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X-RAY RUNS: Apply for Beamtime

2017  May 17 - June 29

2017  October 11 - December 21
2017  Proposal deadline: 08/01/17
2017  BTR deadline: 09/10/17

 


Abstracts

 

Tuesday, June 10th
"Structural Biology of the Actin Cytoskeleton – Three Short Stories"

Roberto Dominguez
Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 728 Clinical Research Bldg., 415 Curie Blvd., Philadelphia, PA 19104

Abstract: Many bacterial pathogens use the actin cytoskeleton of host eukaryotic cells for invasion and motility. The Rickettsia surface protein Sca2 mimics eukaryotic formins by promoting the formation of actin comet tails for Rickettsia motility. It had been proposed that Sca2 was structurally and functionally related to eukaryotic formins. A crystal structure and biochemical analysis unexpectedly revealed a novel fold and a fundamentally new mechanism for actin tail formation (Madasu et al., PNAS 2013).

CARMIL is a 1,370-aa cytoskeleton regulatory protein that plays crucial roles in cell motility and tissue development. The crystal structure of CARMIL1-668 and a SAXS envelope of CARMIL1-878 reveal an unexpected membrane-binding domain and suggest a mechanism for dimerization and membrane binding (Zwolak et al. Nature Communications 2013).

Chromatin-remodeling complexes are assembled around a catalytic subunit that contains a central ATPase domain and flanking sequences that recruit auxiliary proteins. The catalytic subunits of SWI/SNF remodelers recruit actin-related proteins (Arp) 7/9 as auxiliary subunits. In the complex, Arp7/9 is additionally associated with another subunit, Rtt102. Structural analysis by small-angle x-ray scattering shows that when bound to Rtt102, the complex of Arp7/9 with the catalytic subunit of SWI/SNF remodelers assumes a more stable compact conformation (Turegun et al., J Biol Chem 2013).

"The crystal structure of canine parvovirus capsids interacting with neutralizing antibody fragment"

Lindsey J. Organtini1, Sho Iketani2, Colin R. Parrish2, Susan Hafenstein1

1 Department of Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
2 Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA

Abstract: Canine parvovirus 2 (CPV-2) causes severe illness in canines and is highly contagious. While a vaccine is available, the disease is still common in puppies due to lack of vaccination or to interference with vaccine from maternal antibodies. Previously, a panel of neutralizing antibodies was developed and used to map two major antigenic sites on the virus capsid, and examined in biochemical and structural studies. Only two of the eight antibodies were able to neutralize virus as the fragment antibody binding (Fab) portion alone: antibodies E (B5A8) and F (B6D5), which shared a common germline sequence. The cryo-EM structures of these two virus-Fab complexes were solved previously to a resolution of 12-14Å, and shown to have overlapping but distinct footprints on the capsid surface. To achieve a high-resolution structure for elucidation of the neutralization mechanism of the Fab, CPV-2 capsids were co-crystallized with the Fab fragment generated from the MAb E antibody.

The CPV-Fab structure crystallized in the space group C121 with unit cell dimensions of a = 358.6, b = 354.5, c = 854.1. The co-crystal structure was solved to a resolution of 3.5Å. The Fab binds to a region of the virus comprised of three distinct but intertwined molecules of the capsid coat protein. The binding site lies between the icosahedral three-fold and two-fold axes of symmetry. The co-crystal structure identified the details of the interactions between the residues of the virus and Fab, and allowed us to understand the contacts involved. Of the interacting residues, the CPV-2 VP2 residue 300 was identified to make contact with the Fab molecule. VP2 residue 300 has previously been shown to be a determinant of host range and is also within the receptor footprint. Either Fab interaction with this site on the viral capsid, or the interactions with the interacting VP2 molecules may explain the ability of MAb E to neutralize the virus as a Fab alone, unlike other neutralizing antibodies of the same virus. In addition, we have cloned and expressed the variable domains of MAb E from a baculovirus scFv-Fc fusion protein, and mutated several of the residues in the interacting surface, allowing a better understanding of how the interactions control the binding and neutralization.

