Structure and dynamics of single-isoform recombinant Neuronal Human Tubulin

Microtubules are polymers that cycle stochastically between polymerization and depolymerization i.e., they exhibit 'dynamic instability'. This behavior is crucial for cell division, motility and differentiation. While studies in the last decade have made fundamental breakthroughs in our understanding of how cellular effectors modulate microtubule dynamics, analysis of the relationship between tubulin sequence, structure and dynamics has been held back by a lack of dynamics measurements with and structural characterization of homogenous, isotypically pure, engineered tubulin. Here we report for the first time the cryo-EM structure and in vitro dynamics parameters of recombinant isotypically pure human tubulin. α1A/βIII is a purely neuronal tubulin isoform. The 4.2 Å structure of unmodified human α1A/βIII microtubules shows overall similarity to that of heterogeneous brain microtubules, but is distinguished by subtle differences at polymerization interfaces, which are hotspots for sequence divergence between tubulin isoforms. In vitro dynamics assays show that, like mosaic brain microtubules, recombinant homogenous microtubules undergo dynamic instability but they polymerize slower and catastrophe less frequently. Interestingly, we find that epitaxial growth of α1A/βIII microtubules from heterogeneous brain seeds is inefficient, but can be fully rescued by incorporating as little as 5% of brain tubulin into the homogenous α1A/βIII lattice. Our study establishes a system to examine the structure and dynamics of mammalian microtubules with well-defined tubulin species and is a first and necessary step towards uncovering how tubulin genetic and chemical diversity is exploited to modulate intrinsic microtubule dynamics

MARK4 controls ischaemic heart failure through microtubule detyrosination.

Myocardial infarction is a major cause of premature death in adults. Compromised cardiac function after myocardial infarction leads to chronic heart failure with systemic health complications and a high mortality rate1. Effective therapeutic strategies are needed to improve the recovery of cardiac function after myocardial infarction. More specifically, there is a major unmet need for a new class of drugs that can improve cardiomyocyte contractility, because inotropic therapies that are currently available have been associated with high morbidity and mortality in patients with systolic heart failure2,3 or have shown a very modest reduction of risk of heart failure4. Microtubule detyrosination is emerging as an important mechanism for the regulation of cardiomyocyte contractility5. Here we show that deficiency of microtubule-affinity regulating kinase 4 (MARK4) substantially limits the reduction in the left ventricular ejection fraction after acute myocardial infarction in mice, without affecting infarct size or cardiac remodelling. Mechanistically, we provide evidence that MARK4 regulates cardiomyocyte contractility by promoting phosphorylation of microtubule-associated protein 4 (MAP4), which facilitates the access of vasohibin 2 (VASH2)-a tubulin carboxypeptidase-to microtubules for the detyrosination of α-tubulin. Our results show how the detyrosination of microtubules in cardiomyocytes is finely tuned by MARK4 to regulate cardiac inotropy, and identify MARK4 as a promising therapeutic target for improving cardiac function after myocardial infarction.BHF fellowship grant (FS/14/28/30713), Issac Newton Trust Grant (18.40u), and Cambridge BHF Centre of Research Excellence grants (RE/13/6/30180 and RE/18/1/34212)

Influence of electropolishing and anodic oxidation on morphology, chemical composition and corrosion resistance of niobium

The work presents results of the studies performed on electropolishing of pure niobium in a bath that contained: sulphuric acid, hydrofluoric acid, ethylene glycol and acetanilide. After the electropolishing, the specimens were subjected to anodic passivation in a 1 mol dm- 3 phosphoric acid solution at various voltages. The surface morphology, thickness, roughness and chemical composition of the resulting oxide layers were analysed. Thusly prepared niobium samples were additionally investigated in terms of their corrosion resistance in Ringer's solution. The electropolished niobium surface was determined to be smooth and lustrous. The anodisation led to the growth of barrier-like oxide layers, which were enriched in phosphorus species. © 2014 Elsevier B.V.Russian Foundation for Basic Research, RFBR: 13-08-96007; Ural Branch, Russian Academy of Sciences, UB RAS: 12-T-2-1009This work was supported by the Polish Ministry of Science and Education under the “Diamond Grant” programme, research project no. DI 2012 024142 . We acknowledge also the partial support of the Ural Division of the Russian Academy of Sciences (Project 12-T-2-1009 ) and the Russian Foundation for Basic Research (Project 13-08-96007 )

