The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Mitchell Lewis - One of the best experts on this subject based on the ideXlab platform.
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Complexes with DNA and Inducer
2014Co-Authors: Mitchell Lewis, M A Kercher, Geoffrey Chang, Nancy C Horton, H C Pace, Maria A Schumacher, Richard G BrennanAbstract:The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor, a product of the lacl gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-3-D-1-thiogalactoside (IPTG) and the lac repressor complexed with a 21-base pair Symmetric Operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three /ac repressor recognition sites in a stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quaternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites on the genomic DNA. More than 30 years ago, Jacob and Monod (1) introduced the E. coli lactose operon as a model for gene regulation. The mode
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crystallographic analysis of lac repressor bound to natural Operator o1
Journal of Molecular Biology, 2001Co-Authors: Charles E Bell, Mitchell LewisAbstract:Abstract Previous structures of Lac repressor bound to DNA used a fully Symmetric “ideal” Operator sequence that is missing the central G·C base-pair present in the three natural Operator sequences. Here we have determined the X-ray crystal structure of a dimeric Lac repressor bound to a 22 base-pair DNA with the natural Operator O1 sequence and the anti-inducer ONPF, at 4.0 A resolution. The natural Operator is bent in the same way as the Symmetric sequence, due to the binding of the hinge helices of the repressor to the minor groove at the central GCGG sequence of O1 . Comparison of the structures of the repressor bound to the natural and Symmetric Operators shows very similar overall structures, with only slight rearrangements of the headpiece domains of the repressor. Analysis of crystals with iodinated DNA shows that the Operator is uniquely positioned and allows for the sequence registration of the DNA relative to the repressor to be determined. The kink in the Operator is centered between the left half-site and the central G·C base-pair of O1 . Our results are most consistent with a previously proposed model in which, relative to the complex with the Symmetric Operator, the repressor accommodates binding to the natural Operator sequence by shifting the position of the right headpiece by one base-pair step towards the center of O1 .
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a closer view of the conformation of the lac repressor bound to Operator
Nature Structural & Molecular Biology, 2000Co-Authors: Charles E Bell, Mitchell LewisAbstract:Crystal structures of the Lac repressor, with and without isopropylthiogalactoside (IPTG), and the repressor bound to Operator have provided a model for how the binding of the inducer reduces the affinity of the repressor for the Operator. However, because of the low resolution of the Operator-bound structure (4.8 A), the model for the allosteric transition was presented in terms of structural elements rather than in terms of side chain interactions. Here we have constructed a dimeric Lac repressor and determined its structure at 2.6 A resolution in complex with a Symmetric Operator and the anti-inducer orthonitrophenylfucoside (ONPF). The structure enables the induced (IPTG-bound) and repressed (Operator-bound) conformations of the repressor to be compared in atomic detail. An extensive network of interactions between the DNA-binding and core domains of the repressor suggests a possible mechanism for the allosteric transition.
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lac repressor Operator complex
Current Opinion in Structural Biology, 1997Co-Authors: M A Kercher, Ponzy Lu, Mitchell LewisAbstract:Abstract For many years the lac operon of Escherichia coli has been the paradigm for gene regulation. Recently, the structures of the lac repressor core bound to isopropyl-β- D -1-thiogalactoside (IPTG), the intact apo lac repressor, the intact lac repressor complexes with IPTG and a 21-base-pair Symmetric Operator, and the refined headpiece of the repressor have been determined. These structures have provided a framework for understanding a wealth of biochemical and genetic information. An analysis of these structures, as well as a description of their function and a comparison to homologous proteins, is now possible.
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crystal structure of the lactose operon repressor and its complexes with dna and inducer
Science, 1996Co-Authors: Mitchell Lewis, M A Kercher, Geoffrey Chang, Nancy C Horton, H C Pace, Maria A Schumacher, Richard G BrennanAbstract:The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor, a product of the lacI gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-β-D-1-thiogalactoside (IPTG) and the lac repressor complexed with a 21-base pair Symmetric Operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three lac repressor recognition sites in a stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quaternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites on the genomic DNA.
Duca Alessandro - One of the best experts on this subject based on the ideXlab platform.
