08/02/2020: 4:00 PM
- 5:00 PM
The ACA holds three evening poster sessions. Poster sessions are organized by the Poster Chairs and feature presentations covering a range of crystallography topics. Poster presentations may not seem as prominent as oral presentations, but they offer a terrific opportunity to interact with other scientists in your field in a structured way.
Crystallization of novel polyglycine hydrolases found in the fungal response against plant defensive chitinases
Polyglycine hydrolases (PGH) are a novel class of enzymes that are secreted by fungal families in response to plant-fungal defense; a major component of which are chitinases that target the fungal cell wall without harming the plant. ES-chitinase modifying protein (ES-Cmp) and FS-chitinase modifying protein (FS-Cmp), are two identified PGHs of particular interest that are secreted by Epicoccum sorghi and Fusarium solani respectively. These proteases have a specificity for cleaving N-terminal to glycine-glycine bonds resulting in deactivated plant chitinases. Our work focuses on structure determination of these proteases for inhibitory studies. Despite minimal sequence and motif identity between ES-Cmp and FS-Cmp, both share analogous cleavage activity deviating only in specific glycine recognition. Crystal conditions have been confirmed for FS-Cmp and a native data set was collected to 2.0 angstroms. Current work is focused on crystallizing selenomethionine incorporated proteases to determine phases and solve the structures.
, University of Waterloo Waterloo, ON
, United States Department of Agriculture (USDA ARS) Peoria, IL
, United States Department of Agriculture (USDA ARS) Peoria, IL
, Dept of Biology, Univ of Waterloo
Recent advances in serial electron crystallography
Electron crystallography of three-dimensional nanocrystals (3D ED), also called MicroED, has known many successes in the last decade or so, with the development of new acquisition protocols. The introduction of these methods created new opportunities for structure determination, notably in the study of materials that do not form large well-ordered crystals. While 3D ED is conceptually similar to single-crystal x-ray diffraction (SCXRD), another hallmark of XRD techniques, serial crystallography, found little echo in the field of electron crystallography until recently. We proposed an implementation of serial electron crystallography in a scanning transmission electron microscope . The method consist in collecting still diffraction patterns from randomly-oriented nanocrystals dispersed on a TEM grid by shifting a parallel nanobeam.
We present recent progress and ongoing work in making serial electron crystallography more robust and accessible. A data analysis pipeline optimized with parallel processing was developed based on the CrystFEL suite, which is complemented by our python package diffractem. The framework of the Instamatic library was extended toward a portable implementation of the method. Supervised machine learning, in combination with vector analysis, was applied to serial crystallography datasets to extract structural information about the crystalline lattice, in order to decrease the amount of a priori knowledge required by experiments. Finally, recent attempts at structure solution on a wide variety of molecules (e.g. macromolecules, nanoporous materials, etc.) will be discussed.
 Bücker, R, et al, "Serial protein crystallography in an electron microscope", Nature Communications 11, (2020).
Investigation of Disease-causing Mutations in Sucrase-Isomaltase
Sucrase-Isomaltase (SI) is an intestine-localized eukaryotic enzyme that breaks down a variety of disaccharides and oligosaccharides into monosaccharides, through the cleavage of α-1,2 , α-1,4 and α-1,6 glycosidic bonds. Congenital Sucrase-Isomaltase Deficiency (CSID) is a genetic metabolic disorder which affects the expression or function of SI and impacts an individual's ability to digest certain carbohydrates. Symptoms of CSID include diarrhea, abdominal pain and an intolerance to carbohydrates such as sucrose and starch. Common CSID mutations found in 83% of CSID patients of European descent include G1073D, V577G, F1745C and R1124X.
The objective of this project is to investigate the disease-causing mutations of SI. The effect of a single change of residue may affect the stability of SI and/or a structural feature which is responsible for its enzymatic activity. The CSID protein mutants will be investigated by testing the protein stability and substrate affinity to determine the cause of the lack of enzymatic activity. The stability of the expressed CSID protein mutants will be assessed through exposure to a variety of temperature and pH, over different periods of time to determine whether the lack of enzymatic activity is a result of a lack of structural integrity. Since these point mutations are not located within the catalytic active site, measuring the substrate affinity will help clarify whether the lack of enzymatic activity is a result of an indirect structural effect on the catalytic site or a lack of substantial substrate affinity. These investigations into protein stability and substrate affinity of the protein mutants will provide a clearer insight on the effect of these disease-causing mutations on the structure and function of SI.
Psychiatric risk peptide of DISC1 inhibits kinase GSK3β, Structural investigation using crystallography
Disrupted in Schizophrenia 1 (DISC1) is a candidate risk gene in several major mental illnesses, e.g. depression, bipolar disorder, and schizophrenia. The full-length DISC1 protein comprises of 854 amino acids, consisting of many dynamic and disordered regions. DISC1 acts as a scaffold protein. It interacts with a large group of proteins, forming a sizeable protein-protein-interaction network. This interaction network has been implicated in coordination of various stages of the brain development. One of those important interactors is the enzyme, glycogen synthase kinase 3β (GSK3β). As a target for lithium, GSK3β itself is implicated in bipolar disorder. The interaction of DISC1 and GSK3β was discovered at the cross-section of the canonical Wnt/β-catenin signalling, which controls the proliferation of neural progenitors. DISC1 specifically inhibits GSK3β's function in this pathway via a direct physical interaction. The most potent GSK3b inhibitory region has been mapped to a small region in the N-terminus (residue 195-238) of DISC1. This 44-amino acid region (hD1) can inhibit GSK3b in an ATP non-competitive manner. We have obtained different crystal forms of GSK3b bound to hD1 and another peptide that partially shares binding site with hD1 based on biochemical and biophysical data. As obtaining crystallographic data of these new crystal forms is put on hold due to Covid-19, we are also evaluating whether negative stained electron microscopy can be used to identify large conformational changes of GSK3b induced by hD1 binding
SYNTHESIS AND STRUCTURAL CHARACTERIZATION OF LaMnO3+δ AND La0.8AE0.2MnO3+δ (AE=Ca, Sr, Ba) PEROVSKITES FOR CATALYTIC OXIDATION OF VOLATILE ORGANIC COMPOUNDS
Perovskite oxides have the general formula ABO3, where A is typically an alkaline earth (AE) or a lanthanide and B is a transition-metal. This family of compounds is probably the most studied one in the last decades since understanding the structure-properties correlation is of fundamental and technological interest . Despite the simplicity of the crystalline structure, the size variation of A and B cations creates an immense structural variety and generates deviations respect the ideal structure through changes in the crystal symmetry, that leads to the appearance of interesting properties. These properties are the origin of multiple applications, mostly related to energy conversion, adsorption and catalysis, among others.