"XANES and XRF Imaging of Iconic Works by Pablo Picasso, Edvard Munch, Henri Matisse, and Adriaen Coorte: Case Studies in Paint Alteration and Painting Technique"

Jennifer L. Mass, Arthur R. Woll, Apurva Mehta, Florian Meirer, Emeline Pouyet, Marine Cotte, Alyssa Hull, Robin Kirkham, Anthony Kuczewski, Gareth Moorhead, Chris Ryan, Peter Siddons, Katrien Keune, Patricia Favero, Carol Pottash, Annelies Van Loon, David Agyeman-Budu, Robert Gordon, Adam Finnefrock, Erich Uffelman, Barbara Buckley, Jonathan Church, Robert Opila, and Catherine Matsen
University of Delaware

Abstract: Despite extensive research into various aspects of Pablo Picasso's working methods and materials, and detailed analyses of a handful of his later paintings, comprehensive technical analysis of a work from his Blue Period has not been carried out. The Blue Room (1901, The Phillips Collection, Washington, DC) has been known for several years to have another painting, a portrait, beneath the presentation surface, also thought to have been carried out in 1901. This presentation will describe initial results of a comprehensive analysis of The Blue Room, including combined results from portable x-ray fluorescence (XRF), Raman spectroscopy, FTIR, and scanning electron microscopy x-ray microanalysis, along with synchrotron-radiation (SR) based XRF mapping of the entire painting. The SR-XRF maps were obtained at the CHESS using a new version of the 384-sensor Maia detector. The goals of this measurement were to determine the elemental distribution of the combined painting, and the feasibility of distinguishing features of the presentation surface and buried works in this and other, similar Picasso works of the same period. Several features of the buried portrait are distinguishable in the XRF maps, which may assist the ongoing interpretation of this painting.

For works of this same time period, cadmium carbonate (CdCO3) has been identified in the altered cadmium yellow (CdS) paints observed in Impressionist, early modernist, and post-Impressionist paintings including The Blue Room. When it is concentrated at the surface of the paint layer, CdCO3 appears to result from the photo-alteration of CdS. However, in other cases CdCO3 is distributed throughout the paint layer. This is significant because CdCO3 is highly insoluble (Ksp of 1.0 ×10-12), and if it were formed solely as a result of photo-alteration it would not be expected to migrate away from the painting's surface. In Edvard Munch's c. 1910 The Scream (The Munch Museum, Oslo), it has recently been proposed that CdCO3 is present because this compound was used in the indirect wet process synthesis of CdS (through, for example, the reaction of CdCO3 and Na2S). This would mean that the CdCO3 is a residual starting reagent rather than a photo-alteration product. Such an interpretation is supported by the identification of CdCO3 in the unaltered cadmium yellow paints of early modernist works such as Henri Matisse's Flower Piece (The Barnes Foundation, 1906). To address this question of CdCO3's role, apparently non-degraded cadmium yellow paint from Henri Matisse's Flower Piece was studied using x-ray microspectroscopy and microdiffraction at ESRF ID21 and Petra III.

Moving from the early 20th century to the early 18th century, mechanisms of pigment alteration in Still Life with Five Apricots by Adriaen Coorte (1704) (Royal Picture Gallery Mauritshuis, The Hague, The Netherlands) will be discussed. Arsenic sulfide pigments orpiment (As2S3) and realgar (As4S4), are well known to shift color under exposure to visible light. Realgar undergoes photo-induced polymorphism and turns bright yellow (pararealgar) to colorless (As2O3, arsenolite), whereas orpiment photo-oxidizes and becomes colorless (arsenolite). These transformations, as well as the characterization of the reaction products and their mobilities will be discussed. Confocal microspectroscopy of the painting was carried out at APS using the CHESS-developed spoked channel array focusing optic. These results and also X-ray microspectroscopy carried out at ESRF ID21 and SSRL will be discussed. Comparison of the Coorte XANES spectra and their prinicipal components with published spectra and As reference compounds were carried out, and results will be presented along with the implications for the preservation of this important work.

