Solution Structure

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Dinshaw J. Patel - One of the best experts on this subject based on the ideXlab platform.

  • Solution Structure of p22 transcriptional antitermination n peptide box b rna complex
    Nature Structural & Molecular Biology, 1998
    Co-Authors: Andrey Gorin, Ronnie Frederick, Xiaomei Ye, Abdelali Kettani, Weidong Hu, Ananya Majumdar, Dinshaw J. Patel
    Abstract:

    We have determined the Solution Structure of a 15-mer boxB RNA hairpin complexed with a 20-mer basic peptide of the N protein involved in bacteriophage P22 transcriptional antitermination. Complex formation involves adaptive binding with the N peptide adopting a bent α-helical conformation that packs tightly through hydrophobic and electrostatic interactions against the major groove face of the boxB RNA hairpin, orienting the open opposite face for potential interactions with host factors and/or RNA polymerase. Four nucleotides in the boxB RNA hairpin pentaloop form a stable GNRA like tetraloop structural scaffold on complex formation, allowing the looped out fifth nucleotide to make extensive hydrophobic contacts with the bound peptide. The guanidinium group of a key arginine is hydrogen-bonded to the guanine in a loop-closing sheared G·A mismatch and to adjacent backbone phosphates. The identified intermolecular contacts account for the consequences of N peptide and boxB RNA mutations on bacteriophage transcriptional antitermination.

  • Solution Structure of P22 transcriptional antitermination N peptide–box B RNA complex
    Nature Structural & Molecular Biology, 1998
    Co-Authors: Andrey Gorin, Ronnie Frederick, Xiaomei Ye, Abdelali Kettani, Weidong Hu, Ananya Majumdar, Dinshaw J. Patel
    Abstract:

    We have determined the Solution Structure of a 15-mer boxB RNA hairpin complexed with a 20-mer basic peptide of the N protein involved in bacteriophage P22 transcriptional antitermination. Complex formation involves adaptive binding with the N peptide adopting a bent α-helical conformation that packs tightly through hydrophobic and electrostatic interactions against the major groove face of the boxB RNA hairpin, orienting the open opposite face for potential interactions with host factors and/or RNA polymerase. Four nucleotides in the boxB RNA hairpin pentaloop form a stable GNRA like tetraloop structural scaffold on complex formation, allowing the looped out fifth nucleotide to make extensive hydrophobic contacts with the bound peptide. The guanidinium group of a key arginine is hydrogen-bonded to the guanine in a loop-closing sheared G·A mismatch and to adjacent backbone phosphates. The identified intermolecular contacts account for the consequences of N peptide and boxB RNA mutations on bacteriophage transcriptional antitermination.

  • Solution Structure of the Covalent Duocarmycin A-DNA Duplex Complex
    Journal of molecular biology, 1995
    Co-Authors: Chin Hsiung Lin, Dinshaw J. Patel
    Abstract:

    Duocarmycin A is an antitumour antibiotic that binds covalently to the minor groove N-3 position of adenine with sequence specificity for the 3'-adenine in a d(A-A-A-A) tract in duplex DNA. The adenine ring becomes protonated on duocarmycin adduct formation resulting in charge delocalization over the purine ring system. We report on the Solution Structure of duocarmycin A bound site specifically to A12 (designated *A12+) in the sequence context d(T3-T4-T5-T6).d(A9-A10-A11-*A12+) within a hairpin duplex. The Solution Structure was solved based on a combined NMR-molecular dynamics study including NOE based intensity refinement. The A and B-rings of duocarmycin are positioned deep within the walls of the minor groove with the B-ring (which is furthest from the covalent linkage site) directed towards the 5'-end of the modified strand. Duocarmycin adopts an extended conformation and is aligned at approximately 45 degrees to the helix axis with its non-polar concave edges interacting with the floor of the minor groove while its polar edges are sandwiched within the walls of the minor groove. The T3.*A12+ modification site pair forms a weak central Watson-Crick hydrogen bond in contrast to all A.T and G.C pairs, which align through standard Watson-Crick pairing in the complex. The helical parameters are consistent with a minimally perturbed right-handed duplex in the complex with minor groove width and x-displacement parameters indicative of a B-form helix. A striking feature of the complex is the positioning of duocarmycin A within the walls of the minor groove resulting in upfield shifts of the minor groove sugar protons, as well as backbone proton and phosphorus resonances in the DNA segment spanning the binding site.

