ACA 2012

Boston, MA, USA, July 2012
www. amercrystalassn.org
taken from ACA RefleXions, Fall 2012

Exciting Structures

Speakers in Exciting Structures. Front row: Hua Li, Jason Stagno, Sozanne Solmaz, Sung-il Yoon, Dinesh Yernool. Back row: Eric Armstrong, Dirk Zajonc, Douglas Davies, Charles Dann, Graeme Conn.

J. Stagno (NCI) described the first RNA supercoil structure ever observed. As in most nucleic acid-containing crystals, the double-stranded RNA duplexes form pseudo-continuous helices. However, Stagno's helices adopt a coiled-coil plectonemic RNA supercoil, mediated by the RNA binding protein NusB. This remarkable structure provides novel insights into high-density nucleic acid structures, suggesting how protein-mediated RNA supercoiling may facilitate the packaging of viral RNA genomes.

D. Yernool (Purdue) presented studies of a DNA-protein complex from a bacterial two-component signal transduction system, shedding light on the mechanism by which the phosphorylation signal is communicated, the role of interdomain surfaces in regulation of gene expression, and the basis of the increased affinity of activated RRs for DNA.

D. Davies (Emerald Bio) described the first structure of an in vitro evolved 'SOMAmer' (slow off-rate modified aptamer) in complex with its protein target. SOMAmers expand the chemical diversity of nucleic acids through incorporation of modified groups such as amino acid-like side chains. This SOMAmer binds its target protein (a growth factor) through shape complementarity and hydrophobic interactions, mimicking the interaction of the target protein with its receptor. The structure may help identify high-affinity ligands for proteins that are recalcitrant to selection using standard nucleic acids.

S. Solmaz (Rockefeller U.) described her ambitious effort to model the transport channel of the nuclear pore complex. Her model of the entire transport channel, a 12.3 MDa complex, adhered to its overall shape and symmetry determined by electron microscopy, accounts for the remarkable range of pore dynamics necessary for the accommodation of a wide variety of cargo sizes. Her movie showing the contraction of the channel's ring diameter from ∼40 nm to ∼20 nm, with a concomitant 150% increase in height from 4 nm to 6 nm, was a session highlight.

H. Li (UT Southwestern Medical Center) presented recent studies of the sodium/calcium exchanger (NCX) and a welcome foray into the field of electrophysiology. Li finds one Ca and three probable Na binding sites clustered at the center of the outward-facing NCX from Methanococcus jannaschii, and two channels where extracellular ions could gain access to these sites. S. Yoon (Kangwon National U.) presented the first and only structure of a toll-like recepter (TLR) bound to a ligand, the D1-D2-D3 domain of Salmonella flagellin. Rearrangement of a protruding loop within TLR facilitated flagellin accommodation within the binding pocket and resulted in subsequent dimerization of the complex via the receptor's C-terminal tails, allowing downstream activation to ensue.

D. Zajonc (La Jolla Inst. for Allergy and Immunology) focused on glycolipid antigen recognition by type 1 versus type 2 natural killer T (NKT) cells. Many of the key residues responsible for T-cell recepter (TCR) binding were shown to be conserved in other known sulfatide-reactive TCR's, suggesting a common structural modality that enables recognition of this class of self-antigens.

C. Dann III (Indiana U.) talked about the potential of novel antifolates to target the human folate receptor (hFR) and extend this class of therapeutics into a new generation of cancer treatments. Dann described a membrane-anchored protein in its apo form and with folates and antifolates bound and at acidic and neutral pH. By designing drugs whose sole entry into cells occurs via the hFR endocytic pathway, they hope to circumvent the dose-limiting toxicity of traditional antifolates.

Enzyme Mechanisms

Speakers in Enzyme Mechanisms. Zachary Wood, Eric Montemayor, Karen Allen, Nicholas Silvaggi, Adrian Goldman, Hideki Aihara, Rebecca Page and Xiaojing Yang. Inset: Catherine Drennan.

C. Drennan (MIT) described the long-awaited structure of the protein components required for the methyl transfer from folic acid (vitamin B9) to vitamin B12, a reaction necessary for acetogenesis. Her structure revealed the conformational changes required for the methyl transfer between these B vitamins. H. Aihara (U. of Minnesota) discussed a eukaryotic DNA repair enzyme TDP2 that plays a critical role in resistance to DNA damage, and is a potential drug target for chemotherapy. The structure of TDP2 and the mechanism of its substrate recognition have been elusive. The Aihara laboratory determined the structures of TDP2 in the presence and absence of DNA substrate. TDP2 has a narrow groove that selectively accommodates the 5′-terminus of a single-stranded DNA, a novel mode of DNA binding. R. Page (Brown U.) discussed how ser/thr phosphatases (PSP) achieve specificity in the cell. Although more than 420 genes in the human genome encode for serine/threonine kinases, less than 40 genes encode for PSPs. Most PSPs are tightly regulated by their interaction with targeting and inhibitor proteins. Page described her PP1:targeting and CN:inhibitory protein complexes, showing PSP interacting proteins direct PSP activity via inhibition of substrate sites rather than the active site. E. Montemayor (UT Health Science Center-San Antonio) discussed the intron debranching enzyme (Dbr1) in complex with several RNA compounds that mimic the branchpoint structure in lariat RNA. A combination of cell-based functional assays, in vitro activity assays, inductively coupled plasma mass spectrometry and X-ray anomalous diffraction methods were used to support a new proposal for the mechanism of Dbr1, in which a dinuclear metal-binding center alternates between single and double metal ion configurations. The findings clarify the role of Dbr1 in retrotransposon and retrovirus replication, and suggest evolutionary relationships between retrotransposons, retroviruses and pre-mRNA splicing.

