Abstracts of the scientific posters submitted to the 2018 CHESS Users' Meeting listed alphabetically by last name of the PI.
Collimating Channel Arrays Development at CHESS for high resolution confocal x-ray fluorescence microscopy
CHESS, Cornell University
Exploring Reaction Pathways in the Synthesis of Block Copolymer-Derived Mesoporous Superconducting Nitrides via in situ SAXS/WAXS
Extracting Cation Site Occupation in Spinels through X-ray Absorption and X-ray Emission Spectroscopy
Cation site occupation is an important determinant of materials properties, especially in a complex system with multiple cations such as in ternary spinels. Many methods for extracting the cation site information have been explored in the past, including analysis of spectra obtained through x-ray absorption spectroscopy (XAS). In this work, we select CoxMn3-xO4 spinel phase nanoparticles contaminated with impure CoO phases as a model spinel system for testing the effectiveness of different methods used for determining cation site occupation. We take advantage of the spin and oxidation state sensitive Kβ1,3 peak obtained using x-ray emission spectroscopy (XES) and demonstrate that XES is a powerful and reliable technique for determining site occupation as well as other crystal geometry and electronic features. Comparison between the XAS and XES techniques reveal that XES provides not only the site occupation information that XAS reports, but also additional information on the valence states of the cations at each site. Additionally, the percent error for EXAFS is as high as 35% whereas for XES, the error determined is consistently smaller than 10%. Thus, we conclude that XES is a superior and a far more accurate method in extracting cation site occupation in spinel crystal structures.
Understanding an RNA Helix-Junction-Helix Construct by SAXS refinement of MD Models
RNA molecules have intrinsic flexibility in small components like junctions and bulges. It is of significant structural interest to solve the molecular ensemble and determine how small flexible components impact global fold. We show that small angle X-ray scattering (SAXS) offers conformational insights into an RNA Helix-Junction-Helix (HJH). We further use ensemble optimization method (EOM) to refine all-atom molecular simulations (MD) models. The results are supported by previous smFRET study.
Oligopeptide transporter 3, OPT3, is required for copper homeostasis in Arabidopsis thaliana
Ju-Chen Chia1§, Rong Huang4, Arthur Woll4, Louisa Smieska4, Marta Faulkner1, Jiapei Yan1, Chen Jiao2, Zhangjun Fei2, Miguel Piñeros3, Leon V. Kochian3†, Olena K. Vatamaniuk1
1Section of Crop and Soil Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853; 2Boyce Thompson Institute for Plant Research, Ithaca, NY 14553, USA; 3Robert W. Holley Center for Agriculture and Health, USDA-ARS; †Current address: Global Institute for Food Security, University of Saskatchewan, Saskatoon, S7N 5A8, Canada.
Copper (Cu) is an essential element for plant growth and development but is toxic when accumulated in cells in access. Thus, plants developed sophisticated mechanisms to regulate cellular Cu acquisition and source-to-sink delivery to avoid deficiency and prevent toxicity. The mechanism of Cu acquisition into roots has been well studied. However, transport systems responsible for the phloem-based Cu delivery to sink tissues remain poorly understood. Here, we show that phloem-localized Arabidopsis thaliana iron (Fe) transporter, OPT3, recognized for its role in source-to-sink Fe delivery and shoot-to-root communication of Fe status, also contributes to Cu transport. Specifically, RNA-seq analyses revealed that young leaves (sinks) of the opt3-3 mutants manifested the molecular symptoms of Cu deficiency including the upregulation of the expression of genes involved in cellular Cu acquisition and the downregulation of the expression of Cu binding proteins involved in the metabolic re-utilization of cellular copper reserves. These results suggest that in addition to Fe, OPT3 might be also involved in source-to-sink Cu delivery. Consistent with this suggestion was finding that young leaves of the opt3-3 mutant contained 80% less Cu than young leaves of wild type plants, while Cu concentration in mature leaves of the opt3-3 mutant was similar to that of mature leaves of wild type. In addition, we found that the opt3-3 mutant was more sensitive to Cu deficiency than wild type plants re-informing the role of OPT3 in Cu homeostasis in A. thaliana. Finally, 2D-SXRF and SXRF-based computed tomography uncovered how Arabidopsis OPT3 affects Cu accumulation in both vegetative and reproductive tissues. Taken together, our data assign a novel function to OPT3 in source-to-sinks delivery of Cu.
