Matching Items (55)
Description
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.
ContributorsLi, Dianfan (Author) / Stansfeld, Phillip J. (Author) / Sansom, Mark S. P. (Author) / Keogh, Aaron (Author) / Vogeley, Lutz (Author) / Howe, Nicole (Author) / Lyons, Joseph A. (Author) / Aragao, David (Author) / Fromme, Petra (Author) / Fromme, Raimund (Author) / Basu, Shibom (Author) / Grotjohann, Ingo (Author) / Kupitz, Christopher (Author) / Rendek, Kimberley (Author) / Weierstall, Uwe (Author) / Zatsepin, Nadia (Author) / Cherezov, Vadim (Author) / Liu, Wei (Author) / Bandaru, Sateesh (Author) / English, Niall J. (Author) / Gati, Cornelius (Author) / Barty, Anton (Author) / Yefanov, Oleksandr (Author) / Chapman, Henry N. (Author) / Diederichs, Kay (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Seibert, M. Marvin (Author) / Caffrey, Martin (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-12-17
Description
Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.
ContributorsEdlund, Petra (Author) / Takala, Heikki (Author) / Claesson, Elin (Author) / Henry, Leocadie (Author) / Dods, Robert (Author) / Lehtivuori, Heli (Author) / Panman, Matthijs (Author) / Pande, Kanupriya (Author) / White, Thomas (Author) / Nakane, Takanori (Author) / Berntsson, Oskar (Author) / Gustavsson, Emil (Author) / Bath, Petra (Author) / Modi, Vaibhav (Author) / Roy Chowdhury, Shatabdi (Author) / Zook, James (Author) / Berntsen, Peter (Author) / Pandey, Suraj (Author) / Poudyal, Ishwor (Author) / Tenboer, Jason (Author) / Kupitz, Christopher (Author) / Barty, Anton (Author) / Fromme, Petra (Author) / Koralek, Jake D. (Author) / Tanaka, Tomoyuki (Author) / Spence, John (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Boutet, Sebastien (Author) / Nango, Eriko (Author) / Moffat, Keith (Author) / Groenhof, Gerrit (Author) / Ihalainen, Janne (Author) / Stojkovic, Emina A. (Author) / Schmidt, Marius (Author) / Westenhoff, Sebastian (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2016-10-19
Description
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
ContributorsNogly, Przemyslaw (Author) / Panneels, Valerie (Author) / Nelson, Garrett (Author) / Gati, Cornelius (Author) / Kimura, Tetsunari (Author) / Milne, Christopher (Author) / Milathianaki, Despina (Author) / Kubo, Minoru (Author) / Wu, Wenting (Author) / Conrad, Chelsie (Author) / Coe, Jesse (Author) / Bean, Richard (Author) / Zhao, Yun (Author) / Bath, Petra (Author) / Dods, Robert (Author) / Harimoorthy, Rajiv (Author) / Beyerlein, Kenneth R. (Author) / Rheinberger, Jan (Author) / James, Daniel (Author) / Deponte, Daniel (Author) / Li, Chufeng (Author) / Sala, Leonardo (Author) / Williams, Garth J. (Author) / Hunter, Mark S. (Author) / Koglin, Jason E. (Author) / Berntsen, Peter (Author) / Nango, Eriko (Author) / Iwata, So (Author) / Chapman, Henry N. (Author) / Fromme, Petra (Author) / Frank, Matthias (Author) / Abela, Rafael (Author) / Boutet, Sebastien (Author) / Barty, Anton (Author) / White, Thomas A. (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Neutze, Richard (Author) / Schertler, Gebhard (Author) / Standfuss, Jorg (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-08-22
Description
Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices.
