RSS 1.0Faculty, Student Works & Conferences School of Pharmacy
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The Advancement of Current Computational HDX-MS Analysis Methodologies Through Two Novel Packages: DCIPD and HExD-IPAEX1 and EX2 Deconvolution: Hydrogen-Deuterium exchange mass spectrometry (HDX-MS) analyzes the structural dynamics of proteins in solution through the monitoring of the time dependent exchange of the backbone amide Hydrogen with Deuterium. An exchange that is governed by the intrinsic rate of exchange (κchem) such that the closing rate (κcl) is far slower than κchem is determined to be an EX1 kinetic regime, in which all amide Hydrogens involved will be deuterated before folding. Within EX1 kinetics a bimodal isotopic distribution can arise. Bimodality within a spectra represents a mixture of EX1 and EX2 kinetics, which can be deconvoluted to obtain further insight into the system. The current program for Bimodal Deconvolution known as HxExpresss, while beneficial, lacks efficiency and ease of use. The HExD-IPA package, as presented in this poster, aims to remove those issues. Computational Integration with Experimental HDX-MS Data: In recent years, there has been a substantial interest in the integration of high-resolution computational methodologies such as MD simulations with the low resolution in vitro HDX-MS data. HDXer (HDX ensemble reweighting) is a computational software which aids in providing an objective, and quantitative, interpretation of computationally generated structural ensembles using HDX-MS data. HDXer uses a maximum entropy reweighting approach to reweight the modeled ensembles to the experimental HDX-MS data. The current methodology used to select optimal reweighting value involves the subjective determination of the inflection point from the elbow curve of Work (Bias Applied) vs Mean Standard Error (MSE) to select the optimal Work applied. The DCIPD package was developed to objectively determine the inflection point while providing a computationally more efficient methodology exploration of the Work applied.
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The Regulatory Role of the Heme-Binding Protein PhuS in Pseudomonas aeruginosaPseudomonas aeruginosa is a gram-negative opportunistic pathogen that can cause life-threatening nosocomial infections in immunocompromised patients. P. aeruginosa requires iron for survival and infection and has evolved several mechanisms to sense and acquire iron from the host including the utilization of heme. PhuS is a cytoplasmic heme binding protein that regulates extracellular heme flux into P. aeruginosa through its conformational flexibility enabling it to exist in functionally distinct forms. The data presented indicates fluctuations in extracellular heme flux through PhuS can disrupt iron homeostasis through the altered expression of the prrF1/prrH sRNA network.