"Ordered Structure Rearrangements in Heated Gold Nanocrystal Superlattices"

Brian Goodfellow
Dow Chemical, formerly Brian Korgel Group, University of Texas

Abstract: TBA

"Graphene as a protein crystal mounting material to reduce background scatter"

Jennifer Wierman
Cornell University

Abstract: The overall signal-to-noise ratio per unit dose for X-ray diffraction data from protein crystals can be improved by reducing the mass and density of all material surrounding the crystals. In some cases, such as microcrystallography, background reduction is a necessity. Our paper demonstrated a path towards the practical ultimate in background reduction by use of atomically thin graphene sheets as a crystal mounting platform for protein crystals. The results show the potential for graphene in protein crystallography and other cases where X-ray scatter from the mounting material must be reduced and specimen dehydration prevented, such as in coherent X-ray diffraction imaging of microscopic objects. This sets a precedent and guide for the future in serial crystallography at current synchrotron sources, including CHESS.

"High-quality nanomaterials: from single quantum dot to their superstructures"

Ou Chen
Massachusetts Institute of Technology

Abstract: Nanocrystal materials are emerging as an important class of tools that are revolutionizing both fundamental science and technological applications due to their many unique properties. In particular, quantum dots nanocrystals have demonstrated their great potential to be applied in a wide variety of applications as a unique emissive material. In my talk, I will first describe my experimental effort for the synthesis and characterization of a new generation of nanocrystal quantum dots. These dots for the first time combine, in one material, all the best performance metrics desired in quantum dot nanomaterials. In the second part of my talk, I will show how we can use colloidal nanocrystals as building blocks to generate higher-order architectures in assemblies. I will use magneto-fluorescent multifunctional supernanoparticles which self-assemble from quantum dots and magnetic nanoparticles as a model system to demonstrate the synthesis, superstructure, property characterizations and their potential biological applications.

"Emergence of charge density wave domain walls above the superconducting dome in 1T-TiSe2"

Peter Abbamonte
University of Illinois at Urbana-Champaign

Abstract: Superconductivity (SC) in so-called "unconventional superconductors" is nearly always found in the vicinity of another ordered state, such as antiferromagnetism, charge density wave (CDW), or stripe order. This suggests a fundamental connection between superconductivity and fluctuations in some other order parameter. In this talk I will describe our use of high-pressure x-ray scattering at C Line at CHESS to directly study the CDW order in the layered dichalcogenide TiSe2, which was previously shown to exhibit SC when the CDW is suppressed by pressure or intercalation of Cu atoms. We succeeded in suppressing the CDW fully to zero temperature, establishing for the first time the existence of a quantum critical point (QCP) at Pc = 5.1 ± 0.2 GPa, which is more than 1 GPa beyond the end of the superconducting region. Unexpectedly, at P = 3 GPa we observed a reentrant, weakly first order, incommensurate phase, indicating the presence of a Lifshitz tricritical point somewhere above the superconducting dome. Our study suggests that SC in TiSe2 may not be connected to the QCP itself, but to the formation of CDW domain walls.

Wednesday, June 11th - WORKSHOP I
"Measuring and Modeling Grain Average Strain in Titanium"

T.J. Turner1, P.A. Shade1, J.C. Schuren1, J.B. Bernier2, F. Li2, B. Blank3, J. Almer4, P. Kenesei4, U. Lienert5, R.M. Suter6

1Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA
2Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
3PulseRay, Beaver Dams, NY, 14812, USA
4Advanced Photon Source, Argonne National Laboratory, Argonne, IL, 60439, USA
5DESY-Petra III, Hamburg, Germany
6Carnegie Mellon University, Pittsburgh, PA, 15213, USA