ContributorsOberthuer, Dominik (Author) / Knoska, Juraj (Author) / Wiedorn, Max O. (Author) / Beyerlein, Kenneth R. (Author) / Bushnell, David A. (Author) / Kovaleva, Elena G. (Author) / Heymann, Michael (Author) / Gumprecht, Lars (Author) / Kirian, Richard (Author) / Barty, Anton (Author) / Mariani, Valerio (Author) / Tolstikova, Aleksandra (Author) / Adriano, Luigi (Author) / Awel, Salah (Author) / Barthelmess, Miriam (Author) / Dorner, Katerina (Author) / Xavier, P. Lourdu (Author) / Yefanov, Oleksandr (Author) / James, Daniel (Author) / Nelson, Garrett (Author) / Wang, Dingjie (Author) / Calvey, George (Author) / Chen, Yujie (Author) / Schmidt, Andrea (Author) / Szczepek, Michael (Author) / Frielingsdorf, Stefan (Author) / Lenz, Oliver (Author) / Snell, Edward (Author) / Robinson, Philip J. (Author) / Sarler, Bozidar (Author) / Belsak, Grega (Author) / Macek, Marjan (Author) / Wilde, Fabian (Author) / Aquila, Andrew (Author) / Boutet, Sebastien (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Scheerer, Patrick (Author) / Lipscomb, John D. (Author) / Weierstall, Uwe (Author) / Kornberg, Roger D. (Author) / Spence, John (Author) / Pollack, Lois (Author) / Chapman, Henry N. (Author) / Bajt, Sasa (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2017-03-16
Description
It is the intent of this research to determine the feasibility of utilizing industrial byproducts in cementitious systems in lieu of Portland Cement to reduce global CO2 emissions. Class C and Class F Fly Ash (CFA and FFA, respectively) derived from industrial coal combustion were selected as the replacement materials for this study. Sodium sulfate and calcium oxide were used as activators. In Part 1 of this study, focus was placed on high volume replacement of OPC using sodium sulfate as the activator. Despite improvements in heat generation for both CFA and FFA systems in the presence of sulfate, sodium sulfate was found to have adverse effects on the compressive strength of CFA mortars. In the CFA mixes, strength improved significantly with sulfate addition, but began to decrease in strength around 14 days due to expansive ettringite formation. Conversely, the addition of sulfate led to improved strength for FFA mixes such that the 28 day strength was comparable to that of the CFA mixes with no observable strength loss. Maximum compressive strengths achieved for the high volume replacement mixes was around 40 MPa, which is considerably lower than the baseline OPC mix used for comparison. In Part 2 of the study, temperature dependency and calcium oxide addition were studied for sodium sulfate activated systems composed of 100% Class F fly ash. In the presence of sulfate, added calcium increased reactivity and compressive strength at early ages, particularly at elevated temperatures. It is believed that sulfate and calcium react with alumina from fly ash to form ettringite, while heat overcomes the activation energy barrier of fly ash. The greatest strengths were obtained for mixes containing the maximum allowed quantity of calcium oxide (5%) and sodium sulfate (3%), and were around 12 MPa. This is a very low compressive strength relative to OPC and would therefore be an inadequate substitute for OPC needs.
ContributorsTweedley, Shannon Elizabeth (Author) / Neithalath, Narayanan (Thesis director) / Mamlouk, Michael (Committee member) / Civil, Environmental and Sustainable Engineering Programs (Contributor) / Barrett, The Honors College (Contributor) / School of Sustainable Engineering and the Built Environment (Contributor)
Created2014-05
Description
The civil engineering curriculum includes the engineering fields of environmental, geotechnical, hydrology, structural, and transportation. A particular focus on the structural engineering curriculum outline involves courses in mathematics, engineering mechanics, structural analysis, and structural design. The core structural analysis and design course at Arizona State University (CEE 321) is a transition course to connect realistic structural design and analysis concepts to an engineering foundation created by the first and second year mathematics and mechanics courses. CEE 321 is styled after a flipped classroom model and students are assessed through quizzes, midterms, design projects, and a final exam. Student performance was evaluated for the Spring 2013 and Fall 2013 semesters through an error analysis technique designed to categorize student mistakes based on type of error and related topic. This analysis revealed that student's basic engineering mechanics skills improved throughout the course as well as identified the areas that students struggle in. The slope-deflection and direct stiffness methods of analysis and calculating cross-sectional properties are the primary areas of concern. Using appropriate technology in the engineering classroom has the potential to enhance the learning environment and address the areas of inadequacy identified by the performance analysis. A survey of CEE 321 students demonstrated that technology is a highly integrated and useful portion of student's lives. Therefore, the engineering classroom should reflect this. Through the use of analysis and design software, students are able to begin to develop design intuition and understanding while completing realistic engineering projects in their third year of undergraduate studies. Additionally, incorporating internet resources into and outside of the classroom allows students to be connected to course content from any web-enabled device of their choice. Lecture videos posted online covering the course content were requested by many CEE 321 students and are an emerging resource that supplements the flipped classroom model. The availability of such a tool allows students to revisit concepts that they do not understand or pause, rewind, and replay the lectures when necessary. An expansion of the structural analysis and design online lecture videos for CEE 321 are expected to address and improve the areas that students struggle in as identified by the error analysis.