Volatile Organic Compounds (VOCs) are a group of carbon-based chemicals considered not only as major contributors to air pollution but also one of the main hazardous substances for human health. Due to the great impact they provoke, the scientific community has been in search of an economically viable solution in order to control VOCs emissions. A few decades ago, the catalytic oxidation process arose as an interesting alternative to previously proposed methods, because it achieves greater conversions to CO2 and H2O at lower temperatures, is easier to control and less expensive in the long term. An additional complication of VOCs is that these group includes a wide range of compounds with very different physicochemical properties, what makes it difficult to find a single catalyst for the effective elimination of the majority of them.
Transition metal oxides, specially manganites, have been tested for VOCs oxidation and proved active at low temperatures for several molecules. Among them, manganites with perovskite-like structure are the ones that have exhibited the best performances. This can be attributed to the redox properties of the manganese and the mobility of oxygen in the lattice.
In this work, perovskites LaMnO3 and La0.8AE0.2MnO3 (AE=Ca, Sr, Ba) have been prepared by a simple one-step auto-combustion method and were characterized by X-ray powder diffraction and N2 adsorption-desorption method in order to apply them as catalysts in the complete catalytic oxidation of volatile organic compounds. The studied phases show the expected orthorhombic and rhombohedral perovskite crystal structures, being as-prepared materials stoichiometric oxides that transform irreversibly into (La1-xAEx)1-εMn1-εO3 during a calcination in air at 750 °C. The catalytic experiments, performed using acetone as model VOC, show almost no dependence on the state of the initial sample or AE cation. As-prepared stoichiometric samples slowly convert to cation deficient phases between 200 and 300 °C as supported by in-situ thermo-diffraction experiments. This suggests that the most important factor for the activity of these oxides as catalysts, if not the only one, is the Mn4+/Mn3+ molar ratio in the surface of the samples.
 Merino, N; Barbero, B. et al., J. Catal. 231 (2005) 232-244.
 Kamal, M.; Razzak, S. et al., Atmos. Environ. 140 (2016),117-134.
 B.P. Barbero, J.A. Gamboa & L.E. Cadús, Appl. Catal. B-Environ. 65 (2006) 21-30.
Acknowledgements: the authors acknowledge Agencia Nacional de Investigación e Innovación for financial support (Grant FSE_2015_109493) and the XPD beamline staff of Laboratório Nacional de Luz Síncrotron (LNLS-CNPEM) for the assistance during the experiment XPD20180307.
Natasha Di Benedetto
, Cryssmat-Lab, DETEMA, Facultad de Química, Universidad de la República Montevideo
Carolina De Los Santos
, Área Fisicoquímica, DETEMA, Facultad de Química, Universidad de la República Montevideo, Montevideo
, Área Fisicoquímica, DETEMA, Facultad de Química, Universidad de la República Montevideo, Montevideo
, Cryssmat-Lab, DETEMA, Facultad de Química, Universidad de la República Montevideo, Montevideo
Structure and effector-binding analysis of a PreQ1-III riboswitch suggests a fold that is tolerant to binding pocket mutations.
Riboswitches are metabolite-sensing RNA motifs present mostly in the 5´-leader sequences of bacterial mRNAs, where they control gene regulation. The class-III preQ1 riboswitch is found in bacteria of the Ruminococcaceae family, which compose the human gut microbiome. I am working with the class III riboswitch from Faecalibacterium prausnitzii (Fpr), an anti-inflammatory commensal bacterium whose deficiency has been associated with Crohn's disease. Although the global fold of the preQ1-III riboswitch is unique, ten nucleotide bases that compose the effector binding pocket are structurally identical to those of the class II riboswitch found in Streptococcus pneumoniae (Spn) - the leading cause of bacterial meningitis in adults. Given recent efforts to develop inhibitors that target riboswitches, it has become important to investigate the fundamental molecular mechanisms of riboswitches that bind the same effector but function in commensal versus pathogenic settings, such as the class III and class II preQ1 riboswitches.
A co-crystal structure of the Fpr preQ1-III riboswitch determined by our lab revealed a chemical interaction network that links the effector-binding pocket to the distal Shine-Dalgarno sequence, which functions in downstream gene regulation. We have prepared several mutants, spatially identical mutations in a preQ1-II riboswitch, including A84G, A52G, Δ84, and U8C/A85G to assess whether identical binding pocket mutations are affected by different riboswitch folds. PreQ1 binding analysis by isothermal titration calorimetry (ITC) revealed that the equivalent mutations were better tolerated by the class III riboswitch compared to the class II riboswitch. Moreover, our structures of the A84G (PDB ID: 6XKO) and A52G (PDB ID: 6XKN) mutants reveal that the mutant structures are not significantly different from the published wildtype structure, in accord with ITC experiments. We have prepared crystals of Δ84 and U8C/A85G mutants as well.