Abstract: To meet future design challenges, materials performance analysis must shift to the mesoscale - an intermediate length scale above individual atoms but below the continuum approximation employed for modern design. We present a novel capability that concurrently combines several high-energy x-ray methodologies into a combined experiment called High Energy X-Ray Diffraction Microscopy (HEDM). HEDM provides a nondestructive spatially-resolved probe that can track defect accumulation, grain boundary motion, grain rotations, crack propagation, and the evolution of elastic strain/stress states of individual grains inside bulk materials. The technique is demonstrated for a Ti7-Al specimen undergoing creep deformation. These datasets provide insight into deformation at the mesoscale and embody a quantum leap to develop and validate materials models sensitive to the explicit material structure. Without such localized validation, advanced computational methods will not free modern materials design from its dependency on costly traditional large-scale testing programs. We also present the unique testing equipment, the Rotational and Axial Motion System (RAMS) loadframe, which will be available to the general user population at both Argonne National Laboratory's Advanced Photon Source, as well as Cornell's High-Energy Synchrotron Source. Finally, we present initial crystal plasticity finite element modeling results for the elastic-plastic loading of a titanium sample where the initial model was instantiated from the HEDM data and the grain average stresses compared to those collected during the HEDM experiments.

"Modeling In Situ Loading Diffraction Experiments with Finite Element-Based Models"

Paul Dawson
Sibley School of Mechanical and Aerospace Engineering, Cornell University

Abstract: FEpX is a specialty finite element code for simulating the mechanical behavior of polycrystalline solids at the level of aggregates of grains. The number of grains in an aggregate can range from just one to on the order of 100,000. The code is intended for investigating the mechanical behavior of polycrystals that exhibit inhomogeneous deformations within and among the crystals, the heterogeneity of stress within a polycrystal, and the role of neighbors on the behaviors of individual grains. When coupled with sample instantiation methods, FEpX can be used effectively to model yielding and flow of materials with complicated phase/grain topologies and morphologies. With these capabilities and diffraction-based post-processing algorithms, FEpX provides a powerful tool for the aiding in the interpretation of in situ loading diffraction experiments.

In this presentation we will provide an overview of FEpX. We first discuss the constitutive equations central to the focus of FEpX. These are equations describe elastic and plastic responses at the single(sub)-grain scale. The behaviors that the equations represent include: nonlinear kinematics capable of handling motions with both large plastic strains and large rotations; anisotropic elasticity based on cubic or hexagonal crystal symmetry; anisotropic plasticity based on rate-dependent slip on a restricted number of systems for cubic or hexagonal symmetry; and the evolution of state variables for crystal lattice orientation and slip system strengths. Next, we will outline how the finite element framework provides spatial distributions for the motion, deformation and stress throughout the aggregate. With these fields determined, we will show how post-processing is used to generate data analogous to diffraction measurements. Finally, we will illustrate combining FEpX with tools for sample instantiation and for comparing simulation with diffraction experiments with HEXD and neutron diffraction experiments with several examples.

"Bridging between High Energy X-Ray Diffraction Experiments and Polycrystal Computations: on the Issue of Polycrystal Representation and Meshing"

Romain Quey
École des Mines de Saint-Étienne, CNRS UMR 5307, France

Abstract: High energy X-ray diffraction techniques enable to characterize the local elastic strains in a deformed polycrystalline material, but also provide, depending on the set up, some information on its microstructure. For example, powder diffraction, 3D X-ray diffraction microscopy (3DXRD) or diffraction contrast tomography (DCT) are such techniques that provide no, partial or full information on the grain arrangement. On the other hand, polycrystal computations by the finite element method always require fully defined and properly meshed microstructures. In the present work, we first introduce a versatile method for optimal polyhedral representation of polycrystals, which can adapt to the different experimental inputs. We then show how the method can be extended to the generation of more complex, multiscale microstructures. Finally, we describe how to mesh the microstructures with high element quality, as required for finite element computations. The presented algorithms are implemented into a free (open-source) software package: Neper (http://neper.sourceforge.net).