X. Yang (U. of Chicago) uses temperature to trap reaction intermediates in phytochromes that convert a light signal into a biological signal via reversible photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) states. Xiaojing used temperature-scan cryocrystallography on photoactive crystals of P. aeruginosa BphP (PaBphP). By applying a trap-pump-trap-probe strategy, they followed the progression of photoreaction in the crystalline state. The higher the pump temperature, the greater the structural relaxation and the further the reaction proceeds. Light-induced difference electron densities at ten temperatures were analyzed, from which three cryo-trapped intermediate structures in the Pfr-to-Pr photoreaction were delineated.

Investigations of two enzymes from family V of the ADCSF.

Z. Wood (U. of Georgia) showed that a large conformational change in a protein can be caused by a small allosteric effector. When the allosteric inhibitor UDP-α-D-xylose binds to the active site of human UDP-α-D-glucose-6-dehydrogenase (hUGDH), the active hexamer is converted into an inactive U-shaped complex, supporting an evolutionary model in which catalytic efficiency is sacrificed to select for unstable hexameric complexes. Combining biochemical and sedimentation velocity studies, Wood finds apo-hUGDH to be a tipping point between the active and inactive states. Apparently, nature selected for a conformation that is suboptimal for catalysis in order that the small chemical difference between the allosteric inhibitor and the substrate can be a conformational switch.

A. Goldman (U. of Helsinki) presented the first sodium-pumping inorganic pyrophosphatase structure, an integral membrane protein from T. maritima (TmPPase). TmPPase has 16 transmembrane helices, all of which extend up to 20 Å above the membrane surface on the cytoplasmic side. An inner ring of six helices forms the hydrolytic centre, coupling the channel to a gate (just below the membrane) and the exit channel.

N. Silvaggi (U. of Wisconsin-Milwaukee) discussed bioinformatic analysis of enzymes in the acetoacetate decarboxylase superfamily (ADCSF), and identification of families having active-site architectures distinct from the prototypical decarboxylases. Members of this family have a new type fold and aldolase activity.

Structural Enzymology - Biology

Speakers in Structural Enzymology. Front row: Cynthia Stauffacher, Flora Meilleur, Celia Goulding, and Philip Anfinrud. Back: Savvas Savvides, David Jeruzalmi, Sean Froese, Brandt Eichman, William Royer, Zachary Wood. Inset: Liang Tang.

P. Anfinrud (NIH) revealed the power of ultrafast time-resolved SAXS/WAXS technology to observe real-time protein conformational changes in solution. He described changes in protein size and shape as photoactive yellow protein (PYP) underwent a photoactivated signaling-state transition. The transition involved a structural change that cannot be accommodated in protein crystals but can be detected by time-resolved Laue crystallography studies in which the PYP chromophore changes from a red-shifted to a blue-shifted spectroscopic intermediate. A water molecule penetrates into the interior of the protein where it forms hydrogen bonds that temporarily block the ground state recovery of PYP. The ability to track large-amplitude structural changes in solution via time-resolved SAXS/WAXS is proving to be a powerful complement to time-resolved Laue diffraction studies.

Ribbon representation of the BARF1:hCSF-1 complex. Hexameric BARF1 binds three hCSF-1 dimers. The oligo-mannose type glycan structures are shown in stick and surface representation. Adapted from Elegheert et al. (2012), Nature Structural and Molecular Biology (doi 10.1038/nsmb.2367).

S. Savvides (Ghent U.) used biophysical and crystallographic approaches to reveal the mechanism by which the viral decoy receptor BARF-1 from the Epstein-Barr virus hijacks our immune system. Savvides found that viral BARF-1 binds CSF-1 at an epitope far from that of the cognate human receptor and locks CSF-1 into a conformation that is unable to bind and signal via the cognate receptor.

C. Goulding (U. California-Irvine) discussed contact dependent growth inhibition (CDI) systems of gram-negative bacteria. CDI occurs when the C-terminal tail of CdiA, CdiA-CT, a toxic protein, is translocated into a target cell to inhibit growth. Related bacteria express immunity proteins (CdiI) that neutralize the CdiA-CT proteins. Goulding's structures of two CdiA-CT/CdiI complexes show that the CdiA-CT toxins are structurally similar, despite very low sequence conservation. However, one is a tRNase and the other a Zn²⁺-dependent DNase. In contrast, the CdiI's are nonhomologous structures, showing that the immunity factors have distinct origins in evolution.

D. Jeruzalmi (Harvard U.) described the nucleotide excision repair pathway (NER) in bacteria, the DNA damage sensor from the NER pathway, and how the sensor may identify the presence of UV damage on DNA. Three crystal structures of various components in the pathway, combined with known biochemistry, provide details of early steps of NER. DNA (native and damaged) is sampled by the open form of UvrA, and sampling involves closing around the DNA to sense its shape. Native DNA passes this airport-style 'pat-down' and is released. Damaged DNA fails the test, and is shunted to the damage-specific stages of the pathway.

B. Royer (U. Mass Medical School) used time-resolved crystallography and meta-analysis of 70 structures to follow cooperative conformational change in the dimeric hemoglobin HbI and reveal the role of water molecules in facilitating the transition between R and T states, in which the helices of the different subunits undergo a scissoring motion to facilitate the cooperative transition between states. B. Eichman (Vanderbilt U.) revealed how the DNA repair enzyme AlkD adopts an unusual conformation that exposes alkylated purines and facilitates base excision, despite the absence of a direct chemical contact between the enzyme and the labile glycosidic bond, a nice explanation of how the DNA itself can facilitate catalysis in a DNA repair enzyme.