ContributorsMika, Krista Nicole (Author) / Rajan, Subramaniam (Thesis director) / Mamlouk, Michael (Committee member) / Civil, Environmental and Sustainable Engineering Programs (Contributor) / Barrett, The Honors College (Contributor)
Created2013-12
Description
The fatigue resistance of asphalt concrete (AC) plays an important role in the service life of a pavement. For predicting the fatigue life of AC, there are several existing empirical and mechanistic models. However, the assessment and quantification of the ‘reliability’ of the predictions from these models is a substantial knowledge gap. The importance of reliability in AC material performance predictions becomes all the more important in light of limited monetary and material resources. The goal of this dissertation research is to address these shortcomings by developing a framework for incorporating reliability into the prediction of mechanical models for AC and to improve the reliability of AC material performance prediction by using Fine Aggregate Matrix (FAM) phase data. The goal of the study is divided into four objectives; 1) development of a reliability framework for fatigue life prediction of AC materials using the simplified viscoelastic continuum damage (S-VECD) model, 2) development of test protocols for FAM in similar loading conditions as AC, 3) evaluation of the mechanical linkages between the AC and FAM mix through upscaling analysis, and 4) investigation of the hypothesis that the reliability of fatigue life prediction of AC can be improved with FAM data modeling.
In this research effort, a reliability framework is developed using Monte Carlo simulation for predicting the fatigue life of AC material using the S-VECD model. The reliability analysis reveals that the fatigue life prediction is very sensitive to the uncertainty in the input variables. FAM testing in similar loading conditions as AC, and upscaling of AC modulus and damage response using FAM properties from a relatively simple homogenized continuum approach shows promising results. The FAM phase fatigue life prediction and upscaling of FAM results to AC show more reliable fatigue life prediction than the fatigue life prediction of AC material using its experimental data. To assess the sensitivity of fatigue life prediction model to uncertainty in the input variables, a parametric sensitivity study is conducted on the S-VECD model. Overall, the findings from this research show promising results both in terms of upscaling FAM to AC properties and the reliability of fatigue prediction in AC using experimental data on FAM.
In this research effort, a reliability framework is developed using Monte Carlo simulation for predicting the fatigue life of AC material using the S-VECD model. The reliability analysis reveals that the fatigue life prediction is very sensitive to the uncertainty in the input variables. FAM testing in similar loading conditions as AC, and upscaling of AC modulus and damage response using FAM properties from a relatively simple homogenized continuum approach shows promising results. The FAM phase fatigue life prediction and upscaling of FAM results to AC show more reliable fatigue life prediction than the fatigue life prediction of AC material using its experimental data. To assess the sensitivity of fatigue life prediction model to uncertainty in the input variables, a parametric sensitivity study is conducted on the S-VECD model. Overall, the findings from this research show promising results both in terms of upscaling FAM to AC properties and the reliability of fatigue prediction in AC using experimental data on FAM.
ContributorsGudipudi, Padmini Priyadarsini (Author) / Underwood, Benjamin S (Thesis advisor) / Kaloush, Kamil (Committee member) / Mamlouk, Michael (Committee member) / Neithalath, Narayanan (Committee member) / Arizona State University (Publisher)
Created2016
Description
The major challenge for any pavement is the freight transport carried by the structure. This challenge is expected to increase in the coming years as freight movements are projected to grow and because these movements account for most of the load related distresses for the pavement. Substantial effort has been devoted to identifying the impacts of these future national freight trends with respect to the environment, economic growth, congestion, and reliability. These are all important aspects relating to the freight question, but an equally important and often overlooked aspect of this issue involves the impact of freight trends on the physical infrastructure. This study analyzes the impact of future freight traffic trends on 26 major interstates representing 68% of the total system mileage and carrying 80% of the total national roadway freight. The pavement segments were analyzed using the Mechanistic Empirical Pavement Design Guide software after collecting the relevant traffic, climate, structural, and material properties. Comparisons were drawn between the expected pavement performance using current design standards for traffic growth and performance predictions that incorporated more detailed freight projections which themselves considered job growth and six key drivers of freight movement. The differences in the resultant performance were used to generate maps that provide a bird’s eye view of locations that are especially vulnerable to future trends in freight movement. The analysis shows that the areas of greatest vulnerability include segments that are directly linked to the busiest ports, and surprisingly those from Atlantic and Central states that provide long distance connectivity, but do not currently carry the highest traffic volumes.
