The Experts below are selected from a list of 327 Experts worldwide ranked by ideXlab platform
Keir C. Neuman - One of the best experts on this subject based on the ideXlab platform.
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comparison of dna decatenation by escherichia coli topoisomerase iv and topoisomerase iii implications for non equilibrium topology simplification
Nucleic Acids Research, 2013Co-Authors: Yeonee Seol, Ashley H. Hardin, Gilles Charvin, Mariepaule Strub, Keir C. NeumanAbstract:Type II topoisomerases are essential enzymes that regulate DNA topology through a strand-passage mechanism. Some type II topoisomerases relax supercoils, unknot and decatenate DNA to below thermodynamic equilibrium. Several models of this non-equilibrium topology simplification phenomenon have been proposed. The Kinetic Proofreading (KPR) model postulates that strand passage requires a DNA-bound topoisomerase to collide twice in rapid succession with a second DNA segment, implying a quadratic relationship between DNA collision frequency and relaxation rate. To test this model, we used a single-molecule assay to measure the unlinking rate as a function of DNA collision frequency for Escherichia coli topoisomerase IV (topo IV) that displays efficient non-equilibrium topology simplification activity, and for E. coli topoisomerase III (topo III), a type IA topoisomerase that unlinks and unknots DNA to equilibrium levels. Contrary to the predictions of the KPR model, topo IV and topo III unlinking rates were linearly related to the DNA collision frequency. Furthermore, topo III exhibited decatenation activity comparable with that of topo IV, supporting proposed roles for topo III in DNA segregation. This study enables us to rule out the KPR model for non-equilibrium topology simplification. More generally, we establish an experimental approach to systematically control DNA collision frequency.
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Non-Equilibrium Topology Simplification by Type II Topoisomerases: A Test of Kinetic Proofreading
Biophysical Journal, 2012Co-Authors: Yeonee Seol, Ashley H. Hardin, Gilles Charvin, Keir C. NeumanAbstract:Type II topoisomerases are essential enzymes that modify DNA topology. These topoisomerases pass a double stranded segment (T-segment) of DNA though a transient double stranded break in a second segment (G-segment). This strand passage mechanism allows type II topoisomerases to unlink, unknot, and relax supercoiled DNA to below equilibrium levels1. The mechanisms underlying this non-equilibrium topology simplification remain speculative. Several theoretical models have been proposed but experimental data has not been able to distinguish among them. One model developed by Yan and Marko2, postulates that the strand passage mechanism of type II topoisomerases is governed by a Kinetic Proofreading process. In practice, this model suggests that type II topoisomerases require two collisions between the T- and G-segments prior to strand passage. The first collision of a T-segment with the enzyme-bound G-segment transiently activates the enzyme and the second collision of the T-segment with the activated enzyme results in strand passage. The model predicts that the strand passage probability scales as the square of the collision rate, which has not been tested. We directly tested this prediction of the Kinetic Proofreading model using a single-crossing DNA unlinking assay. We measured the rate that topoisomerase IV, a bacterial type II topoisomerase, unlinked DNA as a function of the strand collision probability obtained from Monte Carlo simulations of the DNA crossings. The unlinking rate was linearly related to the collision probability, which is inconsistent with the Kinetic Proofreading model.1.Rybenkov, V. V., Ullsperger, C., Vologodskii, A. V. & Cozzarelli, N. R. Simplification of DNA topology below equilibrium values by type II topoisomerases. Science 277, 690-693 (1997).2.Yan, J., Magnasco, M. O. & Marko, J. F. A Kinetic Proofreading mechanism for disentanglement of DNA by topoisomerases. Nature 401, 932-935, doi:10.1038/44872 (1999).
Hong Qian - One of the best experts on this subject based on the ideXlab platform.