F. Meilleur (North Carolina State U.) described IMAGINE, a high-intensity neutron diffraction beam line that will begin operations next spring at ORNL. Flora discussed neutron diffraction studies of xylose isomerase, an enzyme of interest to the biofuel community. L. Tang (U. Kansas) explained how the bacteriophage Sf6 accomplishes the difficult task of packaging DNA into the viral capsid. The terminase is a large protein complex that pumps DNA through the portal protein channel into the capsid, powered by ATP hydrolysis. The terminase small subunit called gp1 assembles into a ring-like octamer and binds the DNA in nucleosome-like fashion, to select viral DNA for packaging. S. Froese (U. Oxford) described details of glycogen biosynthesis, including how the glycogen core protein, glycogenin, nucleates the synthesis by forming a covalent Tyr-glucose bond, and how conformational changes in the catalytic core of the protein and the growing maltosaccharide chain are important to the reaction. He also proposed a mechanism for the glycogen storage disorder XV in which Thr83Met mutation locks the enzyme in a conformational state that is not catalytically competent to initiate glycogen biosynthesis.

Functional Nanomaterials

Speakers in Functional Nanomaterials. Alamgir Karim, Detlef Smilgies, Volker Urban, Kevin Yager and Tad Koga.

Speakers in this session described the study of electronics, piezoelectrics, photo-voltaics and other nano-materials using various techniques including grazing-incidence methods (GISAXS, GIWAXS, and GI-XPCS) that measure thin films.

A. Karim (U. of Akron) described the use of localized but moving hot bands (zone annealing) to control block-copolymer (BCP) nanoscale morphology. Zone annealing can enhance ordering kinetics and orient microphases. Karim demonstrated that extremely sharp thermal gradients enable better control of order and orientation. Optimized annealing can maintain a vertical orientation for the BCP cylinder phase in films up to 1000 nm thick. The process was further refined by adding a polymer (PDMS) capping layer to the thin film being zone annealed. This flexible layer induces in-plane shearing at the film-PDMS interface and is dubbed 'soft-shear' that induces alignment of the BCP layer over the entire macroscopic dimensions of the sample. This remarkable ordering was confirmed using AFM images and GISAXS analysis.

D. Smilgies (CHESS) presented GISAXS and GIWAXS studies of the ordering of thin films, including in situ measurements conducted during film formation. The assembly of oleic acid-coated PbS spheres from solution into films was pathway-dependent. The solvent evaporation rate affected assembly and could be tuned continuously between FCC and BCC superlattices. Shape anisotropy of spherical nanoparticles drove rearrangement of the superlattice; the particles become oriented within the lattice, as confirmed by WAXS measurements. Process history (solvent evaporation, temperature and annealing history, shear etc.) plays an important role in determining the final nanostructure order of thin-film nanomaterials with potential industrial applications.

Macromolecular Science with Scattering Methods

Speakers in Macromolecular Science with Scattering Methods. Front: Tobin Sosnick, Angela Criswell, Rick Russell, Mark Del Campo; back: Kwaku Dayie, Xianyang Fang, Osman Bilsel, Michal Hammel, Xiaobing Zuo.

Solution X-ray scattering (SAXS) has become a major tool for structural biology, brought about by the development of high-flux X-ray sources, large area detectors, and data analysis methods and programs. T. Sosnick (U. Chicago) found that single-molecule fluorescence resonance energy transfer (smFRET) and SAXS produce divergent views of the unfolded states at low denaturant concentrations. SmFRET experiments suggest the chemically unfolded proteins invariably collapse from random coil to more compact dimensions as the denaturant concentration is reduced, while SAXS experiments suggest that such compaction may be rare. The possible cause of this discrepancy was discussed.

R. Russell (U. Texas-Austin) described the interactions between unstructured RNAs and DEAD-box ATP-dependent chaperones that can unwind short helices in structured RNAs and refold the kinetically trapped intermediates.This flexible positively charged tail interacts non-specifically with nucleic acid, tethers the protein to the structured RNA and directs the chaperone protein toward helical unwinding.

X. Fang (NCI-Frederick) described an HIV Rev response RNA element (RRE RNA), that binds to Rev protein to export viral genes from the nucleus to the cytoplasm, which overwhelms the host's defenses. Two Rev protein binding sites, 60 Å from one another, foster oligomerization of Rev proteins for viral gene export. T. K. Dayie (U. Maryland,) described SAXS and NMR studies of SAM-riboswitch RNAs, in which the Shine-Delgano sequence is buried in a pseudo-knot conformation in the apo-form and exposed in the bound form to allow gene expression.

M. Hammel (LBNL) described the highly automated BioSAXS setup and services provided at the SIBLYS beamline FOXS, a program that calculates scattering profiles using the Debye formula. O. Bilsel (U. Mass) described a continuous turbulent flow-based time-resolved BioSAXS setup with BioCAT at Argonne that allows observation of early stages of biomolecular folding processes that would be inaccessible by stopped-flow techniques. M. Del Campo (Rigaku Americas) described a home laboratory SAXS instrument with focusing optics that provides usable data in 5 min to 2 hours with reasonable signal-to-noise.

Complementary Techniques in Structural Biology

Speakers in Complementary Techniques in Structural Biology. Front: David Case, Allan Pang, Arwen Pearson, Allen Orville; back: Joseph Yarbrough, Dagmar Ringe, Lesa Beamer, Edward Snell, Nozomi Ando. Inset: Agnesa Shala.