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Controllability of periodic bilinear quantum systems on infinite graphs
2020Co-Authors: Ammari Kaïs, Duca AlessandroAbstract:In this work, we study the controllability of the bilinear Schr\"odinger equation on infinite graphs for periodic quantum states. We consider the bilinear Schr\"odinger equation $i\partial_t\psi=-\Delta\psi+u(t)B\psi$ in the Hilbert space $L^2_p$ composed by functions defined on an infinite graph $\mathscr{G}$ verifying periodic boundary conditions on the infinite edges. The Laplacian $-\Delta$ is equipped with specific boundary conditions, $B$ is a bounded Symmetric Operator and $u\in L^2((0,T),\mathbb{R})$ with $T>0$. We present the well-posedness of the system in suitable subspaces of $D(|\Delta|^{3/2})$ . In such spaces, we study the global exact controllability and we provide examples involving for instance tadpole graphs and star graphs with infinite spokes.Comment: arXiv admin note: text overlap with arXiv:1811.0427
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Controllability of localized quantum states on infinite graphs through bilinear control fields
2020Co-Authors: Ammari Kaïs, Duca AlessandroAbstract:In this work, we consider the bilinear Schr\"odinger equation $i\partial_t\psi=-\Delta\psi+u(t)B\psi$ in the Hilbert space $L^2(\mathcal{G},\mathbb{C})$ with $\mathcal{G}$ an infinite graph. The Laplacian $-\Delta$ is equipped with self-adjoint boundary conditions, $B$ is a bounded Symmetric Operator and $u\in L^2((0,T),\mathbb{R})$ with $T>0$. We study the well-posedness in suitable subspaces of $D(|\Delta|^{3/2})$ preserved by the dynamics despite the dispersive behaviour of the equation. In such spaces, we study the global exact controllability and the {\virgolette{energetic controllability}}. We provide examples involving for instance infinite tadpole graphs
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CONTROLLABILITY OF PERIODIC BILINEAR QUANTUM SYSTEMS ON INFINITE GRAPHS
American Institute of Physics (AIP), 2020Co-Authors: Ammari Kaïs, Duca AlessandroAbstract:International audienceIn this work, we study the controllability of the bilinear Schrödinger equation on infinite graphs for periodic quantum states. We consider the equation (BSE) $i\partial_t\psi = −\Delta \psi+ u(t)B\psi$ in the Hilbert space $L^2_p$ composed by functions defined on an infinite graph $\mathcal{G}$ verifying periodic boundary conditions on the infinite edges. The Laplacian $−\Delta$ is equipped with specific boundary conditions, $B$ is a bounded Symmetric Operator and $u \in L^2 ((0, T), \mathbb{R})$ with $T > 0$. We present the well-posedness of the (BSE) in suitable subspaces of $L^2_p$. In such spaces, we study the global exact controllability and we provide examples involving tadpole graphs and star graphs with infinite spokes
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Global exact controllability of bilinear quantum systems on compact graphs and energetic controllability
2020Co-Authors: Duca AlessandroAbstract:The aim of this work is to study the controllability of the bilinear Schr\"odinger equation on compact graphs. In particular, we consider the equation (BSE) $i\partial_t\psi=-\Delta\psi+u(t)B\psi$ in the Hilbert space $L^2(\mathscr{G},\mathbb{C})$, with $\mathscr{G}$ being a compact graph. The Laplacian $-\Delta$ is equipped with self-adjoint boundary conditions, $B$ is a bounded Symmetric Operator and $u\in L^2((0,T),\mathbb{R})$ with $T>0$. We provide a new technique leading to the global exact controllability of the (BSE) in $D(|\Delta|^{s/2})$ with $s\geq 3$. Afterwards, we introduce the "energetic controllability", a weaker notion of controllability useful when the global exact controllability fails. In conclusion, we develop some applications of the main results involving for instance star graphs
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Simultaneous global exact controllability in projection of infinite 1D bilinear Schr\"odinger equations
2020Co-Authors: Duca AlessandroAbstract:The aim of this work is to study the controllability of infinite bilinear Schr\"odinger equations on a segment. We consider the equations (BSE) $i\partial_t\psi^{j}=-\Delta\psi^j+u(t)B\psi^j$ in the Hilbert space $L^2((0,1),\mathbb{C})$ for every $j\in\mathbb{N}^*$. The Laplacian $-\Delta$ is equipped with Dirichlet homogeneous boundary conditions, $B$ is a bounded Symmetric Operator and $u\in L^2((0,T),\mathbb{R})$ with $T>0$. We prove the simultaneous local and global exact controllability of infinite (BSE) in projection. The local controllability is guaranteed for any positive time and we provide explicit examples of $B$ for which our theory is valid. In addition, we show that the controllability of infinite (BSE) in projection onto suitable finite dimensional spaces is equivalent to the controllability of a finite number of (BSE) (without projecting). In conclusion, we rephrase our controllability results in terms of density matrices
Charles E Bell - One of the best experts on this subject based on the ideXlab platform.