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cooperativity and specificity in enzyme Kinetics a single molecule time based perspective
Biophysical Journal, 2008Co-Authors: Hong QianAbstract:An alternative theoretical approach to enzyme Kinetics that is particularly applicable to single-molecule enzymology is presented. The theory, originated by Van Slyke and Cullen in 1914, develops enzyme Kinetics from a "time perspective" rather than the traditional "rate perspective" and emphasizes the nonequilibrium steady-state nature of enzymatic reactions and the significance of small copy numbers of enzyme molecules in living cells. Sigmoidal cooperative substrate binding to slowly fluctuating, monomeric enzymes is shown to arise from association pathways with very small probability but extremely long passage time, which would be disregarded in the traditional rate perspective: A single enzyme stochastically takes alternative pathways in serial order rather than different pathways in parallel. The theory unifies dynamic cooperativity and Hopfield-Ninio's Kinetic Proofreading mechanism for specificity amplification.
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phosphorylation energy hypothesis open chemical systems and their biological functions
Annual Review of Physical Chemistry, 2007Co-Authors: Hong QianAbstract:AbstractBiochemical systems and processes in living cells generally operate far from equilibrium. This review presents an overview of a statistical thermodynamic treatment for such systems, with examples from several key components in cellular signal transduction. Open-system nonequilibrium steady-state (NESS) models are introduced. The models account quantitatively for the energetics and thermodynamics in phosphorylation-dephosphorylation switches, GTPase timers, and specificity amplification through Kinetic Proofreading. The chemical energy derived from ATP and GTP hydrolysis establishes the NESS of a cell and makes the cell—a mesoscopic–biochemical reaction system that consists of a collection of thermally driven fluctuating macromolecules—a genetically programmed chemical machine.
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reducing intrinsic biochemical noise in cells and its thermodynamic limit
Journal of Molecular Biology, 2006Co-Authors: Hong QianAbstract:In living cells, the specificity of biomolecular recognition can be amplified and the noise from non-specific interactions can be reduced at the expense of cellular free energy. This is the seminal idea in the Hopfield-Ninio theory of Kinetic Proofreading: The specificity is increased via cyclic network Kinetics without altering molecular structures and equilibrium affinites. We show a thermodynamic limit of the specificity amplification with a given amount of available free energy. For a normal cell under physiological condition with sustained phosphorylation potential, this gives a factor of 10(10) as the upper bound in specificity amplification. We also study an optimal Kinetic network design that is capable of approaching the thermodynamic limit.
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Open-system nonequilibrium steady state: Statistical thermodynamics, fluctuations, and chemical oscillations
Journal of Physical Chemistry B, 2006Co-Authors: Hong QianAbstract:Gibbsian equilibrium statistical thermodynamics is the theoretical foundation for isothermal, closed chemical, and biochemical reaction systems. This theory, however, is not applicable to most biochemical reactions in living cells, which exhibit a range of interesting phenomena such as free energy transduction, temporal and spatial complexity, and Kinetic Proofreading. In this article, a nonequilibrium statistical thermodynamic theory based on stochastic Kinetics is introduced, mainly through a series of examples: single-molecule enzyme Kinetics, nonlinear chemical oscillation, molecular motor, biochemical switch, and specificity amplification. The case studies illustrate an emerging theory for the isothermal nonequilibrium steady state of open systems.
John F Marko - One of the best experts on this subject based on the ideXlab platform.
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Kinetic Proofreading can explain the supression of supercoiling of circular DNA molecules by type-II topoisomerases
Physical Review E - Statistical Nonlinear and Soft Matter Physics, 2001Co-Authors: Jie Yan, Marcelo O. Magnasco, John F MarkoAbstract:The enzymes that pass DNA through DNA so as to remove entanglements, adenosine-triphosphate-hydrolyzing type-II topoisomerases, are able to suppress the probability of self-entanglements (knots) and mutual entanglements (links) between approximately 10 kb plasmids, well below the levels expected, given the assumption that the topoisomerases pass DNA segments at random by thermal motion. This implies that a 10-nm type-II topoisomerase can somehow sense the topology of a large DNA. We previously introduced a "Kinetic Proofreading" model which supposes the enzyme to require two successive collisions in order to allow exchange of DNA segments, and we showed how it could quantitatively explain the reduction in knotting and linking complexity. Here we show how the same model quantitatively explains the reduced variance of the double-helix linking number (supercoiling) distribution observed experimentally.