Structural insights into enzymatic mechanism of methylenetetrahydrofolate reductase (MTHFR) from Sphingobium sp. SYK-6
Methylenetetrahydrofolate reductase (MTHFR) is a flavoprotein that involves nucleic acid and de novo methionine syntheses. MTHFR converts N5, N10-methylene-tetrahydrofolate (CH2-THF) to N5-methyl-tetrahydrofolate (CH3-THF) using NAD(P)H as an electron donor, and this enzyme also has the capability of catalyzing the reverse reaction using an artificial electron acceptor in vitro. Since most MTHFRs show a significantly high enzymatic activity for NAD(P)H, it has been considered that MTHFR only converts CH2-THF to CH3-THF in cells. However, MTHFR from Sphingobium sp. SYK-6 (S6MTHFR), which utilizes lignin-derived aromatic compounds as a sole source of carbon energy, has been considered to catalyze the conversion from CH3-THF to CH2-THF in SYK-6. Although the cellular NAD(P)H concentration is much higher than CH3-THF, the opposite catalytic reaction by S6MTHFR suggests a different substrate specificity from those of typical MTHFRs. Since S6MTHFR shows similarity to other MTHFRs on the sequences, we speculated that structural changes of S6MTHFR in the process of evolution makes S6MTHFR prefer to react with CH3-THF rather than NAD(P)H. Therefore, we initiated to characterize this enzyme by using X-ray crystallography and biochemistry.
In this study, we overexpressed S6MTHFR in Escherichia coli (E. coli) BL21, and purified by anion exchange and size exclusion chromatographies. Diffraction data for native SAD phasing were collected using X-ray wavelength of 2.7 Å at BL-1A of Photon Factory (KEK, Japan). To determine the structure, we limited the resolution to 2.60Å with 1.2 SigAno, 0.074 Rmerge, 51.1 multiplicity, and succeed in native SAD phasing by Crank2 in CCP4. After that, we determined the high-resolution apo and substrate CH3-THF complex structures using the molecular replacement method at 1.5 Å and 1.8 Å resolutions, respectively. The final Rwork/Rfree of the apo and substrate-complex structures were 0.17/0.20 and 0.17/0.21, respectively, by PHENIX.refine. By comparing to other MTHFR structures, S6MTHFR structures show significant differences. One prominent difference is that Cys219 interacts with the 2nd nitrogen atom of CH3-THF in the active site of S6MTHFR, however, such interaction has not been observed in E. coli MTHFR (EcMTHFR). Mutational analysis revealed that the Km value for CH3-THF of the C219A variant of S6MTHFR decreased 10 times compared to the wild type, suggesting Cys219 facilitates CH3-THF binding. Furthermore, structure superposition of S6MTHFR with the NADH-EcMTHFR complex (PDB: 1zpt) suggested that Leu48 and Cys219 inhibit NADH binding to S6MTHFR. Indeed extremely low enzymatic activities of S6MTHFR were detected with NADH, and NADH hardly reduced FAD in S6MTHFR. Our structural and biochemical analysis revealed the molecular mechanism that S6MTHFR only catalyzes the conversion from CH3-THF to CH2-THF.
, Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) Tsukuba
, Department of Bioengineering, Nagaoka University of Technology Nagaoka
, SBRC, IMSS, KEK
, Nagaoka University of Technology
, High Energy Accelerator Research Organization (KEK) Tsukuba
, Department of Bioengineering, Nagaoka University of Technology
, Structural Bio Research Ctr Inst of Materials Structure , High Energy Accelerator Research Org Tsukuba
1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, a Key Target for Novel Antibacterial Development against Acinetobacter baumannii and Klebsiella pneumoniae
Acinetobacter baumannii and Klebsiella pneumoniae are members of the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, K. pneumoniae, A. baumannii, Pseudomonas aeruginosa, and Enterobacter species), a group of multidrug-resistant bacteria which are currently the leading cause of nosocomial infections worldwide. Presently, carbapenem-resistant A. baumannii and K. pneumoniae are classified as urgent threats by the Centers for Disease Control. The bacterial methylerythritol phosphate (MEP) pathway presents an attractive target for antibiotic development, as it is essential for production of vital isoprenoids including ubiquinone, menaquinone, bactoprenols, and bacterial hopanoids. The corresponding mammalian pathway of isoprenoid biosynthesis, the mevalonic acid pathway, is distinct from the MEP pathway. To facilitate antibiotic development against A. baumannii and K. pneumoniae we characterized the first committed MEP pathway enzyme, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (IspC), of A. baumannii and K. pneumoniae. We assessed in vitro IspC activity inhibition and performed antimicrobial susceptibility testing with two IspC inhibitors, fosmidomycin and FR900098. A. baumannii and K. pneumoniae IspC activity was significantly inhibited by fosmidomycin and FR900098, with IC50 values between 19.5 - 45.5 nM. A. baumannii strains AB5075 and AB19606 were susceptible to FR900098 with minimum inhibitory concentrations (MICs) of 256 and 128 µg/ml respectively. The growth of K. pneumoniae strains Kp_NSC-277 and Kp_BAA-1705 was inhibited by both FR900098 and fosmidomycin with MICs in the range of 64-256 µg/ml. Previous studies have shown that cellular penetration of fosmidomycin and FR900098 is limited by their polar nature and/or by cellular uptake via the glycerol 3-phosphate transporter, which may account for the relatively high MICs observed in this study. However, increasing the lipophilicity of fosmidomycin analogs and/or employing a phosphate diester prodrug strategy has been shown to significantly improve their antibacterial activity. In order to enhance inhibitor development, we determined the 2.5 Å crystal structure of IspC from A. baumannii in complex with inhibitor, FR900098, and cofactors NADPH and magnesium. Given that IspC activity was significantly inhibited by fosmidomycin and FR900098, and bacterial growth was inhibited, to a lesser extent, by fosmidomycin or FR900098, we conclude that IspC of A. baumannii and K. pneumoniae is a valid target for antibiotic development. The elucidation of the enzyme-inhibitor binding interactions presented herein will aid structure-based drug design and prodrug strategies for design and development of derivatives with improved antibacterial activity.
