38 research outputs found

    A Network of Conformational Transitions in the Apo Form of NDM‑1 Enzyme Revealed by MD Simulation and a Markov State Model

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    New Delhi metallo-β-lactamase-1 (NDM-1) is a novel β-lactamase enzyme that confers enteric bacteria with nearly complete resistance to all β-lactam antibiotics, so it raises a formidable and global threat to human health. However, the binding mechanism between apo-NDM-1 and antibiotics as well as related conformational changes remains poorly understood, which largely hinders the overcoming of its antibiotic resistance. In our study, long-time conventional molecular dynamics simulation and Markov state models were applied to reveal both the dynamical and conformational landscape of apo-NDM-1: the MD simulation demonstrates that loop L3, which is responsible for antibiotic binding, is the most flexible and undergoes dramatic conformational changes; moreover, the Markov state model built from the simulation maps four metastable states including open, semiopen, and closed conformations of loop L3 as well as frequent transitions between the states. Our findings propose a possible conformational selection model for the binding mechanism between apo-NDM-1 and antibiotics, which facilitates the design of novel inhibitors and antibiotics

    Structural analysis of the MD simulation results.

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    <p>(A) Backbone RMSFs for WT (blue), A130T (red), and A130V (orange) during the MD simulations. (B) Time evolution of the secondary structural elements, based on DSSP classification, of the wild type and mutant proteins. (C) The angle formed by the Cα atoms of D129, A130, and V131. (D) The angle fluctuations for WT (blue), A130T (red), and A130V (orange) during the MD simulations with the corresponding histogram to the side.</p

    Computational Study of Unfolding and Regulation Mechanism of preQ<sub>1</sub> Riboswitches

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    <div><p>Riboswitches are novel RNA regulatory elements. Each riboswitch molecule consists of two domains: aptamer and express platform. The three-dimensional (3D) structure of the aptamer domain, depending on ligand binding or not, controls that of the express platform, which then switches on or off transcriptional or translational process. Here we study the two types of preQ<sub>1</sub> riboswitch aptamers from <em>T. Tengcongensis</em> (denoted as Tte preQ<sub>1</sub> riboswitch for short below) and <em>Bacillus subtilis</em> (denoted as Bsu preQ<sub>1</sub> riboswitch for short below), respectively. The free-state 3D structure of the Tte preQ<sub>1</sub> riboswitch is the same as its bound state but the Bsu preQ<sub>1</sub> riboswitch is not. Therefore, it is very interesting to investigate how these riboswitches realize their different regulation functions. We simulated the unfolding of these two aptamers through all-atom molecular dynamic simulation and found that they have similar unfolding or folding pathways and ligand-binding processes. The main difference between them is the folding intermediate states. The similarity and difference of their unfolding or folding dynamics may suggest their similar regulation mechanisms and account for their different functions, respectively. These results are also useful to understand the regulation mechanism of other riboswitches with free-state 3D structures similar to their bound states.</p> </div

    Effects of mutating of residue A130.

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    <p>(A) Homology modeling of Bbox1 structures highlighting the position and packing of side chain of A130 (i) compared to those of the T130 (ii) and V130 (iii). (B) Backbone RMSDs for WT (blue), A130T (red), and A130V (orange) during the MD simulations.</p

    Structural properties of the MID1 Bbox1 domain.

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    <p>(A) The ensemble of 13 structures generated from NMR-derived restraints (PDB code: 2FFW). (B) Magnitude of the fluctuation represented as eigenvectors of the Bbox1 ensemble of structures. The conformational fluctuations indicate both magnitude and directions (arrows) and are derived from PCA analysis. (C) The fluctuations of the average NMR structure are shown as a function of residue number. (D) Zoomed-in snapshot of the small cavity near residue A130. The blue dots represent the solvent accessible surface.</p

    Regulation functions for two types of preQ<sub>1</sub> riboswitches.

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    <p>Regulation functions for two types of preQ<sub>1</sub> riboswitches.</p

    Secondary and tertiary structures of two types of the preQ<sub>1</sub> riboswitch aptamer domains.

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    <p>The bound preQ<sub>1</sub> is depicted by a licorice representation. The different parts (P1, P2, L1, L2, and L3) are color-coded.</p

    Unfolding pathways and free energy landscapes of Bsu and Tte preQ<sub>1</sub> riboswitch aptamers in presence of the ligands at 400 K: (A) the time evolution of the mean fraction of native contacts in the aptamer during the unfolding simulations.

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    <p>The different curves describe different parts; (B) the two-dimensional unfolding free energy landscapes. The order parameters are the fractions of native contacts for P1-L3 and P2-L1-L2, respectively. The surrounding structures are representatives of the conformations observed during the unfolding processes.</p

    Insights into Ligand Binding to PreQ<sub>1</sub> Riboswitch Aptamer from Molecular Dynamics Simulations

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    <div><p>Riboswitches play roles in transcriptional or translational regulation through specific ligand binding of their aptamer domains. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, preQ<sub>1</sub> riboswitch aptamer domain from <i>Bacillus subtilis</i> is studied by overall 1.5 μs all-atom molecular dynamics simulations We found that the ligand-free aptamer has a stable state with a folded P1-L3 and open binding pocket. The latter forms a cytosine-rich pool in which the nucleotide C19 oscillates between close and open positions, making it a potential conformation for preQ<sub>1</sub> entrance. The dynamic picture further suggests that the specific recognition of preQ<sub>1</sub> by the aptamer domain is not only facilitated by the key nucleotide C19 but also aided and enhanced by other cytosines around the binding pocket. These results should help to understand the details of preQ<sub>1</sub> binding.</p></div

    Illustration of the cytosine clusters.

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    <p>(a) The six cytosines and preQ<sub>1</sub> in the preQ1-bound structure. (b) Cytosines (red) in the entrance of the opened binding pocket in the ligand-free simulation at 600 ns.</p
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