Structural basis for the activation and inhibition of the UCH37 deubiquitylase.

The UCH37 deubiquitylase functions in two large and very different complexes, the 26S proteasome and the INO80 chromatin remodeler. We have performed biochemical characterization and determined crystal structures of UCH37 in complexes with RPN13 and NFRKB, which mediate its recruitment to the proteasome and INO80, respectively. RPN13 and NFRKB make similar contacts to the UCH37 C-terminal domain but quite different contacts to the catalytic UCH domain. RPN13 can activate UCH37 by disrupting dimerization, although physiologically relevant activation likely results from stabilization of a surface competent for ubiquitin binding and modulation of the active-site crossover loop. In contrast, NFRKB inhibits UCH37 by blocking the ubiquitin-binding site and by disrupting the enzyme active site. These findings reveal remarkable commonality in mechanisms of recruitment, yet very different mechanisms of regulating enzyme activity, and provide a foundation for understanding the roles of UCH37 in the unrelated proteasome and INO80 complexes.

High-affinity free ubiquitin sensors for quantifying ubiquitin homeostasis and deubiquitination.

Ubiquitin (Ub) conjugation is an essential post-translational modification that affects nearly all proteins in eukaryotes. The functions and mechanisms of ubiquitination are areas of extensive study, and yet the dynamics and regulation of even free (that is, unconjugated) Ub are poorly understood. A major impediment has been the lack of simple and robust techniques to quantify Ub levels in cells and to monitor Ub release from conjugates. Here, we describe avidity-based fluorescent sensors that address this need. The sensors bind specifically to free Ub, have dissociation constant Kd values down to 60 pM and, together with a newly developed workflow, allow us to distinguish and quantify the pools of free, protein-conjugated and thioesterified forms of Ub from cell lysates. Alternatively, free Ub in fixed cells can be visualized microscopically by staining with a sensor. Real-time assays using the sensors afford unprecedented flexibility and precision to measure deubiquitination of virtually any (poly)Ub conjugate.

Ubiquitin signals proteolysis-independent stripping of transcription factors.

Ubiquitination of transcription activators has been reported to regulate transcription via both proteolytic and nonproteolytic routes, yet the function of the ubiquitin (Ub) signal in the nonproteolytic process is poorly understood. By use of the heterologous transcription activator LexA-VP16 in Saccharomyces cerevisiae, we show that monoubiquitin fusion of the activator prevents stable interactions between the activator and DNA, leading to transcription inhibition without activator degradation. We identify the AAA(+) ATPase Cdc48 and its cofactors as the Ub receptor responsible for extracting the monoubiquitinated activator from DNA. Our results suggest that deubiquitination of the activator is critical for transcription activation. These findings with LexA-VP16 extend in both yeast and mammalian cells to native transcription activators Met4 and R-Smads, respectively, that are known to be oligo-ubiquitinated. The results illustrate a role for Ub and Cdc48 in transcriptional regulation and gene expression that is independent of proteolysis.

The Effect of Hypothyroidism on Bone Loss at Dental Implants.

Hypothyroidism (HT) is an endocrine disorder characterized by abnormally reduced thyroid gland activity and is most commonly of autoimmune etiology. HT is associated with alterations in bone metabolism, and HT patients typically experience decreased bone resorption. The objective of this study was to use dental implants as standardized reference markers to compare the extent of alveolar bone loss in implant patients with and without HT. We examined medical and dental history records and radiographic data from 635 patients receiving 1480 implants during 2000-2017. The rate of bone loss was calculated from differences in radiographic bone levels over time, corrected for radiographic distortion. Peri-implant bone loss from patients with HT was significantly lower than for those without HT (t1252= -3.42; 95% confidence interval= 0.47-1.73; P < .001; M = 0.53 and 1.63 mm/yr, respectively). A similar relationship persisted after excluding smokers and diabetics and after additionally excluding those on systemic steroids, hormone replacement therapy, hormone medications, or autoimmune diseases other than HT. Our data suggest that patients with HT have a decreased rate of bone loss around dental implants and may not be at increased risk for dental implant failure. The decreased bone metabolic rate among patients with HT might contribute to those findings.

Asphaltene Adsorption on Functionalized Solids.