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A Kinetic Proofreading mechanism for disentanglement of DNA by topoisomerases
Nature, 1999Co-Authors: Jie Yan, Marcelo O. Magnasco, John F MarkoAbstract:Cells must remove all entanglements between their replicated chromosomal DNAs to segregate them during cell division. Entanglement removal is done by ATP-driven enzymes that pass DNA strands through one another, called type II topoisomerases. In vitro, some type II topoisomerases can reduce entanglements much more than expected, given the assumption that they pass DNA segments through one another in a random way1. These type II topoisomerases (of less than 10 nm in diameter) thus use ATP hydrolysis to sense and remove entanglements spread along flexible DNA strands of up to 3,000 nm long. Here we propose a mechanism for this, based on the higher rate of collisions along entangled DNA strands, relative to collision rates on disentangled DNA strands. We show theoretically that if a type II topoisomerase requires an initial ‘activating’ collision before a second strand-passing collision, the probability of entanglement may be reduced to experimentally observed levels. This proposed two-collision reaction is similar to ‘Kinetic Proofreading’ models of molecular recognition2,3.
Yeonee Seol - One of the best experts on this subject based on the ideXlab platform.
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comparison of dna decatenation by escherichia coli topoisomerase iv and topoisomerase iii implications for non equilibrium topology simplification
Nucleic Acids Research, 2013Co-Authors: Yeonee Seol, Ashley H. Hardin, Gilles Charvin, Mariepaule Strub, Keir C. NeumanAbstract:Type II topoisomerases are essential enzymes that regulate DNA topology through a strand-passage mechanism. Some type II topoisomerases relax supercoils, unknot and decatenate DNA to below thermodynamic equilibrium. Several models of this non-equilibrium topology simplification phenomenon have been proposed. The Kinetic Proofreading (KPR) model postulates that strand passage requires a DNA-bound topoisomerase to collide twice in rapid succession with a second DNA segment, implying a quadratic relationship between DNA collision frequency and relaxation rate. To test this model, we used a single-molecule assay to measure the unlinking rate as a function of DNA collision frequency for Escherichia coli topoisomerase IV (topo IV) that displays efficient non-equilibrium topology simplification activity, and for E. coli topoisomerase III (topo III), a type IA topoisomerase that unlinks and unknots DNA to equilibrium levels. Contrary to the predictions of the KPR model, topo IV and topo III unlinking rates were linearly related to the DNA collision frequency. Furthermore, topo III exhibited decatenation activity comparable with that of topo IV, supporting proposed roles for topo III in DNA segregation. This study enables us to rule out the KPR model for non-equilibrium topology simplification. More generally, we establish an experimental approach to systematically control DNA collision frequency.
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Non-Equilibrium Topology Simplification by Type II Topoisomerases: A Test of Kinetic Proofreading
Biophysical Journal, 2012Co-Authors: Yeonee Seol, Ashley H. Hardin, Gilles Charvin, Keir C. NeumanAbstract:Type II topoisomerases are essential enzymes that modify DNA topology. These topoisomerases pass a double stranded segment (T-segment) of DNA though a transient double stranded break in a second segment (G-segment). This strand passage mechanism allows type II topoisomerases to unlink, unknot, and relax supercoiled DNA to below equilibrium levels1. The mechanisms underlying this non-equilibrium topology simplification remain speculative. Several theoretical models have been proposed but experimental data has not been able to distinguish among them. One model developed by Yan and Marko2, postulates that the strand passage mechanism of type II topoisomerases is governed by a Kinetic Proofreading process. In practice, this model suggests that type II topoisomerases require two collisions between the T- and G-segments prior to strand passage. The first collision of a T-segment with the enzyme-bound G-segment transiently activates the enzyme and the second collision of the T-segment with the activated enzyme results in strand passage. The model predicts that the strand passage probability scales as the square of the collision rate, which has not been tested. We directly tested this prediction of the Kinetic Proofreading model using a single-crossing DNA unlinking assay. We measured the rate that topoisomerase IV, a bacterial type II topoisomerase, unlinked DNA as a function of the strand collision probability obtained from Monte Carlo simulations of the DNA crossings. The unlinking rate was linearly related to the collision probability, which is inconsistent with the Kinetic Proofreading model.1.Rybenkov, V. V., Ullsperger, C., Vologodskii, A. V. & Cozzarelli, N. R. Simplification of DNA topology below equilibrium values by type II topoisomerases. Science 277, 690-693 (1997).2.Yan, J., Magnasco, M. O. & Marko, J. F. A Kinetic Proofreading mechanism for disentanglement of DNA by topoisomerases. Nature 401, 932-935, doi:10.1038/44872 (1999).