Control of substrate gating and translocation into ClpP by channel residues and ClpX binding

ClpP is a self-compartmentalized protease, which has very limited degradation activity unless it associates with ClpX to form ClpXP or with ClpA to form ClpAP. Here, we show that ClpX binding stimulates ClpP cleavage of peptides larger than a few amino acids and enhances ClpP active-site modification. Stimulation requires ATP binding but not hydrolysis by ClpX. The magnitude of this enhancement correlates with increasing molecular weight of the molecule entering ClpP. Amino-acid substitutions in the channel loop or helix A of ClpP enhance entry of larger substrates into the free enzyme, eliminate ClpX binding in some cases, and are not further stimulated by ClpX binding in other instances. These results support a model in which the channel residues of free ClpP exclude efficient entry of all but the smallest peptides into the degradation chamber, with ClpX binding serving to relieve these inhibitory interactions. Specific ClpP channel variants also prevent ClpXP translocation of certain amino-acid sequences, suggesting that the wild-type channel plays an important role in facilitating broad translocation specificity. In combination with previous studies, our results indicate that collaboration between ClpP and its partner ATPases opens a gate that functions to exclude larger substrates from isolated ClpP.National Institutes of Health (U.S.) (Grant number AI-15706

Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis

Nucleolar Essential Protein 1 (Nep1) is required for small subunit (SSU) ribosomal RNA (rRNA) maturation and is mutated in Bowen–Conradi Syndrome. Although yeast (Saccharomyces cerevisiae) Nep1 interacts with a consensus sequence found in three regions of SSU rRNA, the molecular details of the interaction are unknown. Nep1 is a SPOUT RNA methyltransferase, and can catalyze methylation at the N1 of pseudouridine. Nep1 is also involved in assembly of Rps19, an SSU ribosomal protein. Mutations in Nep1 that result in decreased methyl donor binding do not result in lethality, suggesting that enzymatic activity may not be required for function, and RNA binding may play a more important role. To study these interactions, the crystal structures of the scNep1 dimer and its complexes with RNA were determined. The results demonstrate that Nep1 recognizes its RNA site via base-specific interactions and stabilizes a stem-loop in the bound RNA. Furthermore, the RNA structure observed contradicts the predicted structures of the Nep1-binding sites within mature rRNA, suggesting that the Nep1 changes rRNA structure upon binding. Finally, a uridine base is bound in the active site of Nep1, positioned for a methyltransfer at the C5 position, supporting its role as an N1-specific pseudouridine methyltransferase

On the electropolishing and anodic oxidation of Ti-15Mo alloy

This paper presents research on modifying the surface of Ti-15Mo alloy using electropolishing and anodic passivation. The electropolishing process was carried out in solutions containing sulfuric acid, ethylene glycol, ammonium fluoride and oxalic acid. Whereas a voltage range from 20 to 100 V and a 1 M orthophosphoric acid solution were used during the anodic passivation. The influence of above mentioned processes parameters on the quality of the obtained oxide layer on Ti-15Mo alloy was investigated. The analysis of Ti-15Mo surface after modification was performed using scanning electron microscopy (SEM), atomic force microscopy (AFM), energy-dispersive X-ray spectroscopy (EDX), X-ray photoelectron spectroscopy (XPS), ellipsometry, and mechanical tests. Moreover, the corrosion resistance was investigated using a potentiostatic method in Ringer's solution. It was found that electropolishing leads to an increase in the surface homogeneity and to the form of an oxide layer, which consisted of TiO2 and MoO3. Whereas the oxide layers obtained during anodic passivation were characterized by different properties depending on the applied voltage. The anodic passivation at various voltages (20-100 V) increased the surface wettability (94.5°-87.6°) in comparison to the electropolished sample (97.5°). Moreover, the obtained oxide layer after anodization exhibited a high hardness. The electrolytic polishing and anodic passivation of Ti-15Mo also improved corrosion resistance of the alloy in contact with Ringer's solution. The sample anodized at 80 V presented the highest corrosion resistance by the smallest corrosion current density (1.4 nA cm-2) and the highest polarization resistance (37.4 MΩ cm2). © 2016 Elsevier Ltd. All rights reserved

