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Full-Text Articles in Physical Sciences and Mathematics
Binding Of Telomestatin, Tmpyp4, Bsu6037, And Braco19 To A Telomeric G-Quadruplex-Duplex Hybrid Probed By All-Atom Molecular Dynamics Simulations With Explicit Solvent., Holli-Joi Sullivan, Carolyn Readmond, Christina Radicella, Victoria Persad, Thomas J Fasano, Chun Wu
Binding Of Telomestatin, Tmpyp4, Bsu6037, And Braco19 To A Telomeric G-Quadruplex-Duplex Hybrid Probed By All-Atom Molecular Dynamics Simulations With Explicit Solvent., Holli-Joi Sullivan, Carolyn Readmond, Christina Radicella, Victoria Persad, Thomas J Fasano, Chun Wu
Faculty Scholarship for the College of Science & Mathematics
A promising anticancer therapeutic strategy is the stabilization of telomeric G-quadruplexes using G-quadruplex-binding small molecules. Although many G-quadruplex-specific ligands have been developed, their low potency and selectivity to G-quadruplexes over duplex remains unsolved. Recently, a crystal structure of a telomeric 3' quadruplex-duplex hybrid was reported and the quadruplex-duplex interface was suggested to a good target to address the issues. However, there are no high-resolution complex structures reported for G-quadruplex ligands except for a docked BSU6037. In this study, molecular dynamic (MD) binding simulations with a free ligand were used to study binding poses and dynamics of four representative ligands: telomestatin, …
Heme Dissociation From Myoglobin In The Presence Of The Zwitterionic Detergent N,N-Dimethyl-N-Dodecylglycine Betaine: Effects Of Ionic Liquids, Eric M. Kohn, Joshua Y. Lee, Anthony Calabro, Timothy Vaden, Gregory A. Caputo
Heme Dissociation From Myoglobin In The Presence Of The Zwitterionic Detergent N,N-Dimethyl-N-Dodecylglycine Betaine: Effects Of Ionic Liquids, Eric M. Kohn, Joshua Y. Lee, Anthony Calabro, Timothy Vaden, Gregory A. Caputo
Faculty Scholarship for the College of Science & Mathematics
We have investigated myoglobin protein denaturation using the zwitterionic detergent Empigen BB (EBB, N,N-Dimethyl-N-dodecylglycine betaine). A combination of absorbance, fluorescence, and circular dichroism spectroscopic measurements elucidated the protein denaturation and heme dissociation from myoglobin. The results indicated that Empigen BB was not able to fully denature the myoglobin structure, but apparently can induce the dissociation of the heme group from the protein. This provides a way to estimate the heme binding free energy, ΔGdissociation. As ionic liquids (ILs) have been shown to perturb the myoglobin protein, we have investigated the effects of the ILs 1-butyl-3-methylimidazolium chloride (BMICl), 1-ethyl-3-methylimidazolium acetate (EMIAc), …
Molecular Dynamics Study Of Homo-Oligomeric Ion Channels: Structures Of The Surrounding Lipids And Dynamics Of Water Movement, Thuy Hien Nguyen, Catherine C. Moore, Preston B. Moore, Zhiwei Liu
Molecular Dynamics Study Of Homo-Oligomeric Ion Channels: Structures Of The Surrounding Lipids And Dynamics Of Water Movement, Thuy Hien Nguyen, Catherine C. Moore, Preston B. Moore, Zhiwei Liu
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Molecular dynamics simulations were used to study the structural perturbations of lipids surrounding transmembrane ion channel forming helices/helical bundles and the movement of water within the pores of the ion-channels/bundles. Specifically, helical monomers to hexameric helical bundles embedded in palmitoyl-oleoyl-phosphatidyl-choline (POPC) lipid bilayer were studied. Two amphipathic α-helices with the sequence Ac-(LSLLLSL)3-NH2 (LS2), and Ac-(LSSLLSL)3-NH2 (LS3), which are known to form ion channels, were used. To investigate the surrounding lipid environment, we examined the hydrophobic mismatch, acyl chain order parameter profiles, lipid head-to-tail vector projection on the membrane surface, and the lipid headgroup vector projection. We find that the lipid …