Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center.

Cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. The electron entry site in subunit II is a mixed-valence dinuclear copper center in enzymes that oxidize cytochrome c. This center has been lost during the evolution of the quinoloxidizing branch of cytochrome oxidases but can be restored by engineering. Herein we describe the crystal structures of the periplasmic fragment from the wild-type subunit II (CyoA) of Escherichia coli quinol oxidase at 2.5-A resolution and of the mutant with the engineered dinuclear copper center (purple CyoA) at 2.3-A resolution. CyoA is folded as an 11-stranded mostly antiparallel beta-sandwich followed by three alpha-helices. The dinuclear copper center is located at the loops between strands beta 5-beta 6 and beta 9-beta 10. The two coppers are at a 2.5-A distance and symmetrically coordinated to the main ligands that are two bridging cysteines and two terminal histidines. The residues that are distinct in cytochrome c and quinol oxidases are around the dinuclear copper center. Structural comparison suggests a common ancestry for subunit II of cytochrome oxidase and blue copper-binding proteins.

Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae.

The diphtheria tox repressor (DtxR) of Corynebacterium diphtheriae plays a critical role in the regulation of diphtheria toxin expression and the control of other iron-sensitive genes. The crystal structures of apo-DtxR and of the metal ion-activated form of the repressor have been solved and used to identify motifs involved in DNA and metal ion binding. Residues involved in binding of the activated repressor to the diphtheria tox operator, glutamine 43, arginine 47, and arginine 50, were located and confirmed by site-directed mutagenesis. Previous biochemical and genetic data can be explained in terms of these structures. Conformational differences between apo- and Ni-DtxR are discussed with regard to the mechanism of action of this repressor.

Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove.

Sequence analysis of peptides naturally presented by major histocompatibility complex (MHC) class I molecules has revealed allele-specific motifs in which the peptide length and the residues observed at certain positions are restricted. Nevertheless, peptides containing the standard motif often fail to bind with high affinity or form physiologically stable complexes. Here we present the crystal structure of a well-characterized antigenic peptide from ovalbumin [OVA-8, ovalbumin-(257-264), SIINFEKL] in complex with the murine MHC class I H-2Kb molecule at 2.5-A resolution. Hydrophobic peptide residues Ile-P2 and Phe-P5 are packed closely together into binding pockets B and C, suggesting that the interplay of peptide anchor (P5) and secondary anchor (P2) residues can couple the preferred sequences at these positions. Comparison with the crystal structures of H-2Kb in complex with peptides VSV-8 (RGYVYQGL) and SEV-9 (FAPGNYPAL), where a Tyr residue is used as the C pocket anchor, reveals that the conserved water molecule that binds into the B pocket and mediates hydrogen bonding from the buried anchor hydroxyl group could not be likewise positioned if the P2 side chain were of significant size. Based on this structural evidence, H-2Kb has at least two submotifs: one with Tyr at P5 (or P6 for nonamer peptides) and a small residue at P2 (i.e., Ala or Gly) and another with Phe at P5 and a medium-sized hydrophobic residue at P2 (i.e., Ile). Deciphering of these secondary submotifs from both crystallographic and immunological studies of MHC peptide binding should increase the accuracy of T-cell epitope prediction.

The crystal structure of a bacterial Class II ketol-acid reductolsomerase: Domain conservation and evolution

Ketol-acid reductoisomerase (KARI; EC 1.1.1.86) catalyzes two steps in the biosynthesis of branched-chain amino acids. Amino acid sequence comparisons across species reveal that there are two types of this enzyme: a short form (Class 1) found in fungi and most bacteria, and a long form (Class 11) typical of plants. Crystal structures of each have been reported previously. However, some bacteria such as Escherichia coli possess a long form, where the amino acid sequence differs appreciably from that found in plants. Here, we report the crystal structure of the E. coli enzyme at 2.6 A resolution, the first three-dimensional structure of any bacterial Class 11 KARI. The enzyme consists of two domains, one with mixed alpha/beta structure, which is similar to that found in other pyridine nucleotide-dependent dehydrogenases. The second domain is mainly alpha-helical and shows strong evidence of internal duplication. Comparison of the active sites between KARI of E. coli, Pseudomonas aeruginosa, and spinach shows that most residues occupy conserved positions in the active site. E. coli KARI was crystallized as a tetramer, the likely biologically active unit. This contrasts with P. aeruginosa KARI, which forms a dodecamer, and spinach KARI, a dimer. In the E. coli KARI tetramer, a novel subunit-to-subunit interacting surface is formed by a symmetrical pair of bulbous protrusions.

