Browsing by Subject "interaction"
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Item A structural and energetic description of protein-protein interactions in atomic detail(Texas A&M University, 2007-04-25) Fischer, Tiffany BrinkHere, we present the program QContacts, which implements Voronoi polyhedra to determine atomic and residue contacts across the interface of a protein-protein interaction. While QContacts also describes hydrogen bonds, ionic pair and salt bridge interactions, we focus on QContacts?????? identification of atomic contacts in a protein interface compared against the current methods. Initially, we investigated in detail the differences between QContacts, radial cutoff and Change in Solvent Accessible Surface Area (delta-SASA) methods in identifying pair-wise contacts across the binding interface. The results were assessed based on a set of 71 double cycle mutants. QContacts excelled at identifying knob-in-hole contacts. QContacts, closest atom radial cutoff and the delta-SASA methods performed well at picking out direct contacts; however, QContacts was the most accurate in excluding false positives. The significance of the differences identified between QContacts and previous methods was assessed using pair-wise contact frequencies in a broader set of 592 protein interfaces. The inaccuracies introduced by commonly used radial cutoff methods were found to produce misleading bias in the residue frequencies. This bias could compromise pair-wise potentials that are based on such frequencies. Here we show that QContacts provides a more accurate description of protein interfaces at atomic resolution than other currently available methods. QContacts is available in a web-based form at http://tsailab.tamu.edu/qcons (Fischer et al., 2006).Item Introduction and Selection of Photoperiod Sensitive Sorghum Genotypes for Agronomic Fitness and Biomass Composition(2012-10-19) Hoffmann, LeoIn 2007, U.S. Congress created the "Energy Independence and Security Act" with primary goals focused on increasing the knowledge in production of renewable fuels, increasing the percentages of renewable fuels in the transportation sector and decreasing the emissions of greenhouse gases from fossil fuel sources. To achieve these goals, many species have been pointed as sources of feedstock for the biofuel industry. Photoperiod sensitive (PS) biomass sorghum for the lignocellusosic based conversion is one. In this study, three main objectives were addressed regarding the relative performance for biomass yield and biomass composition of PS biomass sorghum. First, genetic and environmental variation effects on the biomass yield and biomass composition, and usefulness of pre-classification of genotypes by biomass lignin content were evaluated. On the set of genotypes and locations tested, the environmental effect had the largest influence on the biomass composition, yield and its components. Although smaller, the genetic variation effect was significant for most of the traits, some traits had significant genotype by environment GXE interaction. The pre-classification of genotypes according to lignin content proved to be an efficient system of separating genotypes as groups, but failed to be efficient in separating on the entries bases. Assessment of growth patterns for biomass yield and composition, characterized photoperiod sensitive sorghum as capable of producing a harvestable crop as soon as 4 months, but variations in the concentration of constituents and moisture percentage, pointed to a harvest window that can be extended up to the 7th month after planting. Genetic variation was observed in this trail for most agronomic and composition traits, but a strong environmental effect was also observed. Lastly, the influence of three diverse cytoplasm male sterility (CMS) systems in biomass sorghum hybrids was assessed. The presence of A1, A2 or A3 CMS in the hybrids tested in this study had no influence on the biomass yield performance or in the biomass composition. Therefore, any of the CMS systems can be used in the production of biomass sorghum hybrid seed. Also, in this trial the environmental effects were significant and strong for most traits evaluated.Item Investigation of the aerosol-cloud interaction using the WRF framework(2009-05-15) Li, GuohuiIn this dissertation, a two-moment bulk microphysical scheme with aerosol effects is developed and implemented into the Weather Research and Forecasting (WRF) model to investigate the aerosol-cloud interaction. Sensitivities of cloud properties to the representation of aerosol size distributions are first evaluated using a simple box model and a cloud resolving model with a detailed spectral-bin microphysics, indicating that the three-moment method generally exhibits better performance in modeling cloud properties than the two-moment method against the sectional approach. A convective cloud event occurring on August 24, 2000 in Houston, Texas is investigated using the WRF model, and the simulation results are qualitatively in agreement with the measurements. Simulations with various aerosol profiles demonstrate that the response of precipitation to the increase of aerosol concentrations is non-monotonic. The maximal cloud cover, core updraft, and maximal vertical velocity exhibit similar responses as precipitation. The WRF model with the two-moment microphysical scheme successfully simulates the development of a squall line that occurred in the south plains of the U.S. Model experiments varying aerosol concentrations from the clean background case to the polluted continental case show that the aerosol concentrations insignificantly influence the rainfall pattern/distribution, but can remarkably alter the precipitation intensity. The WRF experiment with polluted aerosols predicts 12.8% more precipitation than that with clean aerosols, as well as more intensive rainfall locally. Using the monthly mean cloudiness from the International Satellite Cloud Climatology Project (ISCCP), a trend of increasing deep convective clouds over the north Pacific in winter from 1984 to 2005 is detected. Additionally, through analyzing the results from the Global Precipitation Climatology Project (GPCP) version 2, we also show a trend of increasing wintertime precipitation over the north Pacific from 1984 to 2005. Simulations with the WRF model reveal that the increased deep convective clouds and precipitation are reproduced when accounting for the aerosol effect from the increasing Asian pollution outflow.Item The phiX174 Lysis Protein E: a Protein Inhibitor of the Conserved Translocase MraY(2010-07-14) Zheng, YiMost bacteriophages release progeny virions at the end of the infection cycle by lysis of the host. Large phages with double-stranded DNA genomes use a multigene strategy based on holins, small membrane proteins, and bacteriolytic enzymes, or endolysins. Holins mediate the control of endolysin activity and thus the timing of lysis. Phages with small genomes only encode a single protein for cell lysis. There are three known unrelated single protein lysis systems: the ?X174 E protein, the MS2 L protein, and the Q? A2 protein. None of these phages encodes a cell wall degrading activity, and previous work has shown that the lytic activity of E stems from its ability to inhibit the host enzyme, MraY, which catalyzes the formation of lipid I, the first lipid intermediate in cell wall synthesis. The purpose of the work described in this dissertation was to characterize the ?X174 E-mediated inhibition of MraY using genetic and biochemical strategies. A fundamental question was why no large phages use the single gene system. This was addressed by constructing a recombinant phage, ?E, in which the holin-endolysin based lysis cassette of ? was replaced with E. ?E was compared with ? in genetic and physiological experiments, with the results indicating that the holin-endolysin system increases fitness in terms of adjusting lysis timing to environmental conditions. Using ?E, physiological experiments were conducted to characterize the interaction between E and MraY in vivo. Transmembrane domains (TMD) 5 and 9 have been identified as the potential E binding site by isolating MraY mutants resistant to E inhibition. The five Eresistant MraY mutants were found to fall into three classes, which reflect the apparent affinity of the mutant proteins for E. Finally, an assay for MraY activity employing the dansylated UDP-MurNAc-pentapeptide and phytol-P, was used to demonstrate the inhibition of MraY by purified E protein. It was determined that E is a non-competitive inhibitor for MraY in respect with both substrates. A model for E-mediated inhibition of MraY was proposed, in which E binds to TMDs 5 and 9 in MraY and thus inactivates the enzyme by inducing a conformational change.