D. Case (Rutgers U.) described extending molecular dynamics simulations from individual molecules to crystal lattices for small peptides and showed clear potential to improve solvent modeling in macromolecular structures. A. Orville (BNL) showed how combining single-crystal spectroscopy, diffraction and X-ray fluorescence was providing a picture of nitrogen fixation in root nodules. J. Yarbrough (U. Florida), an undergraduate recipient of an ACA Travel Award, used circular dichroism and differential scanning calorimetry to follow the unfolding of a viral capsid induced by pH variation. N. Ando (MIT) used SAXS, X-ray crystallography, electron microscopy and analytical ultracentrifugation to show that ribonucleotide reductase existed as a mixture of transient species with distributions modulated by allosteric effectors. Each technique supported evidence from the others and provided unique information, completing the overall picture of the structural mechanism.

Combining structural information with theoretical predictions of perturbed titration curves for individual amino acids, D. Ringe (Brandeis U.) showed how residues outside the active site can control reactivity. Lesa Beamer (U. of Missouri) combined NMR and crystallographic information into context and to better understand connections between structure, dynamics and catalysis in phosophohexomutase. Etter lecturer A. Pang (Queen Mary U.) discussed bacterial metabolosome structures formed from hexagonal-shaped tiles made up of different protein subunits. A. Shala (York U.) presented bioinformatic approaches combined with affinity pull-down assays and mutagensis to study periplasmic proteins linked to antibiotic resistance in human pathogens.

Important Science from Small Molecule Structures

Speakers in Important Science from Small Molecule Structures. Larry Falvello, Alberto Albinati, Lawrence Dahl, Mike Hall, Bruce Foxman, Alan Pinkerton, Lee Daniels, Silvia Chiara Capelli, Mark Bowden.

The focus of this session was cluster chemistry, hydrogen storage, topotaxy, displacement parameters, experimental and theoretical electron densities, and reaction mechanisms. L. Dahl (U. Wisconsin) addressed complex bonding questions in his family of Pd clusters, such as the stabilizing influence of an inert electron pair in Tl(I)/Pd(0) compounds. M. Bowden (Pacific North West National Laboratory) discussed boron adducts which have a greater mass density of hydrogen (∼140 g/l) than does liquid H₂ (∼70 g/l). M. Hall (Texas A&M) adressed quantum chemistry and structural aspects of reaction mechanisms in transition metal complexes. He described density functional theory (DFT) as a free lunch, because the quality of the results obtained from properly used DFT is disproportionate to the relative ease with which the calculations can be done. He pointed out that it is possible to get variable results using different functionals and cited a case of an intermediate predicted by DFT, though not experimentally observed. A Pinkerton (U. of Toledo) provided a bridge between theory and high-resolution diffraction analysis with a charge-density study of croconic acid, a high-density organic (ρ = 1.912 g/cm³) which is ferroelectric at and above room temperature. The charge-density analysis explained the intermolecular interactions observed in croconic acid. S. Capelli (Inst. Laue-Langevin) described several applications of normal-mode analysis from mean-square atomic displacement amplitudes, including applications to urea and sucrose, for which the results agree with data from terahertz spectroscopy. Capelli emphasized the distinguishing characteristics of neutron diffraction; elemental contrast distinct from that of X-ray diffraction, scattering lengths independent of resolution, and hydrogen scattering, so much more powerful than scattering by electrons. B. Foxman (Brandeis U.) described thermally induced topotactic reactions and the method of establishing the geometrical relationship between different phases oriented under the same conditions without removing the crystal from the diffractometer.

Cool Structures

Speakers in Cool Structures. Front: Ying-Pin Chen and Elena Forcen-Vazquez, back: Allen Oliver, Lorraine Malaspina, Kevin Gagnon, Faye Bowles, Chun-Hsing Chen, James Hall, Xiaoping Wang.

J. Hall (U. Reading, UK) described DNA intercalation by Ru complexes in a variety of bonding modes. Both Delta and Lambda forms of the complex were found to interact with DNA decamer chains in each of three bonding modes. E. Forcen-Vazquez (U. of Zaragoza) discussed polymeric diversity in copper citrate complexes ranging from one-dimensional chains to three-dimensional extended networks, some of which are single-molecule magnets. Hydration can affect the polymer formation and produce different networks. J. Chen (Indiana U.) synthesized large cyclic structures, cyanostars, from cyano-stilbene, that have cavities suitable for capture of anions of specific sizes. Having five-fold symmetry, these cyanostar complexes pose crystallographic challenges, including disorder. Chen demonstrated how this disorder was resolved.

K. Gagnon (Texas A&M) described one-dimensional inorganic-organic hybrid materials (alkylbisphosphonic acids and zinc acetate), in which chains of tetrahedral zinc atoms cross-linked by octahedral metal atoms form nanometer-size one-dimensional tunnels filled with disordered solvent molecules. The channel size and shape are sensitive to small variations of zinc site occupancy. L. Malaspina (U. Fed Goias) discussed analysis of the disordered structure of a coumarin ester of ambiguous space group. Y.-P. Chen (Texas A&M) discussed controlling the topology of metal organic framework (MOF) structures by changing the molar ratios of the reaction precursors in solution and changing solvent combinations. Chen provided several examples of different MOF frameworks composed of the same building blocks. F. Bowles (UC Davis) discussed cleavage of metal-metal bonds by reaction of metal-metal bonded carbonyl complexes with C₆₀ to produce a new metal-fullerene adduct.

Magnetic Materials

Speakers in Magnetic Materials. Ovidiu Garlea, Ashfia Huq, Susan Herringer, Simon Parsons, Timothy Munsie, John Greedan, Dimitry Khalyavin.

