The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Elio Fried - One of the best experts on this subject based on the ideXlab platform.
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theoretical and experimental study of the stability of a soap film spanning a Flexible Loop
International Journal of Engineering Science, 2015Co-Authors: Aisa Iria, Elio FriedAbstract:Abstract A variational approach is used to study the stability of a soap film spanning a Flexible Loop. The film is modeled as a fluid surface endowed with constant tension and the Loop is modeled as an inextensible and unshearable elastic rod that resists not only bending but also twisting about the tangent to its centerline. The first and second variations of the underlying energy functional are derived, leading to governing equilibrium equations and energetically based stability conditions. The latter conditions are applied to explore the effect of subjecting flat circular configurations to planar and transverse perturbations. Both the areal stretching and the lineal twisting prove to compete against the lineal bending to destabilize such a configuration. Experiments are performed to study post-buckled configurations and to assess the validity of the theoretical predictions.
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theoretical and experimental study of the stability of a soap film spanning a Flexible Loop
arXiv: Soft Condensed Matter, 2014Co-Authors: Aisa Iria, Elio FriedAbstract:A variational model is used to study the stability of a soap film spanning a Flexible Loop. The film is modeled as a fluid surface endowed with constant tension and the Loop is modeled as an elastic rod resistant to both bending and twist. The first and second energy variations of the underlying energy functional are derived, leading to governing equilibrium equations and stability criteria. The latter criteria are employed to explore the stability of flat circular configurations with respect to planar and transverse perturbations. Experiments are performed to study post-buckled configurations and to explore the validity of the theoretical predictions. Imparting a twist to the bounding Loop destabilizes flat circular Loops which are short-enough to be stable when twist-free. Nevertheless, when the circular disk is perturbed merely radially or merely transversely, the stability condition is indifferent to twist. By the equilibrium equations, the twisting angle of a planar equilibrium configuration should be distributed uniformly along the Loop. The stability criteria guarantee that this uniformity is preserved after buckling. The stability with respect to increasing the surface tension of the film or the length of the Loop is sensitive to the cross-sectional thickness of the bounding Loop. However, stability with respect to increasing the total twist is indifferent to that thickness.
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stability and bifurcation of a soap film spanning an elastic Loop
arXiv: Soft Condensed Matter, 2013Co-Authors: Yichao Che, Elio FriedAbstract:The Euler--Plateau problem, proposed by \cite{gm}, concerns a soap film spanning a Flexible Loop. The shapes of the film and the Loop are determined by the interactions between the two components. In the present work, the Euler--Plateau problem is reformulated to yield a boundary-value problem for a vector field that parameterizes both the spanning surface and the bounding Loop. Using the first and second variations of the relevant free-energy functional, detailed bifurcation and stability analyses are performed. For spanning surface with energy density $\sigma$ and a bounding Loop with length $2\pi R$ and bending rigidity $a$, the first bifurcation, during which the spanning surface remains flat but the bounding Loop becomes noncircular, occurs at $\sigma R^3/a=3$, confirming a result obtained previously via an energy comparison. Other bifurcation solution branches, including those emanating from the flat circular solution branch to nonplanar solution branches, are also shown to be unstable.
J S Frase - One of the best experts on this subject based on the ideXlab platform.
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effects of alpha tubulin acetylation on microtubule structure and stability
Proceedings of the National Academy of Sciences of the United States of America, 2019Co-Authors: Lisa Eshunwilso, Rui Zhang, Didie Portra, Maxence V Nachury, Daniel Toso, Thomas Loh, Michele Vendruscolo, Massimiliano Onomi, J S FraseAbstract:Acetylation of K40 in α-tubulin is the sole posttranslational modification to mark the luminal surface of microtubules. It is still controversial whether its relationship with microtubule stabilization is correlative or causative. We have obtained high-resolution cryo-electron microscopy (cryo-EM) reconstructions of pure samples of αTAT1-acetylated and SIRT2-deacetylated microtubules to visualize the structural consequences of this modification and reveal its potential for influencing the larger assembly properties of microtubules. We modeled the conformational ensembles of the unmodified and acetylated states by using the experimental cryo-EM density as a structural restraint in molecular dynamics simulations. We found that acetylation alters the conformational landscape of the Flexible Loop that contains αK40. Modification of αK40 reduces the disorder of the Loop and restricts the states that it samples. We propose that the change in conformational sampling that we describe, at a location very close to the lateral contacts site, is likely to affect microtubule stability and function.
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effects of α tubulin acetylation on microtubule structure and stability
bioRxiv, 2019Co-Authors: Lisa Eshunwilso, Rui Zhang, Didie Portra, Maxence V Nachury, Daniel Toso, Thomas Loh, Michele Vendruscolo, Massimiliano Onomi, J S FraseAbstract:ABSTRACT Acetylation of K40 in α-tubulin is the sole post-translational modification to mark the luminal surface of microtubules. It is still controversial whether its relationship with microtubule stabilization is correlative or causative. We have obtained high-resolution cryo-electron microscopy reconstructions of pure samples of αTAT1-acetylated and SIRT2-deacetylated microtubules to visualize the structural consequences of this modification and reveal its potential for influencing the larger assembly properties of microtubules. We modeled the conformational ensembles of the unmodified and acetylated states by using the experimental cryo-EM density as the structural restraint in molecular dynamics simulations. We found that acetylation alters the conformational landscape of the Flexible Loop that contains αK40. Modification of αK40 reduces the disorder of the Loop and restricts the states that it samples. We propose that the change in conformational sampling that we describe, at a location very close to the lateral contacts site, is likely to affect microtubule stability and function.
Paul T Wingfield - One of the best experts on this subject based on the ideXlab platform.