  • Solution Structure of the human telomeric repeat d ag3 t2ag3 3 g tetraplex
    Structure, 1993
    Co-Authors: Yong Wang, Dinshaw J. Patel
    Abstract:

    Abstract Background: Repeats of G n sequences are detected as single strand overhangs at the ends of eukaryotic chromosomes together with associated binding proteins. Such telomere sequences have been implicated in the replication and maintenance of chromosomal termini. They may also mediate chromosomal organization and association during meiosis and mitosis. Results: We have determined the three-dimensional Solution Structure of the human telomere sequence, d[AG 3 (T 2 AG 3 ) 3 ] in Na + -containing Solution using a combined NMR, distance geometry and molecular dynamics approach (including relaxation matrix refinement). The sequence, which contains four AG 3 repeats, folds intramolecularly into a G-tetraplex stabilized by three stacked G-tetrads which are connected by two lateral loops and a central diagonal loop. Of the four grooves that are formed, one is wide, two are of medium width and one is narrow. The alignment of adjacent G-G-G segments in parallel generates the two grooves of medium width whilst the antiparallel arrangement results in one wide and one narrow groove. Three of the four adenines stack on top of adjacent G-tetrads while the majority of the thymines sample multiple conformations. Conclusions: The availability of the d[AG 3 (T 2 AG 3 ) 3 ] Solution Structure containing four AG 3 human telomeric repeats should permit the rational design of ligands that recognize and bind with specificity and affinity to the individual grooves of the G-tetraplex, as well as to either end containing the diagonal and lateral loops. Such ligands could modulate the equilibrium between folded G-tetraplex Structures and their unfolded extended counterparts.

Brett L. Lucht - One of the best experts on this subject based on the ideXlab platform.

  • role of Solution Structure in solid electrolyte interphase formation on graphite with lipf6 in propylene carbonate
    Journal of Physical Chemistry C, 2013
    Co-Authors: Daniel P Abraham, Arijit Bose, Yanjing Chen, Brett L. Lucht
    Abstract:

    An investigation of the interrelationship of cycling performance, Solution Structure, and electrode surface film Structure has been conducted for electrolytes composed of different concentrations of LiPF6 in propylene carbonate (PC) with a binder-free (BF) graphite electrode. Varying the concentration of LiPF6 changes the Solution Structure, altering the predominant mechanism of electrolyte reduction at the electrode interface. The change in mechanism results in a change in the Structure of the solid electrolyte interface (SEI) and the reversible cycling of the cell. At low concentrations of LiPF6 in PC (1.2 M), electrochemical cycling and cyclic voltammetry (CV) of BF graphite electrodes reveal continuous electrolyte reduction and no lithiation/delithiation of the graphite. The Solution Structure is dominated by solvent-separated ion pairs (Li+(PC)4//PF6–), and the primary reduction product of the electrolyte is lithium propylene dicarbonate (LPDC). At high concentrations of LiPF6 in PC (3.0–3.5 M), elec...

  • role of Solution Structure in solid electrolyte interphase formation on graphite with lipf6 in propylene carbonate
    Journal of Physical Chemistry C, 2013
    Co-Authors: Daniel P Abraham, Arijit Bose, Yanjing Chen, Brett L. Lucht
    Abstract:

    An investigation of the interrelationship of cycling performance, Solution Structure, and electrode surface film Structure has been conducted for electrolytes composed of different concentrations of LiPF6 in propylene carbonate (PC) with a binder-free (BF) graphite electrode. Varying the concentration of LiPF6 changes the Solution Structure, altering the predominant mechanism of electrolyte reduction at the electrode interface. The change in mechanism results in a change in the Structure of the solid electrolyte interface (SEI) and the reversible cycling of the cell. At low concentrations of LiPF6 in PC (1.2 M), electrochemical cycling and cyclic voltammetry (CV) of BF graphite electrodes reveal continuous electrolyte reduction and no lithiation/delithiation of the graphite. The Solution Structure is dominated by solvent-separated ion pairs (Li+(PC)4//PF6–), and the primary reduction product of the electrolyte is lithium propylene dicarbonate (LPDC). At high concentrations of LiPF6 in PC (3.0–3.5 M), elec...