Molecular Weight Distribution Shape: A Versatile Handle for Tailoring Block Copolymer Phase Behavior
Biological Small Angle X-ray Solution Scattering at MacCHESS
MacCHESS, Cornell University
Biological Small Angle X-ray Solution Scattering (BioSAXS) has become a highly popular technology and is widely used in the structural biology community. The continued rapid growth of the method reflects its ease of use, its versatility, and the fact that it yields structural information about molecules in a wide range of true solution conditions. The ability to probe solution behavior is critical to structural biology studies which often rely heavily on crystalline and/or frozen samples. MacCHE
Studying of the Binding of Gases to Proteins by Pressure Cryocooling
Qingqiu Huang, Irina Kriksunov and Doletha M. Szebenyi
MacCHESS, Cornell University, Ithaca, NY 14853, USA
High pressure cryocooling has been developed as an alternative method for cryopreservation of macromolecular crystals and a method to improve the diffraction quality of macromolecular crystals in which crystals are pressurized by helium gas at 200-400MPa and cooled to liquid nitrogen temperature. This method has been extended to study the binding of gases other than helium to proteins at lower pressure (usually <15MPa). An apparatus for lower-pressure cryocooling using various gases has been installed at CHESS. Standard operating procedures have been established for use with gases, such as CO2, O2, krypton and NO2 (0.5% in nitrogen).
Operando X-ray Microscopy and X-ray Diffraction of Lithium Sulfur Batteries
Xin Huang1,2*, Seung-Ho Yu3*, Rong Huang2, Joel. D. Brock1,2, Héctor D. Abruña3
1Cornell High Energy Synchrotron Sources, 2School of Applied and Engineering Physics, 3Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
Lithium-sulfur (Li-S) batteries have been extensively studied because sulfur has a high theoretical specific capacity (1672 mAh/g) and is abundant on earth. However, there are several problems to be solved before practical use of lithium sulfur batteries can be realized. First, sulfur has very low electrical conductivity, so the sulfur must be mixed with a high amount of conductive additives. Second, the reaction between sulfur and lithium produces a series of polysulfide intermediate species that readily dissolve into the electrolyte and migrate to the Li anode, which leads to many problems including shuttle reactions and loss of capacity. Third, the reaction mechanism of the Li-S battery is very complex; the detailed mechanism is not fully understood. The first two problems have been partly solved for the past 5 years, and we need to further understand the detailed reaction mechanism in order to further improve the electrochemical properties of the battery. Here, we apply operando X-ray microscopy and X-ray diffraction to study the evolution of morphology and structure of the sulfur on the cathode while cycling the battery. Our direct observation of dissolution and formation of sulfur and lithium sulfide during cycling gives us tremendously new insights to understand the reaction mechanism.
Simultaneous, Synchrotron Based, Real-time X-ray Reflectivity Using Monochromatic Radiation
CHESS, Cornell University
We describe the development of a synchrotron based, monochromatic, real-time x-ray reflectivity (XRR) measurement technique. We utilize a polycapillary x-ray optic to produce a converging fan of radiation which provides the range of simultaneous incident angles necessary for monochromatic XRR. For sufficiently smooth surfaces, the specular reflection dominates the diffracted signal, and using a 2D detector allows us to collect a portion of the reflectivity curve simultaneously.
Time Resolved Ice Formation in Protein Crystals
Ice formation in protein crystals is a significant obstacle to cryocrystallographic study of protein structure, especially at temperatures near the protein-solvent glass transition. We study ice formation in response to quenches to temperatures down to 180K. We observe a suppression of freezing points, formation of stacking disordered ice, estimate the unfreezable fraction of crystalline solvent, and demonstrate that ice free data sets can be obtained from cryoprotectant-free crystals.
