expression and functional defects in the mitochondrial respiratory chain, indicating that the loss of function of cytochrome c underlies thrombocytopenia. The clinical features of known CYCS variants have been reported to be confined to mild or asymptomatic thrombocytopenia, as was observed for the patient in our study. This study clearly demonstrates that thrombocytopenia can result from CYCS loss-of-function variants.

Instabilities of interfaces between dissimilar metals induced by high pressure torsion

We observed that high pressure torsion (HPT) of a bi-metallic laminate can induce vortex-like folding instabilities of layers. Thus, HPT leads to multiscale swirls which are perpendicular to the anvil axis. These instabilities are similar to folding of metallic surfaces during sliding and to co-axial swirls by HPT. The HPT induced vortex-like instabilities look very similar to the Kelvin-Helmholtz-type flow instabilities in fluids. We demonstrate in this work that this similarity is only apparent, and physical reasons for HPT-induced instabilituies are principally different from those in liquids. We show using finite element simulations that the folding and vortices of metallic layers are driven by plastic instabilities due to local blocking of shear deformation. Thus, HPT of layered samples leads to the multiscale movement of vortices in the material during deformation. These movements resemble turbulent flow of liquids and gases, but they have a completely different physical nature.

Deriving scaling laws in geodynamics using adjoint gradients

Whereas significant progress has been made in modelling of lithospheric and crustal scale processes in recent years, it often remains a challenge to understand which of the many model parameters is of key importance for a particular simulation. Determining this is usually done by manually changing the model input parameters and performing new simulations. For a few cases, such as for folding or Rayleigh-Taylor instabilities, one can use thick-plate stability analysis to derive scaling laws to obtain such insights. Yet, for more general cases, it is not straightforward to do this (apart from running many simulations). Here, we discuss a numerically cheaper approach to compute scaling laws using adjoint gradients. This method determines the gradients of the model solution versus the model parameters, or more precisely, quantifies the influence of a large number of parameters on the simulation. The required computational effort is nearly independent on the number of model parameters, which makes it tractable even for complicated setups. Here we show how these gradients can be used to derive scaling laws. We test the method by reproducing existing scaling laws for a Rayleigh-Taylor instability problem, as well as that of folding of a single layer over a weaker basement. Next, we show the applicability of the method to more complicated multilayer folding setups and a 3D subduction problem with 22 parameters. The results show that the method can, at very little computational overhead, give significant insights in the controlling parameters of geodynamic simulations.

The dynamics of folding instability in a constrained Cosserat medium.

Different from Cauchy elastic materials, generalized continua, and in particular constrained Cosserat materials, can be designed to possess extreme (near a failure of ellipticity) orthotropy properties and in this way to model folding in a three-dimensional solid. Following this approach, folding, which is a narrow zone of highly localized bending, spontaneously emerges as a deformation pattern occurring in a strongly anisotropic solid. How this peculiar pattern interacts with wave propagation in the time-harmonic domain is revealed through the derivation of an antiplane, infinite-body Green’s function, which opens the way to integral techniques for anisotropic constrained Cosserat continua. Viewed as a perturbing agent, the Green’s function shows that folding, emerging near a steadily pulsating source in the limit of failure of ellipticity, is transformed into a disturbance with wavefronts parallel to the folding itself. The results of the presented study introduce the possibility of exploiting constrained Cosserat solids for propagating waves in materials displaying origami patterns of deformation.This article is part of the themed issue ‘Patterning through instabilities in complex media: theory and applications.’

A dipping, thick segment of the Farallon Slab beneath central U.S.

AbstractIt has been hypothesized that much of the crustal deformation attributed to the Laramide orogeny of the southwest North American Cordillera was caused by dynamic effects induced by the flat subduction of a large oceanic plateau that was embedded within the Farallon Plate. Previous studies have identified within the North American mantle a seismic velocity anomaly that plausibly represents the remnants of the subducted plateau. Coupled plate kinematic and dynamic modeling of the anomaly, as well as surface geological findings, identify this anomaly as the subducted conjugate to the Shatsky Rise. Here we find clear evidence for a northeastward dipping (35° dip), thick (up to 400 km thick) slab‐like seismic velocity anomaly within the top of the lower mantle below the central United States. Using a deep focus earthquake below Spain, we find that the observed seismic waveforms recorded with the dense USArray display multipathing indicative of sharp surfaces. Plate tectonic reconstructions in which the anomaly is migrated back in time suggest strong coupling of the plateau‐thickened slab segment to the overriding North America Plate as it was subducted. In combination with the reconstructions, we interpret the structure as arising from eastward dipping Farallon subduction at the western margin of North America during the Cretaceous, in contrast with some recent interpretations. It appears that the plateau area of the slab has been further thickened, which might undergo a combination of pure shear bulk shortening during flat‐slab subduction and/or by a folding instability during penetration into the lower mantle.