, Walter Reed Army Institute of Research Centreville, VA
, George Mason University Manassas, VA
, George Mason University Manassas, VA
, Walter Reed Army Institute of Research Silver Spring, MD
, George Mason University Manassas, VA
, Walter Reed Army Institute of Research Silver Spring, MD
Synthesis, Crystal Structures and Biomedical Application of Ferrocene-Hormone Complexes
Approximately 52% of breast cancer cases are related to over-expression of estrogen receptor (ERα). Conventional metal-based therapeutics drugs, such as cisplatin and derivatives, are still used to inhibit this abnormal cellular proliferation rate. However, cisplatin-based drugs are highly cytotoxic, triggering a series of side effects that become detrimental to the body, due to their lack of selectivity between healthy and cancerous tissue. In 1984, Köpf-Maier, and his co-workers first reported the anticancer properties of ferrocene. This organometallic compound leads to the formation of radical oxygen species that cause oxidative damage to DNA, inducing cell apoptosis. Our research group has recently successfully incorporated ferrocene with estrone, and estradiol at estrogen's rings A and D showing cytotoxic activity on hormone dependent and hormone independent breast cancer cell lines. The ferrocene-hormone complex substituted at estrogen's ring A proved to have cytotoxic activity similar to conventional therapeutic agents such as cisplatin and tamoxifen and dockings studies showed effective interaction. This work seeks to deliver a new approach to enhance the selectivity to target effectively hormones dependent cancers, specifically, ER+ breast cancer. We present a series of novel ferrocene-hormone complexes with its characterization by X-Ray Diffraction (XRD). Computational studies of the interaction of the ferrocene-hormone complexes with ERα protein were performed and demonstrated the possibilities of docking interaction of these drugs in the ligand binding pocket of the ERα.
Optimization of crystallization conditions for PfActII in complex with fragmin F1 domain
Actins are among the most abundant proteins in cells. They form filaments, which are involved in essential processes in the cell, including cell division, transport, motility, and structural functions. Polymerization involves a transition of monomeric (G-form) actin to the filamentous F-form. Conformational changes upon this transition activate ATP hydrolysis in the actin protomer. In apicomplexan parasites, actin filaments are essential for motility and host cell invasion. Unlike other apicomplexan parasites, including Toxoplasma gondii, which have only a single actin isoform, there are two actin isoforms in Plasmodium spp. (ActI and ActII). Plasmodium falciparum (Pf) ActII is one of the most divergent actins in eukaryotes. PfActII is expressed only during gametogenesis and insect cell stages. PfActI is the most studied isoform. Currently, there are no available atomic details of the PfActII filaments. To understand the mechanisms of F-actin ATP hydrolysis, structures at atomic resolution are indispensable. We have obtained crystals of Mg-ADP-PfActII in complex with fragmin domain F1 from Physarum polycephalum. Fragmin belongs to the gelsolin superfamily, and the interaction with actin is Ca2+ dependent. This protein binds to the barbed end actin subunit and induces an F-like conformation in monomeric actin. We are in the process of optimizing the crystallization conditions of Mg-ADP-PfActII-F1. Additionally, we intend to obtain crystals with PfActII in different nucleotide states.
Understanding c-di-GMP Signaling Specificity in Pseudomonas aeruginosa Pel-dependent Biofilms
Background: Biofilms are communities of microbial cells surrounded by an extracellular matrix (ECM) composed primarily of exopolysaccharides (EPS), protein and extracellular DNA (1). The ECM is an important virulence factor that enables the embedded microbes to resist the immune system and antibiotic therapies (2). The opportunistic Gram-negative pathogen Pseudomonas aeruginosa predominantly exists as a biofilm and is commonly found in chronic infections, such as in the lungs of Cystic Fibrosis (CF) patients (3). The Pel polysaccharide is a major contributor to the ECM of clinical P. aeruginosa CF strains. The production of Pel requires the proteins encoded by the pelABCDEFG operon (Figure 1A) (4,5) and its synthesis is positively regulated post-translationally by the binding of cyclic-3',5'-dimeric guanosine monophosphate (c-di-GMP) to PelD (6). Levels of c-di-GMP in the cell are modulated by the opposing activities of diguanylate cyclases and phosphodiesterases (PDEs) (7). As there are > 40 c-di-GMP metabolic enzymes present in P. aeruginosa, the mechanisms by which signalling specificity is achieved remain largely unknown.
Hypothesis: c-di-GMP metabolic enzymes achieve their specificity by interacting directly with c-di-GMP receptors causing conformational changes that effect function.
Results: Using co-immunoprecipitation, mass spectrometry and bacterial two-hybrid approaches we have found that PelD directly interacts with the PDE BifA, which is known to specifically down-regulate Pel biosynthesis (8). Bioinformatics analyses predict that BifA has a periplasmic sensory HmsP domain that is connected to a dual degenerate diguanylate cyclase domain (GGDEF) and an active PDE domain (EAL) by a HAMP signal transduction module (Figure 1B). We have recombinantly expressed and purified the GGDEF and EAL domains of BifA and have demonstrated using isothermal titration calorimetry that this construct binds GTP with a Kd of ~7.7 µM. Using site-directed mutagenesis we have identified residues in the GGDQF sequence motif that are required for GTP binding and found that GTP binding affects the oligomeric state of BifA and its interactions with PelD. Structure determination of the cytoplasmic domains of apo-BifA and its complex with GTP are currently in progress.
Conclusion: Our data suggests a model wherein the degenerate GGDEF domain of BifA functions as a GTP sensor, which in turn regulates not only BifA PDE activity, but also its interactions with target effectors such as PelD.
Significance: There are thousands of DUAL GGDEF-EAL domain proteins spread across all bacterial phyla. Deciphering the interplay between the GGDEF and EAL domains of BifA will aid in the understanding of other DUAL GGDEF-EAL domain proteins that participate in c-di-GMP metabolism to regulate important physiological responses. Additionally, understanding how the PDE activity of BifA is regulated by GTP binding will be key to understanding how it interacts with PelD and exerts its specific control over Pel biosynthesis in P. aeruginosa.