"A combined experiment and simulation approach to investigating microscale initiation and propagation of yielding in duplex stainless steel under biaxial loading"

Andrew Poshadel
Sibley School of Mechanical and Aerospace Engineering, Cornell University

Abstract: The coupling of diffraction experiments and finite element polycrystalline simulations provides a powerful toolset for investigating the micromechanics of structural alloys. A combined experiment and simulation approach was employed to investigate microscale initiation and propagation of yielding in LDX-2101 duplex stainless steel under biaxial loading. Fiberaveraged lattice strains were measured using neutron powder diffraction at the Canadian Neutron Beam Centre. Experiments were performed on hollow, thin-walled specimens, loaded in-situ by a combination of axial force and internal pressurization. Five levels of stress biaxiality, ranging from uniaxial to balanced biaxial, were investigated. Simulations were conducted using FEpX (Finite Element Polycrystals) code to model the experiment. Experimental lattice strains for uniaxial loading provided necessary data to calibrate the model parameters for the dual phase material. Comparisons between experimental and simulated fiber-averaged lattice strains for the remaining four levels of stress biaxiality established confidence in the model.

In addition to fiber-averaged lattice strains, FEpX offers a wealth of complementary micromechanical data to the powder experiment, including stresses and plastic deformation rates. Furthermore, the model is not restricted to fiber averages; spatial distributions can also be examined. These capabilities of the model were employed to investigate the effects of anisotropic strength and stiffness on the initiation and propagation of yielding at the microscale. The levels of anisotropy for both strength and stiffness were shown to have significant effects on yield behavior.

Wednesday, June 11th - WORKSHOP II
"SAX Scattering: Initial Steps Towards 'Seeing' the Replisome"

Farzaneh Tondnevis1, Richard Gillilan2, Linda B. Bloom1 and Robert McKenna1

1Department of Biochemistry and Molecular Biology, University of Florida
2Cornell High Energy Synchrotron Source, Cornell University

Abstract: Clamp loader complexes bind and utilize ATP hydrolysis to load sliding clamps at the primer template junction to ensure processive DNA synthesis. Several X-ray crystal structures of the E. coli clamp loader containing δ', δ and three γ subunits have been determined, but they all lack the ψ and χ subunits that are essential for ssDNA binding protein interactions. In addition several crystal structures of the sliding clamps have also been determined in closed ring conformations. Discussed are our first steps towards using small angle X-ray (SAX) scattering to unraveling the dynamics of the clamp clamp-loader complexes. Presented will be structural insights of the complete E. coli gamma complex clamp loader that provides the location of the χ and ψ subunits and also implies the clamp loader undergoes structural ordering in the presence of ATP in readiness to bind the sliding clamp and DNA. Also presented will be a captured out-of-plane open conformation of the homodimeric E. coli β-clamp in the absence of clamp loader that provides insights into a possible hinge mechanism by which sliding clamps open to bind DNA. These preliminary findings show that it may be possible to use SAX scattering to follow the dynamics of the replisome.

"Studies of RNA folding and function in crowded environments"

Philip Bevilacqua
Penn State University

Abstract: In an effort to relate RNA folding to function under cellular-like conditions, we monitored the self-cleavage reaction of the human hepatitis delta virus-like CPEB3 ribozyme in the background of physiological ionic concentrations and various crowding and cosolute agents. We found that at physiological free Mg2+ concentrations, both crowders and cosolutes stimulate the rate of self-cleavage, but that in 10 mM Mg2+ (conditions widely used for in vitro ribozyme studies) these same additives have virtually no effect on the self-cleavage rate. SAXS experiments reveal a structural basis for this stimulation in that higher-molecular weight crowding agents favor a more compact form of the ribozyme in 0.5 mM Mg2+ that is essentially equivalent to the form under standard ribozyme conditions of 10 mM Mg2+ without a crowder. This finding suggests that at least a portion of the rate enhancement arises from favoring the native RNA tertiary structure. We conclude that cellular-like crowding supports ribozyme reactivity by favoring a compact form of the ribozyme, but only under physiological ionic and cosolute conditions.