Three-dimensional simulations of viscous folding in diverging microchannels

Three dimensional simulations on the viscous folding in diverging microchannels reported by Cubaud and Mason are performed using the parallel code BLUE for multi-phase flows. The more viscous liquid L_1 is injected into the channel from the center inlet, and the less viscous liquid L_2 from two side inlets. Liquid L_1 takes the form of a thin filament due to hydrodynamic focusing in the long channel that leads to the diverging region. The thread then becomes unstable to a folding instability, due to the longitudinal compressive stress applied to it by the diverging flow of liquid L_2. Given the long computation time, we were limited to a parameter study comprising five simulations in which the flow rate ratio, the viscosity ratio, the Reynolds number, and the shape of the channel were varied relative to a reference model. In our simulations, the cross section of the thread produced by focusing is elliptical rather than circular. The initial folding axis can be either parallel or perpendicular to the narrow dimension of the chamber. In the former case, the folding slowly transforms via twisting to perpendicular folding, or it may remain parallel. The direction of folding onset is determined by the velocity profile and the elliptical shape of the thread cross section in the channel that feeds the diverging part of the cell. Due to the high viscosity contrast and very low Reynolds numbers, direct numerical simulations of this two-phase flow are very challenging and to our knowledge these are the first three-dimensional direct parallel numerical simulations of viscous threads in microchannels. Our simulations provide good qualitative comparison of the early time onset of the folding instability however since the computational time for these simulations is quite long, for such viscous threads, long-time comparisons with experiments for quantities such as folding frequency are limited.

Spatially Controlled Folding Instability of Moduli‐Patterned and Bilayered Membrane under Compressive Stresses

Controlled instability-induced pattern formation is achieved by a moduli-patterning method. Local strains in the relatively soft substrate are higher than those in the hard region once pre-strains are applied. Thus, buckling patterns are initiated preferentially in the soft region, inducing spatially controlled instability-induced pattern formation. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Time-Dependent Protein Thermostability Assay.

Membrane protein purification often yields rather unstable proteins impeding functional and structural protein characterization. Low protein stability also leads to low purification yields as a result of protein degradation, aggregation, precipitation, and folding instability. It is often required to optimize buffer conditions through numerous iterations of trial and error to improve the homogeneity, stability, and solubility of the protein sample demanding high amounts of purified protein. Therefore we have set up a fast, simple, and high-throughput time-dependent thermostability-based assay at low protein cost to identify protein stabilizing factors to facilitate the handling and characterization of membrane proteins by subsequent structural and functional studies.

From period-doubling to folding in stiff film/soft substrate system: The role of substrate nonlinearity

Uniaxial compressed stiff films on soft substrates can evolve into the period-doubling and folding instabilities, beyond the onset of sinusoidal wrinkling. The substrate is modeled as a neo-Hookean solid with a pre-stretch prior to film attachment, and its nonlinearity is obtained. Both the pre-stretch and the external nominal strain imposed on the film/substrate system can induce different substrate nonlinearity, and thus have different effects on the post-buckling mode evolution of the system. This study shows that the critical strain of period-doubling instability is linear to the pre-stretch. As the compressive nominal strain increases, the folding mode occurs beyond the onset of period-doubling in both the pre-tension and the pre-compression case, due to the softening/hardening effects for the inward/outward displacements generated by the positive substrate nonlinearity.

Origins of Folding Instabilities on Polycrystalline Metal Surfaces

Mechanical wear and tear is a fact of life as old as tools themselves, yet is still not fully understood. Here large-scale atomistic simulations combined with atomic force microscopy provide a deep microscopic understanding of unconstrained surface plastic flow in polycrystalline metals. These findings suggest that engineering crystallographic surface texture to avoid formation of folds is a way forward in designing wear-resistant metal surfaces.

Influence of pre-existing salt diapirs on 3D folding patterns

The 3D detachment folding instability gives rise to a wide variety of fold shapes (e.g. from dome shape structures to long en-echelon or straight anticlines) as a result of interactions between growing fold segments. The 3D growth of these folds, as well as the wavelength and lateral propagation of folds, is controlled by the physical parameters of a detachment layer and its overburden. However, the existence of initial heterogeneities, such as pre-existing salt plugs within the sedimentary cover, might affect fold development as well.We use numerical modeling to investigate how the fold pattern is affected by pre-existing salt structures. High-resolution 3D folding simulations (with and without pre-existing salt structures) were performed, in which we varied the shape, height and spacing of pre-existing diapirs. In a first geometric setup, we employed a multilayer setup and synthetic diapir distributions in order to study the influence of diapir spacing on fold spacing and patterns. In a second geometric setup, we use a diapir distribution that fits the observed exposed diapir distribution in the southeastern Zagros.Results show that the presence of diapirs does not considerably change the wavelength of the folds, which is in all cases close to the dominant folding wavelength that develops in the absence of diapirs. Yet, the presence of pre-existing structures speeds up the folding instability in those locations and also affects folding patterns as the diapirs localize the initial deformation by accommodating folding above them, which results in the diapirs being located in the core of the folds. If diapir spacing is much smaller than the dominant folding wavelength, diapirs are located in different structural positions such as fold synclines or flanks.

Interplay between metamorphic strengthening and structural softening in inclusion‐bearing layered rocks

AbstractWe employ numerical and analytical methods to investigate the effect of the presence of rigid porphyroblasts such as garnets on layer strengthening and the folding instability. We use a 50% fraction of non‐overlapping, circular‐shaped inclusions with a wide size distribution. These inclusions cause a fourfold effective viscosity increase and can significantly promote the folding instability. This is not only due to the increased viscosity but also due to the layer interface roughness generation driven by relative movement of inclusions. The increase in layer viscosity promotes strengthening of the whole system. However, with progressive fold development, the system undergoes an effective softening that may counteract the strengthening effect of the porphyroblast growth.