Asphaltenes, heavy aromatic components of crude oil, are known to adsorb on surfaces and can lead to pipe clogging or hinder oil recovery. Because of their multicomponent structure, the details of their interactions with surfaces are complex. We investigate the effect of the physicochemical properties of the substrate on the extent and mechanism of this adsorption. Using wetting measurements, we relate the initial kinetics of deposition to the interfacial energy of the surface. We then quantify the long-term adsorption dynamics using a quartz crystal microbalance and ellipsometry. Finally, we investigate the mechanism and morphology of adsorption with force spectroscopy measurements as a function of surface chemistry. We determine different adsorption regimes differing in orientation, packing density, and initial kinetics on different substrate functionalizations. Specifically, we find that alkane substrates delay the initial monolayer formation, fluorinated surfaces exhibit fast adsorption but low bonding strength, and hydroxyl substrates lead to a different adsorption orientation and a high packing density of the asphaltene layer.

Tracking Sulfonated Polystyrene Diffusion in a Chitosan/Carboxymethyl Cellulose Layer-by-Layer Film: Exploring the Internal Architecture of Nanocoatings.

Since chitosan presents the ability to interact with a wide range of molecules, it has been one of the most popular natural polymers for the construction of layer-by-layer thin films. In this study, depth-profiling X-ray photoelectron spectroscopy (XPS) was employed to track the diffusion of sulfonated polystyrene (SPS) in carboxymethyl cellulose/chitosan (CMC/Chi) multilayers. Our findings suggest that the CMC/Chi film does not constitute an electrostatic barrier sufficient to block diffusion of SPS, and that diffusion can be controlled by adjusting the diffusion time and the molecular weight of the polymers that compose the CMC/Chi system. In addition to monitoring the diffusion, it was also possible to observe a process of preferential interaction between Chi and SPS. Thus, the nitrogen N 1s peak, due to functional groups found exclusively in chitosan chains, was the key factor to identifying the molecular interactions involving chitosan and the different polyanions. Accordingly, the presence of a strong polyanion such as SPS shifts the N 1s peak to a higher level of binding energy. Such results highlight that understanding the fundamentals of polymer interactions is a major step to fine-tuning the internal architecture of LbL structures for specific applications (e.g., drug release).

Spontaneous wettability patterning via creasing instability.

Surfaces with patterned wettability contrast are important in industrial applications such as heat transfer, water collection, and particle separation. Traditional methods of fabricating such surfaces rely on microfabrication technologies, which are only applicable to certain substrates and are difficult to scale up and implement on curved surfaces. By taking advantage of a mechanical instability on a polyurethane elastomer film, we show that wettability patterns on both flat and curved surfaces can be generated spontaneously via a simple dip coating process. Variations in dipping time, sample prestress, and chemical treatment enable independent control of domain size (from about 100 to 500 µm), morphology, and wettability contrast, respectively. We characterize the wettability contrast using local surface energy measurements via the sessile droplet technique and tensiometry.

Investigation of the Internal Chemical Composition of Chitosan-Based LbL Films by Depth-Profiling X-ray Photoelectron Spectroscopy (XPS) Analysis.

Chitosan-based thin films were assembled using the layer-by-layer technique, and the axial composition was accessed using X-ray photoelectron spectroscopy with depth profiling. Chitosan (CHI) samples possessing different degrees of acetylation ([Formula: see text]) and molecular weight ([Formula: see text]) produced via the ultrasound-assisted deacetylation reaction were used in this study along with two different polyanions, namely, sodium polystyrenesulfonate (PSS) and carboxymethylcellulose (CMC). When chitosan, a positively charged polymer in aqueous acid medium, was combined with a strong polyanion (PSS), the total positive charge of chitosan, directly related to its [Formula: see text], was the key factor affecting the film formation. However, for CMC/CHI films, the pH of the medium and [Formula: see text] of chitosan strongly affected the film structure and composition. Consequently, the structure and the axial composition of chitosan-based films can be finely adjusted by choosing the polyanion and defining the chitosan to be used according to its DA and [Formula: see text] for the desired application, as demonstrated by the antibacterial tests.

Linkage-specific avidity defines the lysine 63-linked polyubiquitin-binding preference of rap80.