1. Jackson, K.D. et al. (2004). J. Bacteriol., 186(14), 4466-4475.
2. Franklin, M.J. et al. (2011). Front. Microbiol., 2.
3. Abdallah, M. et al. (2014). Arch. Microbiol., 196, 453-472.
4. Mulcahy, L.R. et al. (2014). Microb. Ecol., 68(1), 1-12.
5. Jennings, L.K. et al. (2015). PNAS, 112(36), 11353-11358.
6. Friedman, L. and Kolter, R. (2005). Mol. Micro., 51(3), 675-690.
7. Lee, V.T. et al. (2007). Mol. Micro., 65(6), 1474-1484.
8. Kuchma, S.L. et al. (2007). J. Bacteriol., 189(22), 8165-8178.
The crystal structure of gallic acid decarboxylase from Arxula adeninivorans
Gallic acid decarboxylases (GADC), a protein found in many different types of bacteria and yeast, is an enzyme that decarboxylates gallic acid to form pyrogallol. Gallic Acid is a hydrolysis product of tannins. Tannins are plant metabolites that play a role in plant defense. They are known for their ability to precipitate proteins, being linked to different pathologies, including cancer. Gallic Acids are used in the pharmaceutical industries for their anticancer and antioxidant properties. The initial crystal of GADC in the space group P21212 diffracted at 2.0 Angstrom resolution and had nine molecules in the asymmetric unit. Structure determination by MAD failed, and there is no known homologs structure. A homologous protein (52% amino acid identity) from Aspergillus niger was crystallized and diffracted to 1.8 Angstrom resolution, but the asymmetric unit had 18 molecules (in C2 space group). Another homologous protein (51% amino acid identity) from Madurella mycetomatis also crystallized with only one molecule in the asymmetric unit (in P321 space group); this structure was determined by MAD phasing of the Se-Methione derivatized protein.
Protein cofactors were found biochemically and validated in the crystal structure. Crystal structures revealed cobalt, potassium, and the substrate binding sites in a homotrimer. The potassium, required for activity, is at the center of the trimer, making trigonal prismatic coordination with OD and the carbonyl oxygen of Glu88 from each monomer. It positions the proximal and critical His86, part of a catalytic dyad, in the substrate binding site, through a twist in the connecting beta-strand. Cobalt further activates enzyme activity. Its binding site, formed by residues of two neighboring monomers, is removed from the active site, suggesting an allosteric mechanism of activation. The substrate analog 4-nitrocatechol is involved in a network of hydrogen bond interactions with W35, R39, T60, H86, Y150, and Q192. Mutation of any of these residues abolishes enzyme activity. The reaction is facilitated by His86, which is part of a catalytic dyad with Asp 40.
, Goethe University Frankfurt Greenville, NC
, University of Illinois at Chicago College of Pharmacy Chicago, IL
, East Carolina University, East Carolina Diabetes and Obesity Institute Greenville, NC
, Goethe University Frankfurt Frankfurt am Main
, Goethe University Frankfurt Frankfurt am Main
, East Carolina University / East Carolina Diabetes and Obesity Institute Greenville, NC
Lessons learned from using the MiTeGen In Situ-1™ Crystallization Plate for microgravity protein crystallization
The MiTeGen In Situ-1™ Crystallization Plate is a 96-well crystallization plate whose patented well design has enabled its use as a commercial technology for microgravity protein crystallization. Protein and precipitant reservoirs are physically separated except for a series of microchannels permitting vapor diffusion while strongly inhibiting fluid transfer. This design allows the plate to be safely rotated in any direction and makes the plate amenable for transport to and from the International Space Station (ISS). In their first flight demonstration in April 2016, crystals were observed in 90% of wells in five plates; fluid exchange was observed in less than 1% of wells. In 2018, a subsequent experiment provided an opportunity to evaluate a modular version of the In Situ-1™ Crystallization Plate while simultaneously exploring the ability of ISS crew members to assemble crystallization drops in microgravity. Crystals appeared in both versions of the plate; ISS crew overwhelmingly preferred the Modular In Situ-1™ Crystallization Plate due to its simpler design and ease of use. After return to Earth, the sealing films covering the Modular plates appeared inconsistently applied. Although there was no evidence of fluid exchange, many crystallization drops appeared partially dehydrated. This did not impact crystal diffraction, but it raised concerns regarding current plate sealing methods and which will be addressed in a third iteration of the plate. The In Situ-1™ Crystallization Plates are far from perfect, but the lessons learned from their use demonstrate them to be a robust, commercial alternative to more established microgravity protein crystal growth hardware.
A Consensus Method to Prepare Crystal Structures in the Protein Data Bank for Downstream Applications
The vast majority of biomedical and drug discovery projects begin by accessing the Protein Data Bank (PDB). However, the qualities of the protein structures in the PDB (dating back to 1976) vary greatly, which may impact project duration and cost. We used six industry-standard quality metrics to create an aggregate "Quality Score" from 0% to 100%, and then scored all 120,365 protein-containing X-ray structures in the PDB. Though most structures scored well (67% of structures had a Quality Score >90%), we hypothesized that low Quality Scores may be improved to reduce the overall time and cost of projects utilizing these input proteins. We assessed the ability of Rosetta's Relax preparation algorithm to improve the Quality Scores of 500 unique structures, representing a diverse cross-section of the PDB, by Relaxing and validating each structure and then calculating its Quality Score and RMSD after Relaxation. We tested 21 variations of the Relax protocol on this dataset (n = 493), and identified a Pareto optimal Relax variant that increased all Quality Scores (from an average of 91.8 ± 3.6% to 99.4 ± 0.8%) with sub-Angstrom RMSDs from their starting structures (average Cα RMSD = 0.16 ± 0.61 Å). Future work includes incorporating feedback into our consensus method of preparing X-ray structural models, applying this method to all crystal structures in the PDB, and releasing the results and method to the public. Our Pareto optimal Relax protocol may be broadly used to prepare X-ray structures as high-quality inputs for protein engineering projects, and the prepared database may serve as a high-quality dataset for machine learning and other big data applications.