Structure and physical properties of [µ-Tris(1,4-bis(tetrazol-1-yl)butane-N4,N4‘')iron(II)] Bis(hexafluorophosphate), a new Fe(II) spin-crossover compound with a three-dimensional threefold interlocked crystal lattice

[μ-Tris(1,4-bis(tetrazol-1-yl)butane-N4,N4‘)iron(II)] bis(hexafluorophosphate), [Fe(btzb)3](PF6)2, crystallizes in a three-dimensional 3-fold interlocked structure featuring a sharp two-step spin-crossover behavior. The spin conversion takes place between 164 and 182 K showing a discontinuity at about T1/2 = 174 K and a hysteresis of about 4 K between T1/2 and the low-spin state. The spin transition has been independently followed by magnetic susceptibility measurements, 57Fe-Mössbauer spectroscopy, and variable temperature far and midrange FTIR spectroscopy. The title compound crystallizes in the trigonal space group P30¯(No. 147) with a unit cell content of one formula unit plus a small amount of disordered solvent. The lattice parameters were determined by X-ray diffraction at several temperatures between 100 and 300 K. Complete crystal structures were resolved for 9 of these temperatures between 100 (only low spin, LS) and 300 K (only high spin, HS), Z = 1 [Fe(btzb)3](PF  6)2:  300 K (HS), a = 11.258(6) Å, c = 8.948(6) Å, V = 982.2(10) Å3; 100 K (LS), a = 10.989(3) Å, c = 8.702(2) Å, V = 910.1(4) Å3. The molecular structure consists of octahedral coordinated iron(II) centers bridged by six N4,N4‘ coordinating bis(tetrazole) ligands to form three 3-dimensional networks. Each of these three networks is symmetry related and interpenetrates each other within a unit cell to form the interlocked structure. The Fe−N bond lengths change between 1.993(1) Å at 100 K in the LS state and 2.193(2) Å at 300 K in the HS state. The nearest Fe separation is along the c-axis and identical with the lattice parameter c.

A hydrogen-bonded polar network in the core of the glucagon-like peptide-1 receptor is a fulcrum for biased agonism:lessons from class B crystal structuress

The glucagon-like peptide 1 (GLP-1) receptor is a class B G protein-coupled receptor (GPCR) that is a key target for treatments for type II diabetes and obesity. This receptor, like other class B GPCRs, displays biased agonism, though the physiologic significance of this is yet to be elucidated. Previous work has implicated R2.60190 , N3.43240 , Q7.49394 , and H6.52363 as key residues involved in peptide-mediated biased agonism, with R2.60190 , N3.43240 , and Q7.49394 predicted to form a polar interaction network. In this study, we used novel insight gained from recent crystal structures of the transmembrane domains of the glucagon and corticotropin releasing factor 1 (CRF1) receptors to develop improved models of the GLP-1 receptor that predict additional key molecular interactions with these amino acids. We have introduced E6.53364 A, N3.43240 Q, Q7.49493N, and N3.43240 Q/Q7.49 Q/Q7.49493N mutations to probe the role of predicted H-bonding and charge-charge interactions in driving cAMP, calcium, or extracellular signal-regulated kinase (ERK) signaling. A polar interaction between E6.53364 and R2.60190 was predicted to be important for GLP-1- and exendin-4-, but not oxyntomodulin-mediated cAMP formation and also ERK1/2 phosphorylation. In contrast, Q7.49394 , but not R2.60190 /E6.53364 was critical for calcium mobilization for all three peptides. Mutation of N3.43240 and Q7.49394 had differential effects on individual peptides, providing evidence for molecular differences in activation transition. Collectively, this work expands our understanding of peptide-mediated signaling from the GLP-1 receptor and the key role that the central polar network plays in these events.

Near-infrared spectroscopic study of basic aluminum sulfate and nitrate

The tridecameric Al-polymer [AlO4Al12(OH)24(H2O)12]7+ was prepared by forced hydrolysis of Al3+ up to an OH/Al molar ratio of 2.2. Under slow evaporation crystals were formed of Al13-nitrate. Upon addition of sulfate the tridecamer crystallised as the monoclinic Al13-sulfate. These crystals have been studied using near-infrared spectroscopy and compared to Al2(SO4)3.16H2O. Although the near-infrared spectra of the Al13-sulfate and nitrate are very similar indicating similar crystal structures, there are minor differences related to the strength with which the crystal water molecules are bonded to the salt groups. The interaction between crystal water and nitrate is stronger than with the sulfate as reflected by the shift of the crystal water band positions from 6213, 4874 and 4553 cm–1 for the Al13 sulfate towards 5925, 4848 and 4532 cm–1 for the nitrate. A reversed shift from 5079 and 5037 cm–1 for the sulfate towards 5238 and 5040 cm–1 for the nitrate for the water molecules in the Al13 indicate that the nitrate-Al13 bond is weakened due to the influence of the crystal water on the nitrate. The Al-OH bond in the Al13 complex is not influenced by changing the salt group due to the shielding by the water molecules of the Al13 complex.