Time-resolved SAXS and ensemble modelling reveal Mg orchestration across an RNA folding landscape
Alex Plumridge1, Andrea M. Katz1, George D. Calvey1, Ron Elber2, Serdal Kirmizialtin3, Lois Pollack1
1Cornell University, Ithaca, NY, USA; 2University of Texas at Austin, Austin, TX, USA; 3New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
RNA’s unique folds and motions enable many of its newly discovered functions, yet RNA self-assembly and conformational dynamics are not well understood. Here, we use microfluidic mixing to trigger the Mg induced folding of tp5abc; a representative of the common RNA motif the three helix junction. Time-dependent conformations are measured using time-resolved small angle x-ray scattering (SAXS), and analyzed by pairing ensemble decomposition with all-atom simulations. Detailed structural ensembles, derived at crucial stages of folding, reveal many distinct phases of tp5abcs journey to the native state. Many of these phases rely on the presence of Mg ions, and underscore their unique and varying role(s) in guiding RNA through a complex and rugged landscape.
Protein denaturation under high pressure
CHESS, Cornell University
The effect of high pressure on a leucine rich protein pp32 mutants will be presented. We compliment the NMR results, which provide high-resolution information about the transient structures and conformational dynamics, with SAXS results, which provides low-resolution structure and interaction details over wide range of particle sizes. We found that the effects of internal cavities on the conformational landscape of pp32 are strongly dependent upon their structural and energetic context.
CESR Upgrade for CHESS-U
CLASSE, Cornell University
Synchrotron X-ray Fluorescence (SXRF) microscopy aids to elucidate BdYSL16 involve in Cu distribution and how Cu affects fertility and seed yield in Brachypodium
Cu is an essential micronutrient for plant growth and development (1) It plays an important biological role in photosynthesis, respiration, C and N metabolism, perception of hormones, cell wall remodeling and regulation of the cellular redox state for its function as a cofactor of numerous proteins (2). A deficiency of the Cu leads to stunted growth, distortion of young leaves, and infertility and grain yield reduction in plants (3). Wheat, as one of the most economically important food crops worldwide, is considered as the most sensitive crop to Cu deficiency. However, how Cu affects fertility and seed yield in monocots is poorly understood. Here, we used Brachypodium distachyon as a model plants for wheat to explore the molecular mechanisms of Cu deficiency induced infertility and seed yield reduction. In this report, we focus on a yellow stripe-like transporter BdYSL16 because its homolog in rice is required for Cu distribution to the developing leaves and seeds. Our results showed that knockout of BdYSL16 resulted in impaired distribution of Cu to developing leaves indicated by the higher Cu accumulation in the old leaves but a lower concentration in the young leaves. At the reproductive stage, ysl16 mutant showed significant reduced fertility and seed yield result from its inability to deliver enough Cu to flag leaf, anthers and ovary indicated by Synchrotron X-ray Fluorescence (SXRF) analysis of elements localization.
What's New at MacCHESS
D. Szebenyi, R. Cerione, T.K. Chua, M. Cook, A. Finke, R. Gillilan, J. Hopkins, Q. Huang, I. Kriksunov, W. Miller, D. Rai, D. Schuller, S. Smith and J. Wierman
MacCHESS, Cornell University, Ithaca, New York 14853
MacCHESS conducts both core and collaborative research projects, and supports users doing "Macromolecular diffraction at CHESS". In 2017-2018, users employed CHESS facilities to collect crystallographic and small-angle solution scattering (BioSAXS) data on numerous molecules and complexes of biological interest. A sampling of users' important structural results, reported here, provides insight into how a new drug may combat antibiotic resistance in bacteria, the role of cardiolipin in importing proteins into mitochondria, and a detailed view of an enzyme's active site as it changes during reduction of its catalytic Cu.
Developments in the major focus areas of MacCHESS include:
BioSAXS – hardware and software upgrades have substantially improved the data collection experience; continuing improvements in the RAW processing software have been made; high pressure BioSAXS has been implemented; initial experiments in time-resolved studies using microfluidic mixing chips have shown promise.
Pressure Cryocooling (HPC) – HPC has been applied to trap several different gases, e.g. CO2 in carbonic anhydrase and ODCase, O2 in hemoglobin, and Kr in lysozyme (for phasing); several cases of pressure-induced reduction of disorder have been observed.
Microcrystallography – significant advances have been made in serial microcrystallography, using the intense focused beam at G3 and multicrystal holders from the Miller group (Toronto); the EMC algorithm developed by the Elser group has been used to obtain a structure from serial data rejected by conventional processing software.
Training & Dissemination – the BioSAXS Essentials course continues to provide an excellent foundation for those interested in applying BioSAXS to their projects; a revamped web site has a modern look and provides new features such as video tutorials.