346,487 research outputs found

    Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability

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    Bryan S. Der, Ron Jacak, Brian Kuhlman, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of AmericaChristien Kluwe, Aleksandr E. Miklos, Andrew D. Ellington , Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of AmericaChristien Kluwe, Aleksandr E. Miklos, George Georgiou, Andrew D. Ellington, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of AmericaAleksandr E. Miklos, Andrew D. Ellington , Applied Research Laboratories, University of Texas at Austin, Austin, Texas, United States of AmericaSergey Lyskov, Jeffrey J. Gray, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of AmericaBrian Kuhlman, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of AmericaReengineering protein surfaces to exhibit high net charge, referred to as “supercharging”, can improve reversibility of unfolding by preventing aggregation of partially unfolded states. Incorporation of charged side chains should be optimized while considering structural and energetic consequences, as numerous mutations and accumulation of like-charges can also destabilize the native state. A previously demonstrated approach deterministically mutates flexible polar residues (amino acids DERKNQ) with the fewest average neighboring atoms per side chain atom (AvNAPSA). Our approach uses Rosetta-based energy calculations to choose the surface mutations. Both protocols are available for use through the ROSIE web server. The automated Rosetta and AvNAPSA approaches for supercharging choose dissimilar mutations, raising an interesting division in surface charging strategy. Rosetta-supercharged variants of GFP (RscG) ranging from −11 to −61 and +7 to +58 were experimentally tested, and for comparison, we re-tested the previously developed AvNAPSA-supercharged variants of GFP (AscG) with +36 and −30 net charge. Mid-charge variants demonstrated ~3-fold improvement in refolding with retention of stability. However, as we pushed to higher net charges, expression and soluble yield decreased, indicating that net charge or mutational load may be limiting factors. Interestingly, the two different approaches resulted in GFP variants with similar refolding properties. Our results show that there are multiple sets of residues that can be mutated to successfully supercharge a protein, and combining alternative supercharge protocols with experimental testing can be an effective approach for charge-based improvement to refolding.This work was supported by the Defense Advanced Research Projects Agency (HR-0011-10-1-0052 to A.E.) and the Welch Foundation (F-1654 to A.E.), the National Institutes of Health grants GM073960 (B.K.) and R01-GM073151 (J.G. and S.L.), the Rosetta Commons (S.L.), the National Science Foundation graduate research fellowship (2009070950 to B.D.), the UNC Royster Society Pogue fellowship (B.D.), and National Institutes of Health grant T32GM008570 for the UNC Program in Molecular and Cellular Biophysics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Center for Systems and Synthetic BiologyCellular and Molecular BiologyApplied Research LaboratoriesEmail: [email protected]

    Alcohol-Induced Histone Acetylation Reveals a Gene Network Involved in Alcohol Tolerance

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    Alfredo Ghezzi, Harish R. Krishnan, Linda Lew, Francisco J. Prado III, Darryl S. Ong, Nigel S. Atkinson, Section of Neurobiology and Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas, United States of AmericaSustained or repeated exposure to sedating drugs, such as alcohol, triggers homeostatic adaptations in the brain that lead to the development of drug tolerance and dependence. These adaptations involve long-term changes in the transcription of drug-responsive genes as well as an epigenetic restructuring of chromosomal regions that is thought to signal and maintain the altered transcriptional state. Alcohol-induced epigenetic changes have been shown to be important in the long-term adaptation that leads to alcohol tolerance and dependence endophenotypes. A major constraint impeding progress is that alcohol produces a surfeit of changes in gene expression, most of which may not make any meaningful contribution to the ethanol response under study. Here we used a novel genomic epigenetic approach to find genes relevant for functional alcohol tolerance by exploiting the commonalities of two chemically distinct alcohols. In Drosophila melanogaster, ethanol and benzyl alcohol induce mutual cross-tolerance, indicating that they share a common mechanism for producing tolerance. We surveyed the genome-wide changes in histone acetylation that occur in response to these drugs. Each drug induces modifications in a large number of genes. The genes that respond similarly to either treatment, however, represent a subgroup enriched for genes important for the common tolerance response. Genes were functionally tested for behavioral tolerance to the sedative effects of ethanol and benzyl alcohol using mutant and inducible RNAi stocks. We identified a network of genes that are essential for the development of tolerance to sedation by alcohol.This work was supported by National Institute of Health grant R01 AA018037 to NSA (http://www.nih.gov/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.NeuroscienceWaggoner Center for Alcohol and Addiction ResearchEmail: [email protected] (AG)Email: [email protected] (NSA

    The Legend of Georgia McBride: Change in Light of Passion

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    This thesis describes the research and production processes of the lighting design for the play, The Legend of Georgia McBride by Matthew Lopez, performed in the Johnny Carson Theatre at the Lied Center for Performing Arts from October 2nd through October 13th, 2019. The play was directed by guest artist Steve Scott with scenic design by Marty Wolff, costumes by Rebecca Armstrong, sound design by Jeff O’Brien, technical direction provided by Austin Elledge, and master electrician Joshua Mullady. This thesis contains the entire lighting process including the initial meetings, research, conceptualization, technical rehearsals, critical response, paperwork, and production photos. Advisor: Laurel Shoemake

    Starting a Sober Dorm: Year One Challenges, Successes and Lessons Learned

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    This presentation is an examination of the pilot year of the Healthy Lifestyles Living Learning Community (HL LLC) substance-free housing option for incoming first year students sponsored by The Center for Students in Recovery at The University of Texas at Austin. Presenters will contextualize the history and unfulfilled need for recovery and sober student housing on the UT Austin campus, and will explore the development and implementation of a sober dorm from inception through the end of year one. Attendees will hear a candid assessment of expectations versus realities across multiple domains, including: the application process; selection of an initial cohort; the design and implementation of programming; the challenges of group cohesion and resident assistant empowerment; budget constraints; overall lessons learned; and considerations moving into year two

    The 1991-1992 project summaries

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    The Department of Mechanical Engineering at The University of Texas at Austin participated in seven cooperative design projects this year. Six of the projects were associated with the Johnson Space Center and include the design of a thermal control system for an inflatable lunar habitat module, a vibration isolation system for a space shuttle cycle ergometer, a radiator shading device for a lunar outpost, a reusable astronaut safety tether, a resistive exercise device for use on the space shuttle, and a fleet of autonomous regolith throwing devices for radiation shielding of lunar habitats. The seventh project is associated with the Jet Propulsion Lab and involves the design of a shock absorbing wheel for a small six-wheeled Martian rover vehicle
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