Synthesis of a heparan sulfate mimetic disaccharide with a conformationally locked residue from a common intermediate

A simple mimetic of a heparan sulfate disaccharide sequence that binds to the growth factors FGF-1 and FGF-2 was synthesized by coupling a 2-azido-2-deoxy-D-glucosyl trichloroacetimidate donor with a 1,6-anhydro-2-azido-2-deoxy--D-glucose acceptor. Both the donor and acceptor were obtained from a common intermediate readily obtained from D-glucal. Molecular docking calculations showed that the predicted locations of the disaccharide sulfo groups in the binding site of FGF-1 and FGF-2 are similar to the positions observed for co-crystallized heparin-derived oligosaccharides obtained from published crystal structures.

Raman microscopy of haidingerite Ca(AsO3OH)•H2O and brassite Mg(AsO3OH)•4H2O

Raman spectroscopy has been used to study the arsenate minerals haidingerite Ca(AsO3OH)•H2O and brassite Mg(AsO3OH)•4H2O. Intense Raman bands in haidingerite spectrum observed at 745 and 855 cm-1 are assigned to the (AsO3OH)2- ν3 antisymmetric stretching and ν1 symmetric stretching vibrational modes. For brassite two similarly assigned intense bands are found at 809 and 862 cm-1. The observation of multiple Raman bands in the (AsO3OH)2- stretching and bending regions suggests that the arsenate tetrahedrons in the crystal structures of both minerals studied are strongly distorted. Broad Raman bands observed at 2842 cm-1 for haidingerite and 3035 cm-1 for brassite indicate strong hydrogen bonding of water molecules in the structure of these minerals. OH…O hydrogen bond lengths were calculated from the Raman spectra based on empiric relations.

Azo- and butadiyne-linked 5,10-diarylporphyrins

Porphyrins are one of Nature’s essential building blocks that play an important role in several biological systems including oxygen transport, photosynthesis, and enzymes. Their capacity to absorb visible light, facilitate oxidation and reduction, and act as energy- and electron-transfer agents, in particular when several are held closely together, is of interest to chemists who seek to mimic Nature and to make and use these compounds in order to synthesise novel advanced materials. During this project 26 new 5,10-diarylsubstituted porphyrin monomers, 10 dimers, and 1 tetramer were synthesised. The spectroscopic and structural properties of these compounds were investigated using 1D/2D 1H NMR, UV/visible, ATR-IR and Raman spectroscopy, mass spectrometry, X-ray crystallography, electrochemistry and gel permeation chromatography. Nitration, amination, bromination and alkynylation of only one as well as both of the meso positions of the porphyrin monomers have resulted in the expansion of the synthetic possibilities for the 5,10-diarylsubstituted porphyrins. The development of these new porphyrin monomers has led to the successful synthesis of new azo- and butadiyne-linked dimers. The functionalisation of these compounds was investigated, in particular nitration, amination, and bromination. The synthesised dimers containing the azo bridge have absorption spectra that show a large split in the Soret bands and intense Q-bands that have been significantly redshifted. The butadiyne dimers also have intense, red-shifted Q-bands but smaller Soret band splittings. Crystal structures of two new azoporphyrins have been acquired and compared to the azoporphyrin previously synthesised from 5,10,15- triarylsubstituted porphyrin monomers. A completely new cyclic porphyrin oligomer (CPO) was synthesised comprising four porphyrin monomers linked by azo and butadiyne bridges. This is the first cyclic tetramer that has both the azo and butadiyne linking groups. The absorption spectrum of the tetramer exhibits a large Soret split making it more similar to the azo- dimers than the butadiyne-linked dimers. The spectroscopic characteristics of the synthesised tetramer have been compared to the characteristics of other cyclic porphyrin tetramers. The collected data indicate that the new synthesised cyclic tetramer has a more efficient ð-overlap and a better ground state electronic communication between the porphyrin rings.