"SAXS, NMR and Crystallography: Mechanism of Dimerization of a Glutamate Receptor Domain and the Structure of a Multidomain, Leptospira Protein"

Christopher P. Ptak,1 Ahmed H. Ahmed,1 Ching-Lin Hsieh,2 Yung-Fu Chang,2 and Robert E. Oswald1

1Department of Molecular Medicine, Cornell University
2Population Medicine and Diagnostic Sciences, Cornell University

Abstract: In the two systems that will be discussed, three-dimensional structures of individual domains were solved with either crystallography or NMR spectroscopy. We then used BioSAXS either to quantitate dimerization induced by experimental drugs or to determine higher order structures of multiple domains.

Glutamate receptors are the major excitatory neurotransmitter receptors in vertebrate brain and are involved in a variety of normal and pathological neuronal functions. These proteins function by binding glutamate in an extracellular domain and opening an intrinsic ion channel that allows cations to flow in and out of the neuron. Drugs targeted to a dimer interface extracellular ligand-binding domains have considerable potential for treating memory loss in diseases such as Alzheimer's. We are using BioSAXS to define the envelope of dimers of the ligand-binding domain and to quantitate dimer formation in the presence of a variety of drugs. The approach has provided new insights in to the mechanism of action of these drugs.

Leptospira bacteria are a genus of spirochete with pathogenic species that can infect and cause leptospirosis in humans. Reemerging in the United States, leptospirosis is a neglected tropical disease that can prove fatal. In an initial step toward infection, virulent species attach to proteins found in the extracellular matrix through surface exposed adhesins. Lig proteins are Leptospira-specific adhesins that aid the spirochetes in attaching to the host epithelial cells during infection, thereby playing a critical role in virulence. One of these proteins, LigB, consists of a series of twelve immunoglobulin-like domains. We determined the structure of one of these domains with NMR spectroscopy and have obtained envelopes of a series of dimeric and tetrameric forms using BioSAXS. The initial results suggest that the protein forms a relatively rigid structure most likely defined by the interaction between domains.

"All-Atom Macromolecular Model Refinement via Combined Fit of NMR and SAXS Data"

Alexander Grishaev
National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK), National Institutes of Health

"A combined NMR and SAXS approach to study challenging complexes in translation initiation"

Sabine Akabayov
Biological Chemistry and Molecular Pharmacology, Harvard Medical School

Abstract: Understanding the function and dynamics of biological macromolecules requires knowledge of their 3D structure. Multidimensional Nuclear Magnetic Resonance (NMR) is a versatile biophysical technique providing information about structure, dynamics, and intermolecular interactions at atomic resolution. However, structure determination by NMR has an upper size limit of currently around 50 - 70 kDa and collection of long range distance information can be difficult depending on the sample. SAXS is an ideal complementary method to NMR as it is not limited by size or isotope labeling and does not require backbone assignment.

One major focus in the Wagner lab is the study of translation initiation. The control of translation (mRNA encoded protein synthesis) is crucial for cell proliferation and differentiation. More than ten eukaryotic translation initiation factors are known to be involved in the assembly of the 80S ribosome-RNA complex enabling placement of the initiator Met-tRNA at the correct start codon of the mRNA. We have used SAXS to study the formation of the complexes between initiation factors eIF5 and eIF2ß as well as the complex between eIF4G and eIF4A to support inconclusive data and overcome size limitations.

The combination of SAXS and NMR can unravel the change in macromolecular structure under modified environmental conditions. For example, we showed that SAXS provides a useful tool to show the effect of macromolecular crowding on the structure of proteins.