Linkage-specific polyubiquitin recognition is thought to make possible the diverse set of functional outcomes associated with ubiquitination. Thus far, mechanistic insight into this selectivity has been largely limited to single domains that preferentially bind to lysine 48-linked polyubiquitin (K48-polyUb) in isolation. Here, we propose a mechanism, linkage-specific avidity, in which multiple ubiquitin-binding domains are arranged in space so that simultaneous, high-affinity interactions are optimum with one polyUb linkage but unfavorable or impossible with other polyUb topologies and monoUb. Our model is human Rap80, which contains tandem ubiquitin interacting motifs (UIMs) that bind to K63-polyUb at DNA double-strand breaks. We show how the sequence between the Rap80 UIMs positions the domains for efficient avid binding across a single K63 linkage, thus defining selectivity. We also demonstrate K48-specific avidity in a different protein, ataxin-3. Using tandem UIMs, we establish the general principles governing polyUb linkage selectivity and affinity in multivalent ubiquitin receptors.

Differential ubiquitin binding by the acidic loops of Ube2g1 and Ube2r1 enzymes distinguishes their Lys-48-ubiquitylation activities.

The ubiquitin E2 enzymes, Ube2g1 and Ube2r1, are able to synthesize Lys-48-linked polyubiquitins without an E3 ligase but how that is accomplished has been unclear. Although both E2s contain essential acidic loops, only Ube2r1 requires an additional C-terminal extension (184-196) for efficient Lys-48-ubiquitylation activity. The presence of Tyr-102 and Tyr-104 in the Ube2g1 acidic loop enhanced both ubiquitin binding and Lys-48-ubiquitylation and distinguished Ube2g1 from the otherwise similar truncated Ube2r1(1-183) (Ube2r1C). Replacement of Gln-105-Ser-106-Gly-107 in the acidic loop of Ube2r1C (Ube2r1C(YGY)) by the corresponding residues from Ube2g1 (Tyr-102-Gly-103-Tyr-104) increased Lys-48-ubiquitylation activity and ubiquitin binding. Two E2∼UB thioester mimics (oxyester and disulfide) were prepared to characterize the ubiquitin binding activity of the acidic loop. The oxyester but not the disulfide derivative was found to be a functional equivalent of the E2∼UB thioester. The ubiquitin moiety of the Ube2r1C(C93S)-[(15)N]UB(K48R) oxyester displayed two-state conformational exchange, whereas the Ube2r1C(C93S/YGY)-[(15)N]UB(K48R) oxyester showed predominantly one state. Together with NMR studies that compared UB(K48R) oxyesters of the wild-type and the acidic loop mutant (Y102G/Y104G) forms of Ube2g1, in vitro ubiquitylation assays with various mutation forms of the E2s revealed how the intramolecular interaction between the acidic loop and the attached donor ubiquitin regulates Lys-48-ubiquitylation activity.

Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and in the Ino80 chromatin-remodeling complex.

Deubiquitinating enzymes (DUBs) are proteases that can antagonize ubiquitin-mediated signaling by disassembling ubiquitin-protein conjugates. How DUBs are regulated in vivo and how their substrate specificities are achieved are largely unknown. The conserved DUB Uch37 is found on proteasomes in organisms ranging from fission yeast to humans. Deubiquitination by Uch37 is activated by proteasomal binding, which enables Uch37 to process polyubiquitin chains. Here we show that in the nucleus Uch37 is also associated with the human Ino80 chromatin-remodeling complex (hINO80). In hINO80, Uch37 is held in an inactive state; however, it can be activated by transient interaction of the Ino80 complex with the proteasome. Thus, DUB activities can be modulated both positively and negatively via dynamic interactions with partner proteins. In addition, our findings suggest that the proteasome and the hINO80 chromatin-remodeling complex may cooperate to regulate transcription or DNA repair, processes in which both complexes have been implicated.

Depth-profiling X-ray photoelectron spectroscopy (XPS) analysis of interlayer diffusion in polyelectrolyte multilayers.