, University of Massachusetts Dartmouth, MA
, University of Massachusetts Dartmouth Dartmouth, MA
LabJack-like crystal structures of halogenated 2-phenylbenzimidazoles – are they isostructural?
Investigation of isostructurality is a tool of understanding of the close packing principles. Isostructurality calculations and statistical analyses are efficient tools for finding isostructural crystals. The fine tuning of structural properties can be achieved by application of substituents, changing its placement and/or chemical composition influencing electrostatic and spherical properties. Molecular conformation of flexible molecules may adjust to the supramolecular features.
Crystal structures of 2-phenylbenzimidazole derivatives were analysed, either prepared by covalent synthesis or collected from the CSD. The molecules are substituted on the phenyl ring in ortho, meta and para positions or simultaneously in two different positions with fluorine, chlorine and bromine. The arrangement of the molecules recalls a laboratory Jack of which the height is determined by the halogen substitution.
The molecular arrangements in the crystals are governed by the N-H...N intermolecular interaction. The relative tilt of the hydrogen bonded molecules is determined by the substituents of the 2-phenylbenzimidazole skeleton. We focus on how and to what extent the type and the position of a halogen substituent may affect the crystal structure. We compare a series of increasingly more different structures to test the limits of isostructurality. With the varying substitution the lengths of the unit cell axes, the tilt of the molecules and the supramolecular interactions can be systematically influenced "the lab Jack can be closed or opened".
The flexibility of the structures permits a nearly twofold increase of the length of the unit cell perpendicular to the N-H...N hydrogen bonded chains in the investigated crystals with unchanged space group and Z'. How far can we call these crystals being isostructural?
Figure 1 Superimposed unit cells of the investigated crystals indicating the arrangement of the molecules.
This work was supported by the National Research, Development and Innovation Office-NKFIH through OTKA K124544 and KH129588.
1. Petra Bombicz, Nóra V. May, Dániel Fegyverneki, Avirmed Saranchimeg, Laura Bereczki: Methods for easy recognition of isostructurality - Lab Jack-likecrystal structures of halogenated 2-phenylbenzimidazoles. CrystEngComm DOI: 10.1039/D0CE00410C
Reinvestigation of the crystal structure of bis(3-aminopyridinium) tetrachloridocuprate(II)
The structure of bis(3-aminopyridinium) tetrachloridocuprate(II) (PATMUT) was reported by Kumar, et al. (Cryst. Growth Des. (2005) 5, 651), along with the structure of the 2-aminopyridinium analog (YOPNAS01). Both structures belong to the same space group (triclinic P-1) with very similar lattice constants (within 0.4% of longest cell dimension)--and with atomic coordinates that closely overlay. The published ORTEP diagram for PATMUT also shows an anomalously large ellipsoid for the ring N atom (with this atom not involved in significant hydrogen bonding) and an anomalously small ellipsoid on the C atom ortho to the amino group, which led us to believe that atom mis-assignment had occurred during refinement of PATMUT. Furthermore, the proximity of the amino group to the ring N atom in 2-aminopyridine leads to a preference for mono-protonation in halidometallate systems-the di-protonated cation is unknown. For 3-aminopyridine, in contrast, the di-protonated cation is readily observed in 3-ammoniumpyridinium salts while the mono-protonated cation, when it occurs, is usually found to coordinate the metal through the amino group.
An attempt to grow crystals of bis(3-aminopyridinium) tetrachloridocuprate(II) by slow evaporation of a 2:1 molar ratio of 3-aminopyridine and CuCl2 in a 6 M HCl solution yielded only green, thin, plate-like crystals of 3-ammoniumpyridinum tetrachloridocuprate(II). Recrystallization of these crystals from dry acetonitrile in a thermal gradient tube yielded only orange-red crystals initially, which then gradually re-dissolved to be replaced by green crystals of the 3-ammoniumpyridinium salt. Single crystal X-ray diffraction analysis at 295 K of an orange-red crystal yields the structure bis(3-aminopyridinium) tetrachloridoduprate(II) as triclinic P-1 with a c-axis ~1 Å longer than in PATMUT and very different unit cell angles, yet a cell volume only 0.5% smaller. The CuCl42- anion in this structure has a flattened tetrahedral geometry that is more distorted than in PATMUT (trans-Cl-Cu-Cl = 138.81 and 140.29° versus 130.27 and 136.35°, respectively), while significant hydrogen bonding by the ring N atoms is now also found.
, Dept of Chemistry and Physics, Southeast Missouri State University Cape Girardeau, MO
, Southeast Missouri State University Cape Girardeau, MO
, Southeast Missouri State University Cape Girardeau, MO
A cross-phase reaction coordinate in the formation of a mononuclear copper(II) orotate complex
The reaction of orotic acid with a copper (II) starting material in the presence of CsOH produces crystals of a six-coordinate Jahn-Teller active Cu complex ([b]1[/b], Fig. 1). The initial solid product loses crystallinity when removed from its aqueous mother liquor. When crystals of ([b]1[/b]) are kept in the mother liquid, and the aqueous supernatant is partially evaporated, they evolve to a second anionic mononuclear copper complex, this one four-coordinate, in a solvent-mediated crystal-to-crystal transformation. The crystal structure of this second copper complex ([b]2[/b], Fig. 2) is conserved both within and without the mother liquor. A previously reported nickel complex ([b]3[/b]), isostructural to ([b]1[/b]), is stable at ambient conditions both in the presence and in the absence of mother liquor. Comparisons of the molecular and extended structures, along with TGA data, were used in an attempt to elucidate the comparative stabilities of the isostructural Cu ([b]1[/b]) and Ni ([b]3[/b]) complexes in their respective solids, and the role of the relative stability of ([b]2[/b]) in promoting the further reaction of ([b]1[/b]) after its initial formation. An unusual feature in the anisotropic displacement parameters from the structure analysis of compound ([b]2[/b]) is briefly discussed.