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the solution structure of hiv 1 nef reveals an unexpected fold and permits delineation of the binding surface for the sh3 domain of hck tyrosine protein kinase
Nature Structural & Molecular Biology, 1996Co-Authors: Stephan Grzesiek, Ad Bax, G M Clore, Angela M Gronenborn, Joshua D Kaufman, Ira Palmer, Stephen J Stahl, Paul T WingfieldAbstract:The solution structure of HIV-1 Nef has been solved by multidimensional heteronuclear NMR spectroscopy. The construct employed to circumvent problems associated with aggregation was a double-deletion mutant (delta2-39, delta159-173) in which conformationally disordered regions of the protein at the N terminus and in a long solvent-exposed Flexible Loop were removed, without affecting the properties or structural integrity of the remainder of the protein. Despite the absence of any sequence similarity, the overall fold of Nef is reminiscent of that of the family of winged helix-turn-helix DNA binding proteins. The binding surface of Nef for the SH3 domain of Hck tyrosine protein kinase has been mapped and reveals a non-contiguous (in terms of amino-acid sequence) interaction surface. This unique feature may suggest possible avenues for drug design aimed at inhibiting the interaction between Nef and SH3 domains.
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the solution structure of hiv 1 nef reveals an unexpected fold and permits delineation of the binding surface for the sh3 domain of hck tyrosine protein kinase
Nature Structural & Molecular Biology, 1996Co-Authors: Stephan Grzesiek, G M Clore, Angela M Gronenborn, Joshua D Kaufman, Ira Palmer, Stephen J Stahl, Jinshan Hu, Paul T WingfieldAbstract:The solution structure of HIV-1 Nef has been solved by multidimensional heteronuclear NMR spectroscopy. The construct employed to circumvent problems associated with aggregation was a double-deletion mutant (Δ2–39, Δ159–173) in which conformationally disordered regions of the protein at the N terminus and in a long solvent-exposed Flexible Loop were removed, without affecting the properties or structural integrity of the remainder of the protein. Despite the absence of any sequence similarity, the overall fold of Nef is reminiscent of that of the family of winged helix-turn-helix DNA binding proteins. The binding surface of Nef for the SH3 domain of Hck tyrosine protein kinase has been mapped and reveals a non-contiguous (in terms of amino-acid sequence) interaction surface. This unique feature may suggest possible avenues for drug design aimed at inhibiting the interaction between Nef and SH3 domains.
Kanju Ohsawa - One of the best experts on this subject based on the ideXlab platform.
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crystal structure of 1 deoxy d xylulose 5 phosphate reductoisomerase complexed with cofactors implications of a Flexible Loop movement upon substrate binding
Journal of Biochemistry, 2002Co-Authors: Shunsuke Yajima, Takamasa Nonaka, Tomohisa Kuzuyama, Haruo Seto, Kanju OhsawaAbstract:The key enzyme in the nonmevalonate pathway, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), has been shown to be an effective target of antimalarial drugs. Here we report the crystal structure of DXR complexed with NADPH and a sulfate ion from Escherichia coli at 2.2 A resolution. The structure showed the presence of an extra domain, which is absent from other NADPH-dependent oxidoreductases, in addition to the conformation of catalytic residues and the substrate binding site. A Flexible Loop covering the substrate binding site plays an important role in the enzymatic reaction and the determination of substrate specificity.
Eliot Fried - One of the best experts on this subject based on the ideXlab platform.
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buckling of a soap film spanning a Flexible Loop resistant to bending and twisting
Proceedings of The Royal Society A: Mathematical Physical and Engineering Sciences, 2014Co-Authors: Aisa Biria, Eliot FriedAbstract:A generalization of the Euler–Plateau problem to account for the energy contribution due to twisting of the bounding Loop is proposed. Euler–Lagrange equations are derived in a parametrized setting and a buckling analysis is performed. A pair of dimensionless parameters govern buckling from a flat, circular ground state. While one of these is familiar from the Euler–Plateau problem, the other encompasses information about the ratio of the torsional rigidity to the bending rigidity, the twist density and the size of the Loop. For sufficiently small values of the latter parameter, two separate groups of buckling modes are identified. However, for values of that parameter exceeding the critical twist density arising in Michell's study of the stability of a twisted elastic ring, only one group of buckling modes exists. Buckling diagrams indicate that a Loop with greater torsional rigidity shows more resistance to transverse buckling. Additionally, a twisted Flexible Loop spanned by a soap film buckles at a value of the twist density less that the value at which buckling would occur if the soap film were absent.
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Stability and Bifurcation of a Soap Film Spanning a Flexible Loop
Journal of Elasticity, 2014Co-Authors: Yi-chao Chen, Eliot FriedAbstract:The Euler–Plateau problem, proposed by Giomi and Mahadevan in Proc. R. Soc. Lond. Ser. A, Math. Phys. Eng. Sci. 468, 1851–1864 ( 2012 ), concerns a soap film spanning a Flexible Loop. The shapes of the film and the Loop are determined by the interactions between the two components. In the present work, the Euler–Plateau problem is reformulated to yield a boundary-value problem for a vector field that parameterizes both the spanning surface and the bounding Loop. Using the first and second variations of the relevant free-energy functional, detailed bifurcation and stability analyses are performed. For a spanning surface with energy density σ and a bounding Loop with length 2 πR and flexural rigidity a , the first bifurcation, during which the spanning surface remains flat but the bounding Loop becomes noncircular, occurs at R ^3 σ / a =3, confirming a result obtained previously via an energy comparison. All other bifurcation solution branches emanating from the flat circular solution branch, including those to nonplanar solution branches, are found to be unstable.