204 research outputs found

    Folding Circular Permutants of IL-1ÎČ: Route Selection Driven by Functional Frustration

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    Interleukin-1ÎČ (IL-1ÎČ) is the cytokine crucial to inflammatory and immune response. Two dominant routes are populated in the folding to native structure. These distinct routes are a result of the competition between early packing of the functional loops versus closure of the ÎČ-barrel to achieve efficient folding and have been observed both experimentally and computationally. Kinetic experiments on the WT protein established that the dominant route is characterized by early packing of geometrically frustrated functional loops. However, deletion of one of the functional loops, the ÎČ-bulge, switches the dominant route to an alternative, yet, as accessible, route, where the termini necessary for barrel closure form first. Here, we explore the effect of circular permutation of the WT sequence on the observed folding landscape with a combination of kinetic and thermodynamic experiments. Our experiments show that while the rate of formation of permutant protein is always slower than that observed for the WT sequence, the region of initial nucleation for all permutants is similar to that observed for the WT protein and occurs within a similar timescale. That is, even permutants with significant sequence rearrangement in which the functional-nucleus is placed at opposing ends of the polypeptide chain, fold by the dominant WT “functional loop-packing route”, despite the entropic cost of having to fold the N- and C- termini early. Taken together, our results indicate that the early packing of the functional loops dominates the folding landscape in active proteins, and, despite the entropic penalty of coalescing the termini early, these proteins will populate an entropically unfavorable route in order to conserve function. More generally, circular permutation can elucidate the influence of local energetic stabilization of functional regions within a protein, where topological complexity creates a mismatch between energetics and topology in active proteins

    Orbital overlap effects in electron transfer reactions across a metal nanowire/electrolyte solution interface

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    In this paper, we report on calculations of the orbital overlap between Fe(III) and Cr(III) aquacomplexes and different electrode surfaces: Cu(111), Ag (111), Au(111), Pt(111), and corresponding monatomic wires. The electronic structure of the monocrystalline surfaces and nanowires are described in terms of the electronic spillover and density of electronic states at the Fermi level obtained from periodic density functional theory (DFT) calculations. The transmission coefficients (Îș) characterizing the first stage of outer-sphere electron transfer for the reduction of aquacomplexes are calculated on the basis of Landau–Zener theory as a function of electrode–reactant separation; the electronic transmission coefficients for the [Cr(H2O)6]3+/2+ redox couple were found to be smaller than those for [Fe(H2O)6]3+/2+. Two different intervals can be clearly distinguished for Cu, Au and Pt: “a catalytic region”, where Îș(wire) > Îș(Me slab) and “an inhibition region”, where Îș(wire) < Îș(Me slab). A similar behavior exhibits the coupling constant estimated for a hydrogen atom adsorbed at the Au(111) surface and the Au monatomic wire. These effects originate from some specific features of electronic density profile for metal nanowires: at short distances the electronic density of nanowires is higher compared with the (111) metal surfaces, while at larger separations it decreases more sharply.Fil: Nazmutdinov, Renat R.. Kazan National Research Technological University; RusiaFil: Berezin, Alexander S.. Kazan National Research Technological University; RusiaFil: Soldano, GermĂĄn. Universitat Ulm; Alemania. Consejo Nacional de Investigaciones CientĂ­ficas y TĂ©cnicas; ArgentinaFil: Schmickler, Wolfgang. Universitat Ulm; Alemani

    A statistical learning strategy for closed-loop control of fluid flows

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    This work discusses a closed-loop control strategy for complex systems utilizing scarce and streaming data. A discrete embedding space is first built using hash functions applied to the sensor measurements from which a Markov process model is derived, approximating the complex system’s dynamics. A control strategy is then learned using reinforcement learning once rewards relevant with respect to the control objective are identified. This method is designed for experimental configurations, requiring no computations nor prior knowledge of the system, and enjoys intrinsic robustness. It is illustrated on two systems: the control of the transitions of a Lorenz’63 dynamical system, and the control of the drag of a cylinder flow. The method is shown to perform well

    Plakophilin3 Loss Leads to an Increase in PRL3 Levels Promoting K8 Dephosphorylation, Which Is Required for Transformation and Metastasis

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    The desmosome anchors keratin filaments in epithelial cells leading to the formation of a tissue wide IF network. Loss of the desmosomal plaque protein plakophilin3 (PKP3) in HCT116 cells, leads to an increase in neoplastic progression and metastasis, which was accompanied by an increase in K8 levels. The increase in levels was due to an increase in the protein levels of the Phosphatase of Regenerating Liver 3 (PRL3), which results in a decrease in phosphorylation on K8. The increase in PRL3 and K8 protein levels could be reversed by introduction of an shRNA resistant PKP3 cDNA. Inhibition of K8 expression in the PKP3 knockdown clone S10, led to a decrease in cell migration and lamellipodia formation. Further, the K8 PKP3 double knockdown clones showed a decrease in colony formation in soft agar and decreased tumorigenesis and metastasis in nude mice. These results suggest that a stabilisation of K8 filaments leading to an increase in migration and transformation may be one mechanism by which PKP3 loss leads to tumor progression and metastasis
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