Sponsored by Materials, Neutron and Powder SIG, this session featured materials synthesis, molecular magnets studied under pressure and three different families of compounds which have exciting magnetic properties. J. Greedan (McMaster U.) discussed short- and long-range magnetic order observed in vacancy ordered/disordered perovskite structures. D. Khalyavin (ISIS) described exchange topology in the hexagonal lattice system RBaCo₄O₇, where geometrical frustration gives rise to varied degrees of spin correlation. O. Garlea (ORNL) described the effect of oxygen doping on the structural and magnetic properties of delafossite compounds. The session included studies of molecular-based magnets under pressure, effects of random exchange in ferromagnetic copper chloride chains, and studies of single-crystal holmium titanate.

Prions, Amyloids and 'Friends'

Speakers in Prions, Amyloids and 'Friends'. Front: Christopher Stanley, Gerald Stubbs, William Wan, Hiromi Arai; back: Joseph Orgel, Robyn Stanfield, Sankar Naravan Krishna, Wenji Zheng.

Prions and amyloids are the root cause of or directly associated with systemic and neurological diseases such as Alzheimer's, Parkinson's and Huntington's. J. Orgel (Illinois Inst. of Tech.) provided a brief overview of pathological fibril-forming peptides. C. Stanley (ORNL) presented a time-resolved neutron scattering study of the aggregation kinetics of huntingtin amyloid precursors, revealing a clear distinction between the wild-type and pathological forms of the protein. Using fiber diffraction, Etter Lecturer W. Wan (Vanderbilt U.) detected structural polymorphism in the fungal prionizable element HET-s. When fibrils from this peptide are formed at pH 7.5 they do not display infectious qualities. Fibrils formed at pH 2 do. Significant degradation occurs at low pH, which may well account for the different (and infectious) structure of the HET-s fibrils.

Materials for a Sustainable Future

Speakers in Materials for a Sustainable Future. Front: Andrey Yakovenko, Christopher Cahill, Debasis Banerjee, Greg Halder; back: Winnie Wong-Ng, Hong-Cai Zhou, Karena Chapman, Fernando Uribe-Romo.

The symposium provided an overview of neutron and X-ray scattering studies on materials that address key energy-related problems. H.-C. Zhou (Texas A&M) designed and characterized selective metal-organic frameworks (MOFs) for carbon capture. Carbon capture in MOFs was also addressed by D. Banerjee (Rutgers U.) and W. Wong-Ng (NIST). Studies of uranium-bearing hybrid materials relevant to nuclear energy were presented by C. Cahill (George Washington U.), and K. Chapman (ANL) described a MOF-based trap for hazardous by-products of nuclear energy production. F. Uribe-Romo (Cornell U.) presented his work with porous covalent organic frameworks (COFs), including highly ordered COF thin films for organic photovoltaic devices.

S. Chundawat (Michigan State U.) described a biomass-to-biofuel conversion process, an important route to energy sustainability. Anhydrous liquid ammonia pretreatment reorganizes the hydrogen-bonding network in the crystalline structure, giving the biomass improved enzymatic deconstruction efficiency. H. O'Neill (ORNL) discussed development of a biohybrid photoconversion system that combines natural photosynthetic apparatus with synthetic block copolymers to expedite solar energy conversion. M. Everett (ORNL) described neutron powder diffraction studies of seafloor methane hydrates. She suggests that formation of carbon dioxide hydrates could release methane as an energy source and simultaneously reduce carbon dioxide in the environment. J. Cole (U. of Cambridge) quantified structure-property relationships of materials for dye-sensitized solar cells.

N. Chernova [Binghamton U./Northeastern Center for Chemical Energy Storage (NECCES)] studies atomic-scale processes which govern electrode function in rechargeable batteries (EFRC), using pair-distribution function (PDF) analysis, X-ray absorption spectroscopy, electron microscopy, Li NMR and magnetic properties. O. Borkiewicz (ANL/NECCES) examines the spatial evolution of electrochemical reactions and reaction fronts using in situ X-ray PDF analysis. C. Bridges (ORNL) described his studies of disorder and defects in Li-ion cathode materials.

Diffraction Studies of Animals, Plants and Insect Bodies

Speakers in Diffraction Studies of Animals, Plants and Insect Bodies. Rama Sashank Madhurapantula, Barbara Brodsky, Dan Kirschmer, Joseph Orgel, Jeff Deschamps, Olga Antipova, Tom Irving, Li-Kai Liu and Simon Goodson.

The session focused on studies of animal, plant and insect connective tissues while they were still principally intact. B. Brodsky (Tufts U.) reviewed the history of collagen studies, from early investigations of its helical symmetry through studies of collagen packing and fibril forms, noting the different methods used over the years. Several of the key investigators in the study of collagen and fibrous elements were present in the audience. Etter Lecturer S. Goodson (Cardiff U.) found agreement between the type I collagen packing structure he found in mouse tissue with that previously reported for rat type I collagen packing structure, a model organism specifically suited to the study of human diabetes. D. Kirschner (Boston College) combined X-ray and neutron diffraction of rodent nerve cells to differentiate between CNS and PNS nerves. The scans of rodent nerves, which showed clear and recognizable myelin diffraction, may lead to routine detection of differences in nerve structure, distinguishing pathological from normal conditions.

Complementary Methods

Speakers in Complementary Methods. Jacqueline Cherfils, Christopher Dettmar, Michel Fodje, Julien Cotelesage, Catherine Lawson, Stephen Tomanicik, Shyamosree Bhattacharya, Filip Van Petegem.