 Using the crystal to engineer the molecule: cis-trans-isomer selection in anionic bis(orotate) complexes. Larry R. Falvello, Daniel Ferrer, María Piedrafita, Tatiana Soler and Milagros Tomás. CrystEngComm, 2007, 9, 852-855.
FUNDING: Ministerio de Ciencia e Innovación (Spain, Grant PGC2018-093451-B-I00), the European Union Regional Development Fund, FEDER), and the Diputación General de Aragón, Project M4, E11_20R.
, Dept of Inorganic Chemistry, Univ of Zaragoza Zaragoza
, Department of Inorganic Chemistry and Aragón Materials Science Institute (ICMA), University of Zarag Zaragoza
, Laboratoire de Matériaux, Cristallochimie et Thermodynamique Appliquée, Département de Chimie and Un Tunis and Sfax
, Department of Inorganic Chemistry and Institute for Chemical Synthesis and Homogeneous Catalysis (IS Zaragoza
Evaluation of covalent bond density in molecular crystals using simplified virtual scattering centers: inorganic and complex compounds
The Independent Atom Model (IAM) provides a good estimate for the most of routine crystallographic research. A charge density approach, which additionally describes bonding electrons, requires very high quality data in order to obtain meaningful results.
Here we address a 'gray area' of good quality datasets with 0.5-0.8 Å resolution, which show visible deviation from IAM but are not satisfactory for experimental charge density calculations. The suggested methodology follows the well-known virtual atom method (see [1-3] and numerous references therein. Most probably, the idea of placing a scattering center exactly in the middle of two carbon atoms was first implemented by Rosalind Franklin  and was 'conveniently forgotten' by all subsequent publications in this field.
Virtual scattering centers (VSC) are placed at fixed calculated positions between C, N, and O atoms with 'occupancies' being different for single, double, aromatic, and triple bonds. Scattering is approximated by a single Gaussian which can be justified by a small value of correction. VSCs are treated as isotropic: multiplication of point VSC by Debye-Waller factor yields a single isotropic Gaussian function to describe both effects (no deconvolution of vibrations and charge density). All scattering at VSC is described as anomalous scattering; therefore, there is no change of total number of electrons in a molecule.
Usual IAM software (SHELXL or Jana) was employed. The number of introduced parameters can be as low as one (for overall occupancy of the VSC part of the structure). Introduction of VSCs makes the effect similar to the scattering of one hydrogen atom per 4-5 C-C bonds, which is substantial enough to justify the effort. Alternatively, each bond can be treated separately (number of additional parameters is roughly equal to the number of bonds). This can lead to further improvement. It is possible to handle C-H bonds as well as lone pairs in the same fashion . In this presentation, several inorganic and element-organic molecules were investigated. When it was possible, charge density calculations (MoPro [5}) and/or HARt  calculations  were performed using the same experimental data. Visible improvement of fitting characteristics was achieved, especially for molecules with aromatic fragments.
Some representative examples:
Sulfamic acid resolution 0.37 Å: IAM R=2.1, VSC 1.86. Refinement with HARt  gives R=1.85. All S-O bonds and S-N bond have approximately the same covalent scattering, in agreement with charge density results (MoPro), confirming single covalent bonds in this molecule (plus additional electrostatic interactions).
Several 3d transition metal complexes with large organic part and resolution of 0.58 -0.62 Å showed visible improvement of R factor (e.g, from 2.9 to 2.5), 30% smaller standard deviations of bond lengths, and, more important, much cleaner residual map. After removing most of residual bond density from the Fourier difference map, other sources of deviation such as disorder and experimental and data processing limitations can be addressed. As usual, applicability of this algorithm is limited by Coppens's suitability factor S values.
1] Franklin, R. E. Nature 1950, 165, 71-72.
 Scheringer, C. &. Kutoglu, A. Acta Cryst. 1983, A39, 899-901.
 Afonine, P.; Pichon-Pesme, V; Muzet, N.; Lecomte, C.; Urzhumtsev, A. CCP4 Newsletter on Protein Crystallography, 2002, 41; Afonine, P.V; Grosse-Kunstleve, R.W.; Adams, P D.; Lunin, V. & Urzhumtsev, A. Acta Cryst. 2007, D63, 1194–1197; Dadda, N.; Nassour, A.; Guillot, B.; Benali-Cherif , N. & Jelsch, C. Acta Cryst. 2012, A68, 452–463; Ahmed, M.; Nassour, A.; Noureen, S.; Lecomte, C. & Jelsch, C. Acta Cryst.2016, B72, 75–86; Urzhumtsev A.G.; Lunin V.Y. Crystallography Rev., 2020, 26, 51-55.
 Nazarenko, A.Y. Z. Kristallographie, 2018, 38, S44-S45
 Guillot, B. Viry, L. Guillot, R. Lecomte, C. & Jelsch, C. (2001). J. Appl. Cryst. 34, 214-223
 Fugel, M.; Jayatilaka, D.; Hupf, E.; Overgaard, J.; Hathwar, V. R.; Macchi, P.; Turner, M. J.; Howard, J. A. K.; Dolomanov, O. V.; Puschmann, H.; Iversen, B. B.; Bürgi, H.-B. & Grabowsky, S. IUCrJ 2018, 5, 32–44.