Daniel P Abraham - One of the best experts on this subject based on the ideXlab platform.

  • role of Solution Structure in solid electrolyte interphase formation on graphite with lipf6 in propylene carbonate
    Journal of Physical Chemistry C, 2013
    Co-Authors: Daniel P Abraham, Arijit Bose, Yanjing Chen, Brett L. Lucht
    Abstract:

    An investigation of the interrelationship of cycling performance, Solution Structure, and electrode surface film Structure has been conducted for electrolytes composed of different concentrations of LiPF6 in propylene carbonate (PC) with a binder-free (BF) graphite electrode. Varying the concentration of LiPF6 changes the Solution Structure, altering the predominant mechanism of electrolyte reduction at the electrode interface. The change in mechanism results in a change in the Structure of the solid electrolyte interface (SEI) and the reversible cycling of the cell. At low concentrations of LiPF6 in PC (1.2 M), electrochemical cycling and cyclic voltammetry (CV) of BF graphite electrodes reveal continuous electrolyte reduction and no lithiation/delithiation of the graphite. The Solution Structure is dominated by solvent-separated ion pairs (Li+(PC)4//PF6–), and the primary reduction product of the electrolyte is lithium propylene dicarbonate (LPDC). At high concentrations of LiPF6 in PC (3.0–3.5 M), elec...

  • role of Solution Structure in solid electrolyte interphase formation on graphite with lipf6 in propylene carbonate
    Journal of Physical Chemistry C, 2013
    Co-Authors: Daniel P Abraham, Arijit Bose, Yanjing Chen, Brett L. Lucht
    Abstract:

    An investigation of the interrelationship of cycling performance, Solution Structure, and electrode surface film Structure has been conducted for electrolytes composed of different concentrations of LiPF6 in propylene carbonate (PC) with a binder-free (BF) graphite electrode. Varying the concentration of LiPF6 changes the Solution Structure, altering the predominant mechanism of electrolyte reduction at the electrode interface. The change in mechanism results in a change in the Structure of the solid electrolyte interface (SEI) and the reversible cycling of the cell. At low concentrations of LiPF6 in PC (1.2 M), electrochemical cycling and cyclic voltammetry (CV) of BF graphite electrodes reveal continuous electrolyte reduction and no lithiation/delithiation of the graphite. The Solution Structure is dominated by solvent-separated ion pairs (Li+(PC)4//PF6–), and the primary reduction product of the electrolyte is lithium propylene dicarbonate (LPDC). At high concentrations of LiPF6 in PC (3.0–3.5 M), elec...

Yanjing Chen - One of the best experts on this subject based on the ideXlab platform.

  • role of Solution Structure in solid electrolyte interphase formation on graphite with lipf6 in propylene carbonate
    Journal of Physical Chemistry C, 2013
    Co-Authors: Daniel P Abraham, Arijit Bose, Yanjing Chen, Brett L. Lucht
    Abstract:

    An investigation of the interrelationship of cycling performance, Solution Structure, and electrode surface film Structure has been conducted for electrolytes composed of different concentrations of LiPF6 in propylene carbonate (PC) with a binder-free (BF) graphite electrode. Varying the concentration of LiPF6 changes the Solution Structure, altering the predominant mechanism of electrolyte reduction at the electrode interface. The change in mechanism results in a change in the Structure of the solid electrolyte interface (SEI) and the reversible cycling of the cell. At low concentrations of LiPF6 in PC (1.2 M), electrochemical cycling and cyclic voltammetry (CV) of BF graphite electrodes reveal continuous electrolyte reduction and no lithiation/delithiation of the graphite. The Solution Structure is dominated by solvent-separated ion pairs (Li+(PC)4//PF6–), and the primary reduction product of the electrolyte is lithium propylene dicarbonate (LPDC). At high concentrations of LiPF6 in PC (3.0–3.5 M), elec...