F. Van Petegem (U. British Columbia) combined electron microscopy reconstruction maps and single-crystal X-ray structural models to investigate malignant hyperthermia and cardiac arrhythmias. Comparisons between wild-type and mutant ryanodine receptor models revealed that mutations lead to premature and prolonged opening of the calcium channels, resulting in abnormal calcium release. C. Lawson (Rutgers U.) described the EM Databank, a unified data resource for three-dimensional electron microscopy and a one-stop shop for EM-related data, and the tools for depositing, accessing and visualizing EM-related data. S. Tomanicek (ORNL) described progress with the X-ray structure determination of a metallochaperone-like domain of mercuric reductase (MerA). The MerA structure has two arms with conserved -SH groups, which bind mercury and transfer it to the core for catalysis. J. Cherfils (Centre National de la Recherche Scientifique) described the structure and dynamics of Arf GTPases, important regulators of exo- and endocytocis. A combination of SAXS, NMR, immune-labelling electron microscopy and tryptophan fluorescence revealed structure-based functional differences between Arf1 and Arf6. Etter Lecturer C. Dettmar (Purdue U.) described an instrument for integrating second-order nonlinear imaging of chiral crystals (SONICC) and two-photon excited ultraviolet fluorescence imaging (TPE-UVF) with a synchrotron X-ray diffraction beam line. By combining SONICC and TPE-UVF, the capabilities for imaging tiny crystals with a high depth of field are significantly improved over existing methods. J. Cotelesage (U. Saskatchewan) described how X-ray absorption spectroscopy provides more accurate bond lengths between metals and their ligands than diffraction experiments, as well as information about the oxidation state of metal ligands that is not available from diffraction experiments. He described efforts to integrate online X-ray absorption spectroscopy and diffraction at the Canadian Light Source. S. Bhattacharya (U. Wisconsin-Madison) described how X-ray structure determination of wild-type and mutant phytochrome is guiding protein engineering efforts to design a smaller, more compact and more stable fluorescent phytochrome biomarker.

Local Structure and Partially Ordered Systems

Speakers in Local Structure and Partially Ordered Systems. L to R: Branton Campbell, A. M. Abeykoon, Breaunnah Bloomer, Elena Aksel, Daniel Shoemaker, Katharine Page, Mikhail Feygenson and Claire Saunders. (Absent: Co-chair Thomas Proffen.)

Real space maps of static Bi displacements in insulating Bi₂Ti₂O₆O′ and metallic Bi₂Ru₂O₆O′ are viewed along (top) and normal to (bottom) the O-Bi-O bond. Static disorder in both produces hexagonal ring or disk shapes centered on the ideal position, with striking differences in displacement magnitude. D. P. Shoemaker, R. Seshadri, M. Tachibana and A. L. Hector, 'Incoherent Bi off-centering in Bi₂Ti₂O₆O and Bi₂Ru₂O₆O: insulator versus metal', Phys. Rev. B, 84, 064117 (2011).

(Top) A TEM image of ∼100 nm Au nanoparticles. Black dots are the nanoparticles on the grid and the large white areas are the holes in the grid. (Middle) A background-subtracted electron diffraction image, collected from the same region of the sample using 200 keV electrons. (Bottom) The one-dimensional electron diffraction pattern obtained by integrating around the diffraction rings. The inset shows a magnified region of the integrated electron diffraction pattern, as indicated by the dotted lines. M. Abeykoon, C. D. Malliakas, P. Juhas, E. S. Bozin, M. G. Kanatzidis and S. J. L. Billinge, 'Quantitative nanostructure characterization using atomic pair distribution functions obtained from laboratory electron microscopes', Z. Kristallogr. 227, 248-256 (2012).

D. Shoemaker (ANL) demonstrated how data-driven reverse Monte Carlo simulations can create large-box models to capture atomic disorder in complex materials while separate constraints (PDF, Bragg, bond valence) can be satisfied simultaneously. Among his examples were complex oxides, crystal growth, and semiconducting chalcogenides. M. Abeykoon (BNL) showed that, using the pair distribution function (PDF), data of sufficient quality for quantitative analysis of nanoparticle structures can be obtained with a transmission electron microscope (TEM). The ease of data collection and ubiquity of TEMs could make this an important tool in the characterization of nanostructured materials if the barriers to data processing can be overcome. B. Campbell (Bringham Young U.) fits local structure models to three-dimensional volumes of single-crystal X-ray diffuse scattering data in relaxor ferroelectrics. He discussed Huang scattering from point defects that produce long-range distortion fields in the surrounding material, which Campbell explained were, 'much like those that troubled the sleep of the princess in the story of The Princess and the Pea' (!). M. Feygenson (ORNL) related how PDF analysis can provide quantitative information about the local arrangement of atoms, enabling studies of defects, surface relaxation and local disorder in nanomaterials. Etter Lecturer E. Aksel (U. of Florida) discussed local deviations from the average structure of Na_0.5Bi_0.5TiO₃ ferroelectric ceramics. Undergraduate B. Bloomer (LANL/Howard U.) demonstrated local structural changes occurring during geopolymerization synthesis, and undergraduate C. Saunders (ORNL/Duquesne U.) discussed instrument resolution effects on PDFs.

In situ Parametric Studies

Speakers in In situ Parametric Studies. L to R: Antonio dos Santos, Scott Misture, Kamila Wiaderek, Garrett Granroth, Dermot O'Hare, Mario Wriedt, Peter Khalifah. Inset: Xiang-quiang Chu.

D. O'Hare (Oxford U.) has designed a custom-built cell that allows the study of reactions in situ, using energy-dispersive and monochromatic X-rays. The flux growth of Bi₅Ti₃Fe_(1−x)Mn_xO₁₅ Aurivillius phase under different experimental conditions was monitored and it was observed that product formation is preceded by the formation of an intermediate phase. M. Wriedt (Texas A&M) described a copper-based metal-organic framework material containing neutral nitrogen-rich moieties, for which a single reaction led to the formation of three crystal forms of different hydration states. The crystal and hydration states are interchangeable and dependent on temperature and humidity, and water content alters magnetic properties. G. Granroth (ORNL) used the Sequoia time-of-flight spectrometer at the Spallation Neutron Source to determine the magnetic structures of two high-field magnetic phases of MnWO₄, a multiferroic material with a magnetic phase diagram of at least six phases.

