Browsing by Author "Huang, Jing"

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    CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field
    Kognole, Abhishek A.; Lee, Jumin; Park, Sang-Jun; Jo, Sunhwan; Chatterjee, Payal; Lemkul, Justin A.; Huang, Jing; MacKerell, Alexander D.; Im, Wonpil (Wiley, 2021-12-07)
    Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. In addition, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. The capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.
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    Functional Polymers Containing Semi-Rigid Alternating Sequences
    Huang, Jing (Virginia Tech, 2017-12-12)
    Alternating copolymers represent a special class of copolymers in which the two comonomers copolymerize in a regular alternating sequence along the polymer chain. Of particular interest in our group are the stilbene-maleic anhydride/maleimide alternating copolymers. These copolymers possess sterically congested backbones and precisely placed functional groups arising from the strictly alternating copolymerization. The research in this dissertation is focused on the synthesis, characterization, and potential application of functionalized copolymers that contain semi-rigid alternating copolymer sequences. The fluorescence properties of a series of non-conjugated, tert-butyl carboxylate functionalized alternating copolymers were investigated. Extraordinarily high fluorescent intensity with excellent linearity was observed for the di-tert-butyl group-containing stilbene and maleic anhydride alternating copolymer in THF. We attributed the origin of the strong fluorescence to the “through space” π – π interactions between the phenyl rings from the stilbene and C=O groups from the anhydride. The fluorescence was maintained when the copolymer was deprotected and hydrolyzed and the resulting carboxylic acid-functionalized copolymer was dissolved in water at neutral pH. The tert-butyl carboxylate functionalized alternating copolymer sequences were incorporated into highly crosslinked polymer networks using suspension polymerization. After removing the tert-butyl groups by acidic hydrolysis, the surface area of the networks increased significantly. Using this facile two-step strategy, we were able to achieve nanoporous polymers with BET surface area up to 817 m2/g and carboxylic acid-functionalized surfaces. The BET surface area of deprotected polymers increased with increasing crosslinking density, and the stilbene-containing polymers showed systematically higher BET surface area than the styrene-containing polymers due to the stiffness of the alternating sequences. The resulting nanoporous polymers have potential to be employed as solid sorbents for CO2. The same tert-butyl carboxylate functionalized alternating copolymer sequences were also incorporated into microgels via miniemulsion polymerization. The miniemulsion technique ensured the successful synthesis of microgels with ~100 nm diameter using solid stilbene and maleimide monomers. The resulting tert-butyl carboxylate-containing microgels were converted into carboxylic acid-containing aqueous microgels by acid hydrolysis. These aqueous microgels showed good and reversible lead and copper ion adsorption capacities. Amine-functionalized nanoporous polymers were synthesized by the post-modification of highly-crosslinked divinylbenzene-maleic anhydride polymers. High amine-contents were achieved by covalently attaching multiamines to the acid-chloride functionalized polymer surface. The resulting polymers showed medium to high BET surface areas (up to 500 m2/g) and high CO2 capture capacities.
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    Transport and Metabolism Behavior of Brazilein during Its Entrance into Neural Cells
    Zhao, Shuang; Wang, Xin-Pei; Jiang, Jing-Fei; Chai, Yu-Shuang; Tian, Yu; Feng, Tian-Shi; Ding, Yi; Huang, Jing; Lei, Fan; Xing, Dong-Ming; Du, Li-Jun (PLOS, 2014-10-02)
    Brazilein, a natural small molecule, shows a variety of pharmacological activities, especially on nervous system and immune system. As a potential multifunctional drug, we studied the distribution and the transport behavior and metabolic behavior of brazilein in vivo and in vitro. Brazilein was found to be able to distribute in the mouse brain and transport into neural cells. A metabolite was found in the brain and in the cells. Positive and negative mode-MS/MS and Q-TOF were used to identify the metabolite. MS/MS fragmentation mechanisms showed the methylation occurred at the10-hydroxyl of brazilein (10-O-methylbrazilein). Further, catechol-O- methyltransferase (COMT) was confirmed as a crucial enzyme correlated with the methylated metabolite generation by molecular docking and pharmacological experiment.