ContributorsNagarajan, Sathish Kannan (Author) / Underwood, Shane (Thesis advisor) / Kaloush, Kamil (Committee member) / Mamlouk, Michael (Committee member) / Arizona State University (Publisher)
Created2016
Description
This study examines the outcomes of roundabouts in the State of Arizona. Two types of roundabouts are introduced in this study, single-lane roundabouts and double-lane roundabouts. A total of 17 roundabouts across Arizona were chosen upon several selection criteria and according to the availability of data for roundabouts in Arizona. Government officials and local cities’ personnel were involved in this work in order to achieve the most accurate results possible. This thesis focused mainly on the impact of roundabouts on the accident rates, accident severities, and any specific trends that could have been found. Scottsdale, Sedona, Phoenix, Prescott, and Cottonwood are the cities that were involved in this study. As an overall result, both types of roundabouts showed improvements in decreasing the severity of accidents. Single-lane roundabouts had the advantage of largely reducing the overall rate of accidents by 18%, while double-lane roundabouts increased the accident rate by 62%. Although the number of fatalities was very small, both types of roundabouts were able to stop all fatalities during the analysis periods used in this study. Damage rates increased by 2% and 60% for single-lane and double-lane roundabouts, respectively. All levels of injury severities dropped by 44% and 16% for single-lane and double-lane roundabouts, respectively. Education and awareness levels of the public still need to be improved in order for people to be able to drive within the roundabouts safely.
ContributorsSouliman, Beshoy (Author) / Mamlouk, Michael (Thesis advisor) / Kaloush, Kamil (Committee member) / Zhou, Xuesong (Committee member) / Arizona State University (Publisher)
Created2016
Description
ABSTRACT Pre-treated crumb rubber technologies are emerging as a new method to produce asphalt rubber mixtures in the field. A new crumb rubber modifier industrially known as "RuBind" is one such technology. RuBindTM is a "Reacted and Activated Rubber" (RAR) that acts like an elastomeric asphalt extender to improve the engineering properties of the binder and mixtures. It is intended to be used in a dry mixing process with the purpose of simplifying mixing at the asphalt plant. The objectives of this research study were to evaluate the rheological and aging properties of binders modified with RuBindTM and its compatibility with warm mix technology. Two binders were used for this study: Performance Grade (PG) 70-10 and PG 64-22, both modified with 25% by weight of asphalt binder. Laboratory test included: penetration, softening point, viscosity, Dynamic Shear Rheometer (DSR) and Bending Beam Rheometer (BBR). Tests were conducted under original, short and long -term aging conditions. Observations from the test results indicated that there is a better improvement when RuBindTM is added to a softer binder, in this case a PG 64-22. For short-term aging, the modified binder showed a similar aging index compared to the control. However, long term aging was favorable for the modified binders. The DSR results showed that the PG 64-22 binder high temperature would increase to 82 °C, and PG 70-10 would be increased to 76 °C, both favorable results. The intermediate temperatures also showed an improvement in fatigue resistance (as measured by the Superpave PG grading parameter |G*|sinä). Test results at low temperatures did not show a substantial improvement, but the results were favorable showing reduced stiffness with the addition of RuBindTM. The evaluation of warm mix additive using EvothermTM confirmed the manufacturer information that the product should have no negative effects on the binder properties; that is the modified binder can be used in a warm mix process. These results were encouraging and the recommendation was to continue with a follow up study with mixture tests using the RuBindTM modified binders.
ContributorsMedina, Jose R. (Jose Roberto) (Author) / Kaloush, Kamil (Thesis advisor) / Underwood, Shane (Thesis advisor) / Mamlouk, Michael (Committee member) / Stempihar, Jeffrey (Committee member) / Arizona State University (Publisher)
Created2014