S. Misture (Alfred U.) described in situ studies of transition metal oxides with potential applications in fuel cells. Electrochemical activity was monitored at high temperatures and under controlled atmosphere, mimicking the operation environment of fuel cells. P. Khalifah (SUNY Stony Brook) discussed degradation of LiFeBO₃, a high-capacity battery material. The crystal structure was redetermined based on a four-dimensional modulated space group C2/c(1/200)00. It was found that modulation hindered Li mobility and that the performance of LiFeBO₃ can be improved by reducing this modulation. K. Wiaderek (ANL) studied the structure and size of nanoparticles in iron-based battery materials under operational conditions. A ripening of the nanoparticles observed upon cycling may contribute to observed performance degradation.

X.-Q. Chu (ORNL) discussed the use of quasi-elastic neutron scattering to study the relaxational dynamics of hen egg white lysozyme and an inorganic pyrophosphatase. The slow dynamics of these globular proteins could be adequately modeled by the mode-coupling theory that predicts a logarithmic decay of the relaxation time.

From Constructs to Crystals

Speakers in From Constructs to Crystals. Front: Eric Ortland, Zygmunt Derewenda, David Waugh and Miki Senda; Glen Spraggon, Todd Green, Nicholas Noimaj, Patrick Shaw Stewart and George Lountos.

This session addressed membrane protein expression, purification and crystallization (N. Noinaj, NIDDK /NIH), using the maltose binding protein as a fusion partner which has become a staple of protein purification (D. Waugh, NCI), the ins-and-outs of protein and nucleic acid production and crystallization (T. Green, U. Alabama), and enhancing the crystallizability of proteins via surface entropy reduction (Z. Derewenda, U. Virginia). Noted that replacing bulky hydrophobic residues with alanine may improve protein solubility and stability.

Functional Materials and Technology

Speakers in Functional Materials and Technology. Front: Elinor Spencer, Margot Fabian, Craig Bridges, and James Kaduk; back Emil Bozin, Tiffany Kinnibrugh, Hans-Conrad zur Loye, and Andrey Yakovenko. (Max Kaganyuk not shown.)

The high-pressure behaviour of the three-dimensional copper carbonate framework {[Cu(CO₃)₂](CH₆N₃)₂}_n by Elinor C. Spencer, Nancy L. Ross and Ross J. Angel, J. Mater. Chem. (2012), 22, 2074-2080, DOI: 10.1039/C2JM15206A, published online Dec. 2011.

The session began by looking at inorganic solids synthesized using high-temperature (fluxes) or hydrothermal (supercritical water) solvents. H. zur Loye (U. South Carolina) showed that metal hydroxides are very effective for the growth of high-quality mixed metal oxide single crystals. E. Bozin (BNL) showed by PDF techniques that Ir⁴⁺ dimers exist locally in Cu(Ir_1−xCr_x)₂S₄, even though long-range order is absent.

With high-pressure single-crystal studies, E. Spencer (Virgina Tech) showed that three-dimensional metal-organic hybrid materials can be as strong as zeolites.

T. Kinnibrugh (Texas A&M) used powder diffraction techniques to characterize the structural changes on dehydration of potentially nanoporous Zn phosphonate compounds. Combining X-ray and neutron PDF measurements and reverse Monte Carlo simulations, M. Fabian (LANL) showed that the glassy networks in MoO₃-Bi₂O₃-WO₃ systems are built up of distorted MoO₄ tetrahedra and mixed WO₃/WO₄ or BO₃/BO₄ structural units.

A. Yakovenko (Texas A&M) showed that structure envelope density maps can be used to determine the pore structure and locations of guest molecules in MOFs.

Membrane Proteins: Start to Finish

Speakers in Membrane Proteins: Start to Finish. Robert Stroud, Robert Fischetti, Vadim Cherezov, Eugene Chun, Tommi Kajander, Ehud Landau, and Nicholas Noinaj.

Membrane proteins that perform essential cellular functions are major drug targets and challenging candidates for structural analysis. Financial support for major initiatives has produced exciting structures of ion channels, G protein-coupled receptors, transporters and other membrane protein families. This session was devoted to persistent challenges in this important field. R. Stroud (UCSF) discussed expression systems for production of eukaryotic membrane proteins and his structure determination of components of a zinc pump belonging to a superfamily of membrane proteins.

About 15 years ago, E. Landau (U. of Zürich) and J. Rosenbusch (Biozentrum) began crystallizing membrane proteins using a greasy lipidic mesophase known as lipidic cubic phase (LCP). At the time, some considered this method to be revolutionizing, while others believing it would be a 'one-trick pony', suitable only for a specific class of proteins. The LCP crystallization method has contributed more than 100 membrane protein structures to the PDB, including 32 proteins from at least seven different families, including the highly challenging superfamily of G protein-coupled receptors. While it takes an effort to perfect LCP technologies, labs that took the plunge have been highly successful and the perspectives look bright for newcomers.

N. Noinaj (NIDDK) talked about nits and grits of his work on structural determination of components of a β-barrel assembly complex. Significant progress has been made during the last few years at synchrotron beamlines, allowing for data collection on ever smaller crystals of more challenging targets. R. Fischetti (GM/CA CAT, APS) described instrument developments of particular relevance to studies of membrane proteins, including a SONICC system for detection and alignment of optically invisible small crystals.