Functional organic thin films often demand precise control over the nanometer-level structure. Interlayer diffusion of materials may destroy this precise structure; therefore, a better understanding of when interlayer diffusion occurs and how to control it is needed. X-ray photoelectron spectroscopy paired with C60(+) cluster ion sputtering enables high-resolution analysis of the atomic composition and chemical state of organic thin films with depth. Using this technique, we explore issues common to the polyelectrolyte multilayer field, such as the competition between hydrogen bonding and electrostatic interactions in multilayers, blocking interlayer diffusion of polymers, the exchange of film components with a surrounding solution, and the extent and kinetics of interlayer diffusion. The diffusion coefficient of chitosan (M = ∼100 kDa) in swollen hydrogen-bonded poly(ethylene oxide)/poly(acrylic acid) multilayer films was examined and determined to be 1.4*10(-12) cm(2)/s. Using the high-resolution data, we show that upon chitosan diffusion into the hydrogen-bonded region, poly(ethylene oxide) is displaced from the film. Under the conditions tested, a single layer of poly(allylamine hydrochloride) completely stops chitosan diffusion. We expect our results to enhance the understanding of how to control polyelectrolyte multilayer structure, what chemical compositional changes occur with diffusion, and under what conditions polymers in the film exchange with the solution.

Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling.

Polyubiquitin chain topology is thought to direct modified substrates to specific fates, but this function-topology relationship is poorly understood, as are the dynamics and subcellular locations of specific polyubiquitin signals. Experimental access to these questions has been limited because linkage-specific inhibitors and in vivo sensors have been unavailable. Here we present a general strategy to track linkage-specific polyubiquitin signals in yeast and mammalian cells, and to probe their functions. We designed several high-affinity Lys63 polyubiquitin-binding proteins and demonstrate their specificity in vitro and in cells. We apply these tools as competitive inhibitors to dissect the polyubiquitin-linkage dependence of NF-κB activation in several cell types, inferring the essential role of Lys63 polyubiquitin for signaling via the IL-1ß and TNF-related weak inducer of apoptosis (TWEAK) but not TNF-α receptors. We anticipate live-cell imaging, proteomic and biochemical applications for these tools and extension of the design strategy to other polymeric ubiquitin-like protein modifications.

Sustainable drag reduction in turbulent Taylor-Couette flows by depositing sprayable superhydrophobic surfaces.

We demonstrate a reduction in the measured inner wall shear stress in moderately turbulent Taylor-Couette flows by depositing sprayable superhydrophobic microstructures on the inner rotor surface. The magnitude of reduction becomes progressively larger as the Reynolds number increases up to a value of 22% at Re=8.0×10(4). We show that the mean skin friction coefficient C(f) in the presence of the superhydrophobic coating can be fitted to a modified Prandtl-von Kármán-type relationship of the form (C(f)/2)(-1/2)=Mln (Re(C(f)/2)(1/2))+N+(b/Δr)Re(C(f)/2)(1/2) from which we extract an effective slip length of b≈19 µm. The dimensionless effective slip length b(+)=b/δ(ν), where δ(ν) is the viscous length scale, is the key parameter that governs the drag reduction and is shown to scale as b(+)∼Re(1/2) in the limit of high Re.

Designing Robust Hierarchically Textured Oleophobic Fabrics.

Commercially available woven fabrics (e.g., nylon- or PET-based fabrics) possess inherently re-entrant textures in the form of cylindrical yarns and fibers. We analyze the liquid repellency of woven and nanotextured oleophobic fabrics using a nested model with n levels of hierarchy that is constructed from modular units of cylindrical and spherical building blocks. At each level of hierarchy, the density of the topographical features is captured using a dimensionless textural parameter D(n)*. For a plain-woven mesh comprised of chemically treated fiber bundles (n = 2), the tight packing of individual fibers in each bundle (D2* ≈ 1) imposes a geometric constraint on the maximum oleophobicity that can be achieved solely by modifying the surface energy of the coating. For liquid droplets contacting such tightly bundled fabrics with modified surface energies, we show that this model predicts a lower bound on the equilibrium contact angle of θ(E) ≈ 57° below which the Cassie­Baxter to Wenzel wetting transition occurs spontaneously, and this is validated experimentally. We demonstrate how the introduction of an additional higher order micro-/nanotexture onto the fibers (n = 3) is necessary to overcome this limit and create more robustly nonwetting fabrics. Finally, we show a simple experimental realization of the enhanced oleophobicity of fabrics by depositing spherical microbeads of poly(methyl methacrylate)/fluorodecyl polyhedral oligomeric silsesquioxane (fluorodecyl POSS) onto the fibers of a commercial woven nylon fabric.

Optimization of amine-rich multilayer thin films for the capture and quantification of prostate-specific antigen.

