Ying-Hua Chung

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Reactive oxygen species (ROS) have important functions in cell signaling and, when present at overly high levels, may cause oxidation of important biological molecules. Kinetic models to study diffusion of ROS inside of mitochondria often assume dynamics similar to that in solution. However, it is well-known that separation of proteins in the cytosol or(More)
In this article, we characterize the behavior of water on the surface of a diverse group of carbohydrates and attempt to determine the role of saccharide size, linkage, and branching as well as secondary structure on the dynamics and structure of water at the surface. In order to better understand the similarities and differences in the behavior of the(More)
In this study, we present a general-purpose methodology for deriving the three-dimensional (3D) arrangement of multivalent transmembrane complexes in the presence of their ligands. Specifically, we predict the most likely families of structures of the experimentally intractable trimeric asialoglycoprotein receptor (ASGP-R), which consists of human hepatic(More)
An umbrella sampling method for the calculation of free energies for helical transitions is presented. The method biases structures toward helices of a desired radius and pitch. Although computationally complex, the method has negligible overhead in actual applications. To illustrate the method, calculations of the helical free energy landscape of several(More)
Functional characterization of the lysine acetylation pathway requires quantitative measurement of the modification abundance at the stoichiometry level. Here, we developed a systematic workflow for global untargeted identification of site-specific Lys acetylation stoichiometries in mammalian cells. Our strategy includes an optimized protocol for in vitro(More)
Using free-energy simulations, we have shown that RevErbα-induced DNA deformation preferentially occurs by induced fit rather than by conformational selection, even though the DNA is only slightly distorted in the complex. Our study shows that information on the sequence of binding events is needed to establish whether conformational selection or induced(More)
The difference in lifetime with respect to hydrolysis of two covalent syalosyl-enzyme intermediates of two difluorinated sialic acid analogues ( 1 and 2) bound to Trypanosoma rangeli sialidase is rationalized based on quantum mechanical calculations. The two intermediates differ only in a single functional group, acetamide in the sialidase- 1 complex and(More)
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