  • role of Solution Structure in solid electrolyte interphase formation on graphite with lipf6 in propylene carbonate
    Journal of Physical Chemistry C, 2013
    Co-Authors: Daniel P Abraham, Arijit Bose, Yanjing Chen, Brett L. Lucht
    Abstract:

    An investigation of the interrelationship of cycling performance, Solution Structure, and electrode surface film Structure has been conducted for electrolytes composed of different concentrations of LiPF6 in propylene carbonate (PC) with a binder-free (BF) graphite electrode. Varying the concentration of LiPF6 changes the Solution Structure, altering the predominant mechanism of electrolyte reduction at the electrode interface. The change in mechanism results in a change in the Structure of the solid electrolyte interface (SEI) and the reversible cycling of the cell. At low concentrations of LiPF6 in PC (1.2 M), electrochemical cycling and cyclic voltammetry (CV) of BF graphite electrodes reveal continuous electrolyte reduction and no lithiation/delithiation of the graphite. The Solution Structure is dominated by solvent-separated ion pairs (Li+(PC)4//PF6–), and the primary reduction product of the electrolyte is lithium propylene dicarbonate (LPDC). At high concentrations of LiPF6 in PC (3.0–3.5 M), elec...

Arijit Bose - One of the best experts on this subject based on the ideXlab platform.

  • role of Solution Structure in solid electrolyte interphase formation on graphite with lipf6 in propylene carbonate
    Journal of Physical Chemistry C, 2013
    Co-Authors: Daniel P Abraham, Arijit Bose, Yanjing Chen, Brett L. Lucht
    Abstract:

    An investigation of the interrelationship of cycling performance, Solution Structure, and electrode surface film Structure has been conducted for electrolytes composed of different concentrations of LiPF6 in propylene carbonate (PC) with a binder-free (BF) graphite electrode. Varying the concentration of LiPF6 changes the Solution Structure, altering the predominant mechanism of electrolyte reduction at the electrode interface. The change in mechanism results in a change in the Structure of the solid electrolyte interface (SEI) and the reversible cycling of the cell. At low concentrations of LiPF6 in PC (1.2 M), electrochemical cycling and cyclic voltammetry (CV) of BF graphite electrodes reveal continuous electrolyte reduction and no lithiation/delithiation of the graphite. The Solution Structure is dominated by solvent-separated ion pairs (Li+(PC)4//PF6–), and the primary reduction product of the electrolyte is lithium propylene dicarbonate (LPDC). At high concentrations of LiPF6 in PC (3.0–3.5 M), elec...

  • role of Solution Structure in solid electrolyte interphase formation on graphite with lipf6 in propylene carbonate
    Journal of Physical Chemistry C, 2013
    Co-Authors: Daniel P Abraham, Arijit Bose, Yanjing Chen, Brett L. Lucht
    Abstract:

    An investigation of the interrelationship of cycling performance, Solution Structure, and electrode surface film Structure has been conducted for electrolytes composed of different concentrations of LiPF6 in propylene carbonate (PC) with a binder-free (BF) graphite electrode. Varying the concentration of LiPF6 changes the Solution Structure, altering the predominant mechanism of electrolyte reduction at the electrode interface. The change in mechanism results in a change in the Structure of the solid electrolyte interface (SEI) and the reversible cycling of the cell. At low concentrations of LiPF6 in PC (1.2 M), electrochemical cycling and cyclic voltammetry (CV) of BF graphite electrodes reveal continuous electrolyte reduction and no lithiation/delithiation of the graphite. The Solution Structure is dominated by solvent-separated ion pairs (Li+(PC)4//PF6–), and the primary reduction product of the electrolyte is lithium propylene dicarbonate (LPDC). At high concentrations of LiPF6 in PC (3.0–3.5 M), elec...