It is demonstrated that poly(allylamine hydrochloride)/poly(styrenesulfonate) (PAH/SPS) multilayer films can be successfully tailored for the capture and detection of small biomolecules in dilute concentrations. Based on in vitro results, these films could be potentially applied for rapid and high-throughput diagnosis of dilute biomarkers in serum or tissue. PAH presents functional amino groups that can be further reacted with desired chemistries in order to create customizable and specific surfaces for biomolecule capture. A variety of film assembly characteristics were tested (pH, molecular weight of PAH, and ionic strength) to tune the biotinylation and swelling behavior of these films to maximize detection capabilities. The resultant optimized biotinylated PAH/SPS 9.3/9.3 system was utilized in conjunction with quantum dots (Qdots) to capture and detect a dilute biomarker for prostate cancer, prostate-specific antigen (PSA). Compared to previous work, our system presents a good sensitivity for PSA detection within the clinically relevant range of 0.4-100 ng/mL.

Tuning the properties of mucin via layer-by-layer assembly.

Multilayer films consisting of bovine submaxillary mucin (BSM) and poly(allylamine hydrochloride) (PAH) were prepared on various substrates using layer-by-layer assembly. The effects of both the assembly pH and ionic strength on multilayer characteristics were investigated by assessing film thicknesses (10-80 nm), surface wetting characteristics, and cell repulsion. Also, the dynamic assembly behavior was monitored using quartz crystal microbalance with dissipation monitoring (QCM-D) to further understand the effect of assembly pH on film characteristics. Assembly studies revealed that substantial amounts of BSM adhere to the outermost surface only at low pH conditions. The resulting multilayer films assembled at low pH conditions were found to exhibit hydrophilic and cell repellent behavior. In addition, it was found that batch-to-batch variations of the biopolymer BSM could dramatically alter properties.

Multifunctional inverted nanocone arrays for non-wetting, self-cleaning transparent surface with high mechanical robustness.

A multifunctional surface that enables control of wetting, optical reflectivity and mechanical damage of nanostructured interfaces is presented. Our approach is based on imprinting a periodic array of nanosized cones into a UV-curable polyurethane acrylate (PUA), resulting in a self-reinforcing egg-crate topography evenly distributed over large areas up to several cm(2) in size. The resulting surfaces can be either superhydrophilic or superhydrophobic (through subsequent application of an appropriate chemical coating), they minimize optical reflection losses over a broad range of wavelengths and a wide range of angles of incidence, and they also have enhanced mechanical resilience due to greatly improved redistribution of the normal and shearing mechanical loads. The transmissivity and wetting characteristics of the nanoscale egg-crate structure, as well as its resistance to mechanical deformation are analyzed theoretically. Experiments show that the optical performance together with self-cleaning or anti-fogging behavior of the inverted nanocone topography is comparable to earlier designs that have used periodic arrays of nanocones to control reflection and wetting. However the egg-crate structures are far superior in terms of mechanical robustness, and the ability to replicate this topography through several generations is promising for large-scale commercial applications where multifunctionality is important.

Sugar-mediated disassembly of mucin/lectin multilayers and their use as pH-Tolerant, on-demand sacrificial layers.

The layer-by-layer (LbL) assembly of thin films on surfaces has proven to be an extremely useful technology for uses ranging from optics to biomedical applications. Releasing these films from the substrate to generate so-called free-standing multilayer films opens a new set of applications. Current approaches to generating such materials are limited because they can be cytotoxic, difficult to scale up, or have undesirable side reactions on the material. In this work, a new sacrificial thin film system capable of chemically triggered dissolution at physiological pH of 7.4 is described. The film was created through LbL assembly of bovine submaxillary mucin (BSM) and the lectin jacalin (JAC) for a (BSM/JAC) multilayer system, which remains stable over a wide pH range (pH 3-9) and at high ionic strength (up to 5 M NaCl). This stability allows for subsequent LbL assembly of additional films in a variety of conditions, which could be released from the substrate by incubation in the presence of a competitive inhibitor sugar, melibiose, which selectively disassembles the (BSM/JAC) section of the film. This novel multilayer system was then applied to generate free-standing, 7 µm diameter, circular ultrathin films, which can be attached to a cell surface as a "backpack". A critical thickness of about 100 nm for the (BSM/JAC) film was required to release the backpacks from the glass substrate, after incubation in melibiose solution at 37 °C for 1 h. Upon their release, backpacks were subsequently attached to murine monocytes without cytotoxicity, thereby demonstrating the compatibility of this mucin-based release system with living cells.