Neel H Shah - One of the best experts on this subject based on the ideXlab platform.
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slow phosphorylation of a tyrosine residue in lat optimizes t cell ligand discrimination
Nature Immunology, 2019Co-Authors: Wanlin Lo, Sara A Rubin, Ian R Fallahee, Neel H Shah, Veronika Horkova, Ondrej Stepanek, John Kuriyan, Weiguo Zhang, Arthur WeissAbstract:Self–non-self discrimination is central to T cell-mediated immunity. The Kinetic Proofreading model can explain T cell antigen receptor (TCR) ligand discrimination; however, the rate-limiting steps have not been identified. Here, we show that tyrosine phosphorylation of the T cell adapter protein LAT at position Y132 is a critical Kinetic bottleneck for ligand discrimination. LAT phosphorylation at Y132, mediated by the kinase ZAP-70, leads to the recruitment and activation of phospholipase C-γ1 (PLC-γ1), an important effector molecule for T cell activation. The slow phosphorylation of Y132, relative to other phosphosites on LAT, is governed by a preceding glycine residue (G131) but can be accelerated by substituting this glycine with aspartate or glutamate. Acceleration of Y132 phosphorylation increases the speed and magnitude of PLC-γ1 activation and enhances T cell sensitivity to weaker stimuli, including weak agonists and self-peptides. These observations suggest that the slow phosphorylation of Y132 acts as a Proofreading step to facilitate T cell ligand discrimination. TCR ligation activates the tyrosine kinase ZAP-70 to phosphorylate the adapter LAT, which then coordinates TCR proximal signaling cascades. Weiss and colleagues show LAT-Y132 is critical to TCR ligand discrimination, as its phosphorylation represents a rate-limiting step in T cell activation due to a conserved glycine residue at position 131.
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slow phosphorylation of a tyrosine residue in lat optimizes t cell ligand discrimination
Nature Immunology, 2019Co-Authors: Sara A Rubin, Ian R Fallahee, Neel H Shah, Veronika Horkova, Ondrej Stepanek, Weiguo Zhang, Leonard I Zon, John KuriyanAbstract:Self-non-self discrimination is central to T cell-mediated immunity. The Kinetic Proofreading model can explain T cell antigen receptor (TCR) ligand discrimination; however, the rate-limiting steps have not been identified. Here, we show that tyrosine phosphorylation of the T cell adapter protein LAT at position Y132 is a critical Kinetic bottleneck for ligand discrimination. LAT phosphorylation at Y132, mediated by the kinase ZAP-70, leads to the recruitment and activation of phospholipase C-γ1 (PLC-γ1), an important effector molecule for T cell activation. The slow phosphorylation of Y132, relative to other phosphosites on LAT, is governed by a preceding glycine residue (G131) but can be accelerated by substituting this glycine with aspartate or glutamate. Acceleration of Y132 phosphorylation increases the speed and magnitude of PLC-γ1 activation and enhances T cell sensitivity to weaker stimuli, including weak agonists and self-peptides. These observations suggest that the slow phosphorylation of Y132 acts as a Proofreading step to facilitate T cell ligand discrimination.