Etter Student Lecturer E. Chun (Scripps Research Inst.) developed a fusion partners toolchest for stabilization and crystallization of G protein-coupled receptors (GPCR). Chun described in detail the procedures followed to identify a fusion partner that would cocrystallize with GPCR and yield the best structure to date of a GPCR (1.8 Å resolution), The same fusion partner was used to determine a structure of the nociceptin/orphanin FQ opioid receptor.

T. Kajander (U. of Helsinki) described his studies of Na-pumping pyrophosphatase from Thermotoga maritima at 2.6 Å resolution in a resting state and with a bound product that shed light on the sodium pumping mechanism and suggested that the protein has evolved through gene triplication. The session including reports on the details of the structure determinations of five new membrane proteins was supported by contributions from Avanti Polar Lipids and TTP LabTech.

Pharmaceutical Research and Development

Speakers in Pharmaceutical Research and Development. Noa Marom, Matthew Peterson, Eugene Cheung, Eric Chan, Magali Hickey, Mark Oliveira, and Peter Wood. (Patrick Connelly not shown.)

P. Connelly (Vertex Pharmaceuticals) showed examples of combining crystallographic, computational and thermodynamic data to guide drug design. P. Wood (CCDC) presented an assessment of isostructurality in pharmaceutical salts, highlighting the lack of similarity and predictability between crystal structures of most sodium and potassium salts of drug-like molecules. E. Cheung (Amgen) illustrated the differences between thermal expansion, dehydration and form change using variable-temperature powder diffraction data. N. Marom (U. Texas, Austin) described advances in dispersion correction schemes employed in DFT computations, with case studies on several polymorphic systems. E. Chan (Bristol Meyers Squibb) discussed models of the diffuse scattering from single crystals of two aspirin polymorphs, highlighting the power of the diffuse scattering method in comparison to routine analysis of diffraction data. M. Oliveira (Alkermes) described the structure of an opioid modulator and a structural and computational analysis of closely related analogs.

Structure-Guided Drug Discovery

Speakers in Structure-Guided Drug Discovery. Front: Jaeok Park, Helen Berman, Shraddha Thakkar and Stephen Burley; back: Stefan Knapp, Gregg Crichlow, Alan Hruza, David Eisenberg.

S. Knapp (Oxford U./Structural Genomics Consortium) presented studies targeting epigenetic effecter domains of the bromodomain family. H. Berman (Rutgers U./PDB) described advances in data management of small molecule ligands, antibiotics and peptide inhibitors in the PDB. D. Eisenberg (UCLA) presented efforts to find small-molecule inhibitors of amyloid formation. A. Hruza (Merck Research Laboratory) explained how modest resolution X-ray structures of the aurora kinase catalytic domain allowed structure-based design of imidazo[1,2-a]pyrazine inhibitors.

Etter Lecturer S. Thakkar (U. of Arkansas) discussed her structure-based design of anti-methamphetamine single-chain antibodies.

Data Collection with the Pros

Speakers in Data Collection with the Pros. Andrew Torelli, Edward Collins, Zbigniew Dauter, James Holton and Raj Rajashankar.

The 'Blackboard' sessions at this year's meeting focused on best practices for data collection and included a real-time demonstration of data collection on SER-CAT's ID beam line at ANL (Z. Dauter, NCI), a discussion of critical sources of error found in crystallographic data that can make the difference between solvable and intractable data led by J. Holton (UCSF/BMB/PBD) and instruction on collecting data using the six million detectors that comprise the latest PILATUS X-ray detector arrays (R. Rajashankar, Cornell U.). Links to the Powerpoint slides and videos of the talks can be found on the ACA website. Click on the 'Jobs/Education' link at the top of the ACA home page and then click on the 'Blackboard Sessions' link under the 'A Crystallographer's Resources' section heading. Next year's Blackboard session will address structural validation.

Inorganic Phase Transitions

Speakers in Inorganic Phase Transitions: Stacey Smith, Marcus Bond, Elinor Spencer, Mario Bieringer, Patrick Mercier, Branton Campbell and Saurabh Tripathi.

P. Mercier (NRC, Canada) presented a systematic analysis of the layer-stacking polytypes available within the kaolin system. Ab initio DFT calculations of the energy and enthalpy of each polytype make it possible to rationalize the experimental phase sequence observed up to 60 GPa. E. Spencer (Virginia Tech.) discussed supercells, symmetries, superlattice reflections, volume changes and group-subgroup relationships in two high-pressure phases of the mineral petalite (LiAlSi₄O₁₀). S. Smith (Brigham Young U.) described two types of high-temperature surface area loss, the location of the La atoms in La-doped gamma-alumina nanoparticles and a potential mechanism for the La-stabilization of the gamma phase. M. Bieringer (U. of Manitoba) described phases in the Sc_1−xLu_xVO₃ perovskite family. He found that the smaller Sc cation results in a disordered bixbyite structure, while the larger Lu cation results in a perovskite phase. High-pressure stabilization of the Sc-rich perovskite phases made it possible to track the physical properties of the family across the boundary between stability and metastability. S. Tripathi (Central Michigan U.) discussed particle size influence on the ferroelectric polarization of YMnO₃. M. Bond (SE Missouri State U.) explained that, due to strong ligand-ligand interactions, it was concluded that CuBr⁴⁻ salts were incapable of forming the square-planar complex observed in some CuCl⁴⁻ salts. However, a square-planar to flattened-tetrahedral transformation has now been observed in 1,2,6-trimethylpyridinium salts of both CuCl⁴⁻ and CuBr⁴⁻.