Tubulin isoform composition tunes microtubule dynamics

Microtubules polymerize and depolymerize stochastically, a behavior essential for cell division, motility and differentiation. While many studies advanced our understanding of how microtubule-associated proteins tune microtubule dynamics in trans, we have yet to understand how tubulin genetic diversity regulates microtubule functions. The majority of in vitro dynamics studies are performed with tubulin purified from brain tissue. This preparation is not representative of tubulin found in many cell types. Here we report the 4.2Å cryo-EM structure and in vitro dynamics parameters of α1B/βI+βIVb microtubules assembled from tubulin purified from a human embryonic kidney cell line with isoform composition characteristic of fibroblasts and many immortalized cell lines. We find that these microtubules grow faster and transition to depolymerization less frequently compared to brain microtubules. Cryo-EM reveals that the dynamic ends of α1B/βI+βIVb microtubules are less tapered and that these tubulin heterodimers display lower curvatures. Interestingly, analysis of EB1 distributions at dynamic ends suggests no differences in GTP cap sizes. Lastly, we show that the addition of recombinant α1A/βIII tubulin, a neuronal isotype overexpressed in many tumors, proportionally tunes the dynamics of α1B/βI+βIVb microtubules. Our study is an important step towards understanding how tubulin isoform composition tunes microtubule dynamics

Insight into the Mechanisms of Adenovirus Capsid Disassembly from Studies of Defensin Neutralization

Defensins are effectors of the innate immune response with potent antibacterial activity. Their role in antiviral immunity, particularly for non-enveloped viruses, is poorly understood. We recently found that human alpha-defensins inhibit human adenovirus (HAdV) by preventing virus uncoating and release of the endosomalytic protein VI during cell entry. Consequently, AdV remains trapped in the endosomal/lysosomal pathway rather than trafficking to the nucleus. To gain insight into the mechanism of defensin-mediated neutralization, we analyzed the specificity of the AdV-defensin interaction. Sensitivity to alpha-defensin neutralization is a common feature of HAdV species A, B1, B2, C, and E, whereas species D and F are resistant. Thousands of defensin molecules bind with low micromolar affinity to a sensitive serotype, but only a low level of binding is observed to resistant serotypes. Neutralization is dependent upon a correctly folded defensin molecule, suggesting that specific molecular interactions occur with the virion. CryoEM structural studies and protein sequence analysis led to a hypothesis that neutralization determinants are located in a region spanning the fiber and penton base proteins. This model was supported by infectivity studies using virus chimeras comprised of capsid proteins from sensitive and resistant serotypes. These findings suggest a mechanism in which defensin binding to critical sites on the AdV capsid prevents vertex removal and thereby blocks subsequent steps in uncoating that are required for release of protein VI and endosomalysis during infection. In addition to informing the mechanism of defensin-mediated neutralization of a non-enveloped virus, these studies provide insight into the mechanism of AdV uncoating and suggest new strategies to disrupt this process and inhibit infection

Nonequivalent adsorption of pH-responsive dicephalic sugar surfactants at the air/solution interface

The present work contributes to the analysis of the effect of electrolyte and pH on the adsorption of dicephalic N-dodecyl-N,N-bis[(3-D-aldonylamido) propyl]amines (aldonyl = gluconyl and lactobionyl) at the air/water interface. The headgroup of these surfactants consists of two amide groups connected by a central tertiary amine, which may be protonated in an aqueous environment. We performed measurements of surface tension isotherms of aqueous solutions of the studied dicephalics in the presence of NaCl and NaOH and applied the STDE model for evaluation of the experimental results. They showed that the adsorption of the surfactants at the air/water interface was pH- and electrolyte- dependent, since addition of NaCl and NaOH had different effects on the surface activity and critical micelle concentration values (CMC). The theoretical model reflected well the surface tension isotherms obtained for a broad range of surfactants concentration, confirming the theoretical predictions concerning the protonation of tertiary amines, which was additionally supported by the measurements of solution pH