Electron Diffraction for Characterization of Nanocrystal Materials: Beyond the Crystal Structure
Crystalline solids, such as metal, metal oxides, zeolites, and metal-organic frameworks (MOFs), have been intensively investigated both as traditional and state-of-the-art materials. They have been implemented in a wide range of applications from industrial use to laboratorial research. The applications are closely associated with the physical and chemical properties, which are determined by the atomic crystal structures. Thus, structure determination is arguably the most important characterization step for crystalline materials. Although single crystal X-ray diffraction (SCXRD) is the most practiced and routine method for structure determination, the acquisition of adequate data quality from weakly scattering nano- and micro-sized crystals remains a challenge. While powder X-ray diffraction is more suitable technique for handling small crystals, structure determination can be challenging due to severe peak overlap as a consequence of large lattices, complexity of the structures themselves, as well as phase mixtures.
Microcrystal electron diffraction (MicroED) or 3-dimensional electron diffraction (3D ED)[2,3] techniques have shown to be powerful for structural determination of 'intractable' crystals that are too small for SCXRD analysis. These techniques benefit from the strong interaction between electrons and matter. Compared to X-ray, electrons generate much higher signal-to-noise ratios, even when the volume of the crystals are 6 or 7 orders of magnitude smaller. A series of ED patterns can be acquired by tilting a crystal around the goniometer axis of a transmission electron microscope (TEM). After reconstruction of the 3D reciprocal lattice, and extracting intensities, the acquired ED data can be applied as SCXRD-like data for structural analysis.
We have successfully applied the ED techniques for ab initio structure determination of novel nanocrystalline zeolites and MOFs[4–7], and demonstrated that the technique can achieve an accuracy comparable to SCXRD. Because zeolites and MOFs are sensitive to radiation damage, fast data acquisition is key to the analysis. Nowadays, a complete data can be acquired in 15-150 seconds using continuous goniometer tilt, and the electron dose can be limited to below 0.1 e Å-2. As a consequence, important details beyond the crystal structure can be revealed. For example, the preferred positions of solvents can be determined, and hydrogen bonding can be identified between the solvent molecules and the framework. Such key information of guest-host interactions plays a key role in understanding adsorption properties of porous materials. Moreover, using the MicroED/3D ED method, the positions of different metal cations in MOFs can be directly determined, which is crucial for obtaining key knowledge on the catalytic properties. To further automate the structural analysis, serial rotation electron diffraction method was developed for automated data collection, processing, and structure solution. The large number of data makes it possible for quantitative phase analysis, and for detection of minor phases that may not be detectable by X-ray diffraction.
(1) Nannenga, B. L.; Shi, D.; Leslie, A. G. W.; Gonen, T. Nat. Methods 2014, 11 (9), 927–930.
(2) Wan, W.; Sun, J.; Su, J.; Hovmöller, S.; Zou, X. J. Appl. Crystallogr. 2013, 46 (6), 1863–1873.
(3) Kolb, U.; Gorelik, T.; Otten, M. T. Ultramicroscopy 2008, 108 (8), 763–772.
(4) Wang, B.; Rhauderwiek, T.; Inge, A. K.; Xu, H.; Yang, T.; Huang, Z.; Stock, N.; Zou, X. Chem. – Eur. J. 2018, 24 (66), 17429–17433.
(5) Yuan, S.; Qin, J.-S.; Xu, H.-Q.; Su, J.; Rossi, D.; Chen, Y.; Zhang, L.; Lollar, C.; Wang, Q.; Jiang, H.-L.; Son, D. H.; Xu, H.; Huang, Z.; Zou, X.; Zhou, H.-C. ACS Cent. Sci. 2018, 4 (1), 105–111.
(6) Roy, S.; Huang, Z.; Bhunia, A.; Castner, A.; Gupta, A. K.; Zou, X.; Ott, S. J. Am. Chem. Soc. 2019, 141 (40), 15942–15950.
(7) Carraro, F.; Velásquez-Hernández, M. de J.; Astria, E.; Liang, W.; Twight, L.; Parise, C.; Ge, M.; Huang, Z.; Ricco, R.; Zou, X.; Villanova, L.; Kappe, C. O.; Doonan, C.; Falcaro, P. Chem. Sci. 2020, 11, 3397-3404.
(8) Huang, Z.; Ge, M.; Carraro, F.; Doonan, C. J.; Falcaro, P.; Zou, X. Faraday Discuss. 2020, DOI: 10.1039/D0FD00015A.
(9) Wang, B.; Zou, X.; Smeets, S. IUCrJ 2019, 6 (5), 854–867.
, Stockholm University Stockholm
, Stockholm University Stockholm, Sweden
The 1.9Å structure of PA5083 – a 116 residue protein with 1 ordered sulfur - determined by Native-SAD using in-house data and phenix.autobuild recycling.
PA5083 a Rid2 (Reactive Intermediate Deaminase) protein from Pseudomonas aeruginosa known to have broad imine deaminase activity against iminoarginine has been determined to 1.9Å resolution using Native-SAD. The Rid family enzymes are of interest since they play important roles in nutrition, amino acids biosynthesis, mitochondrial maintenance and other biological processes by reducing the accumulation of toxic metabolite intermediates.
The structure determination is noteworthy in that (1) the data were collected in-house ( = 1.5418) and consisted of a single set of 1440 quarter degree images (total rotation 360°, multiplicity 16.6), (2) the 116 residue enzyme has only two sulfur containing residues (Met 1 and Cys 17) giving a Bijvoet ratio 0.374 assuming Met 1 is disordered (it was), (3) the initial results from phenix.autosol gave a "very low" (autosol) FOM of 0.16 with R and Rfree values of 0.5049 and 0.5505 respectively and (4) the structure was built from the initial autosol phases using several rounds of model building with phenix.autobuild. The R and Rfree values for the refined model are 0.200 and 0.233 respectively.
Details of the Native (sulfur atom)-SAD analysis and the PA5083 crystal structure will be presented.
Work supported in part by funds from the University of Georgia Foundation, and the National Institutes of Health (1S10OD021762-01).
Keywords: Native (sulfur atom)-SAD; PA5083; Reactive Intermediate Deaminase; Rid2 Protein; Crystal Structure; Challenging Analysis