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crystallographic analysis of lac repressor bound to natural Operator o1
Journal of Molecular Biology, 2001Co-Authors: Charles E Bell, Mitchell LewisAbstract:Abstract Previous structures of Lac repressor bound to DNA used a fully Symmetric “ideal” Operator sequence that is missing the central G·C base-pair present in the three natural Operator sequences. Here we have determined the X-ray crystal structure of a dimeric Lac repressor bound to a 22 base-pair DNA with the natural Operator O1 sequence and the anti-inducer ONPF, at 4.0 A resolution. The natural Operator is bent in the same way as the Symmetric sequence, due to the binding of the hinge helices of the repressor to the minor groove at the central GCGG sequence of O1 . Comparison of the structures of the repressor bound to the natural and Symmetric Operators shows very similar overall structures, with only slight rearrangements of the headpiece domains of the repressor. Analysis of crystals with iodinated DNA shows that the Operator is uniquely positioned and allows for the sequence registration of the DNA relative to the repressor to be determined. The kink in the Operator is centered between the left half-site and the central G·C base-pair of O1 . Our results are most consistent with a previously proposed model in which, relative to the complex with the Symmetric Operator, the repressor accommodates binding to the natural Operator sequence by shifting the position of the right headpiece by one base-pair step towards the center of O1 .
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a closer view of the conformation of the lac repressor bound to Operator
Nature Structural & Molecular Biology, 2000Co-Authors: Charles E Bell, Mitchell LewisAbstract:Crystal structures of the Lac repressor, with and without isopropylthiogalactoside (IPTG), and the repressor bound to Operator have provided a model for how the binding of the inducer reduces the affinity of the repressor for the Operator. However, because of the low resolution of the Operator-bound structure (4.8 A), the model for the allosteric transition was presented in terms of structural elements rather than in terms of side chain interactions. Here we have constructed a dimeric Lac repressor and determined its structure at 2.6 A resolution in complex with a Symmetric Operator and the anti-inducer orthonitrophenylfucoside (ONPF). The structure enables the induced (IPTG-bound) and repressed (Operator-bound) conformations of the repressor to be compared in atomic detail. An extensive network of interactions between the DNA-binding and core domains of the repressor suggests a possible mechanism for the allosteric transition.
M A Kercher - One of the best experts on this subject based on the ideXlab platform.
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Complexes with DNA and Inducer
2014Co-Authors: Mitchell Lewis, M A Kercher, Geoffrey Chang, Nancy C Horton, H C Pace, Maria A Schumacher, Richard G BrennanAbstract:The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor, a product of the lacl gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-3-D-1-thiogalactoside (IPTG) and the lac repressor complexed with a 21-base pair Symmetric Operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three /ac repressor recognition sites in a stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quaternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites on the genomic DNA. More than 30 years ago, Jacob and Monod (1) introduced the E. coli lactose operon as a model for gene regulation. The mode
-
lac repressor Operator complex
Current Opinion in Structural Biology, 1997Co-Authors: M A Kercher, Ponzy Lu, Mitchell LewisAbstract:Abstract For many years the lac operon of Escherichia coli has been the paradigm for gene regulation. Recently, the structures of the lac repressor core bound to isopropyl-β- D -1-thiogalactoside (IPTG), the intact apo lac repressor, the intact lac repressor complexes with IPTG and a 21-base-pair Symmetric Operator, and the refined headpiece of the repressor have been determined. These structures have provided a framework for understanding a wealth of biochemical and genetic information. An analysis of these structures, as well as a description of their function and a comparison to homologous proteins, is now possible.
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crystal structure of the lactose operon repressor and its complexes with dna and inducer
Science, 1996Co-Authors: Mitchell Lewis, M A Kercher, Geoffrey Chang, Nancy C Horton, H C Pace, Maria A Schumacher, Richard G BrennanAbstract:The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor, a product of the lacI gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-β-D-1-thiogalactoside (IPTG) and the lac repressor complexed with a 21-base pair Symmetric Operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three lac repressor recognition sites in a stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quaternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites on the genomic DNA.
Rianne Kaptein - One of the best experts on this subject based on the ideXlab platform.
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hinge helix formation and dna bending in various lac repressor Operator complexes
The EMBO Journal, 1999Co-Authors: Christian A E M Spronk, Gert E. Folkers, Rolf Boelens, Rainer Wechselberger, Annemarie Noordman, Nienke Van Den Brink, Rianne KapteinAbstract:The hinge-region of the lac repressor plays an important role in the models for induction and DNA looping in the lac operon. When lac repressor is bound to a tight-binding Symmetric Operator, this region forms an alpha-helix that induces bending of the Operator. The presence of the hinge-helices is questioned by previous data that suggest that the repressor does not bend the wild-type Operator. We show that in the wild-type complex the hinge-helices are formed and the DNA is bent, similar to the Symmetric complex. Furthermore, our data show differences in the binding of the DNA binding domains to the half-sites of the wild-type Operator and reveal the role of the central base-pair of the wild-type Operator in the repressor-Operator interaction. The differences in binding to the Operator half-sites are incorporated into a model that explains the relative affinities of the repressor for various lac Operator sequences that contain left and right half-sites with different spacer lengths.