Hydrogen bonding in proton-transfer compounds of 5-sulfosalicylic acid with a series of aliphatic nitrogen Lewis bases

The crystal structures of the proton-transfer compounds of 5-sulfosalicylic acid (3-carboxy-4-hydroxybenzenesulfonic acid) with the aliphatic nitrogen Lewis bases, hydroxylamine, triethylamine, pyrrolidine, morpholine, N-methylmorpholine and piperazine, viz. hydroxyammonium 3-carboxy-4-hydroxybenzenesulfonate (1), triethylaminium 3-carboxy-4-hydroxybenzenesulfonate (2), pyrrolidinium 3-carboxy-4-hydroxybenzenesulfonate monohydrate (3), morpholinium 3-carboxy-4-hydroxybenzenesulfonate monohydrate (4), N-methylmorpholinium 3-carboxy-4-hydroxybenzenesulfonate monohydrate (5) and piperazine-1,4-diium bis(3-carboxy-4-hydroxybenzenesulfonate) hexahydrate (6) have been determined and their comparative structural features and hydrogen-bonding patterns described. Crystals of 4 are triclinic, space group P-1 while the remainder are monoclinic with space group either P21/c (1 - 3) or P21/n (5, 6). Unit cell dimensions and contents are: for 1, a = 5.0156(3), b = 10.5738(6), c = 18.4785(9) Å, β = 96.412(5)o, Z = 4; for 2, a = 8.4998(4), b = 12.3832(6), c = 15.4875(9) Å, β = 102.411(5)o, Z = 4; for 3, a = 6.8755(2), b = 15.5217(4), c = 12.8335(3) Å, β = 92.074(2)o, Z = 4; for 4, a = 6.8397(2), b = 12.9756(5), c = 15.8216(6) Å, α = 90.833(3), β = 95.949(3), γ = 92.505(3)o, Z = 4; for 5, a = 7.0529(3), b = 13.8487(7), c = 15.6448(6) Å, β = 90.190(6)o, Z = 4; for 6, a = 7.0561(2), b = 15.9311(4), c = 12.2102(3) Å, β = 100.858(3)o, Z = 2. The hydrogen bonding generates structures which are either two-dimensional (2 and 5) or three-dimensional (1, 3, 4 and 6). Compound 6 represents the third reported structure of a salt of 5-sulfosalicylic acid having a dicationic piperazine species.

2,3-Dimethoxy-10-oxostrychnidinium 2-(2,4,6-trinitroanilino)benzoate monohydrate : a 1:1 proton-transfer salt of brucine with o-picraminobenzoic acid

In the structure of the 1:1 proton-transfer compound of brucine with 2-(2,4,6-trinitroanilino)benzoic acid C23H27N2O4+ . C13H7N4O8- . H~2~O, the brucinium cations form the classic undulating ribbon substructures through overlapping head-to-tail interactions while the anions and the three related partial water molecules of solvation (having occupancies of 0.73, 0.17 and 0.10) occupy the interstitial regions of the structure. The cations are linked to the anions directly through N-H...O(carboxyl) hydrogen bonds and indirectly by the three water molecules which form similar conjoint cyclic bridging units [graph set R2/4(8)] through O-H...O(carbonyl) and O(carboxyl) hydrogen bonds, giving a two-dimensional layered structure. Within the anion, intramolecular N-H...O(carboxyl) and N H...O(nitro) hydrogen bonds result in the benzoate and picrate rings being rotated slightly out of coplanarity inter-ring dihedral angle 32.50(14)\%]. This work provides another example of the molecular selectivity of brucine in forming stable crystal structures and also represents the first reported structure of any form of the guest compound 2-(2,4,6-trinitroanilino)benzoic acid.

A Raman spectroscopic study of the different vanadate-groups in solid-state compounds, model case : mineral phases vésigniéite, BaCu3(VO4)2(OH)2, and volborthite, Cu3V2O7(OH)2•2H2O

Raman spectroscopy has been used to study vanadates in the solid state. The molecular structure of the vanadate minerals vésigniéite [BaCu3(VO4)2(OH)2] and volborthite [Cu3V2O7(OH)2·2H2O] have been studied by Raman spectroscopy and infrared spectroscopy. The spectra are related to the structure of the two minerals. The Raman spectrum of vésigniéite is characterized by two intense bands at 821 and 856 cm−1 assigned to ν1 (VO4)3− symmetric stretching modes. A series of infrared bands at 755, 787 and 899 cm−1 are assigned to the ν3 (VO4)3− antisymmetric stretching vibrational mode. Raman bands at 307 and 332 cm−1 and at 466 and 511 cm−1 are assigned to the ν2 and ν4 (VO4)3− bending modes. The Raman spectrum of volborthite is characterized by the strong band at 888 cm−1, assigned to the ν1 (VO3) symmetric stretching vibrations. Raman bands at 858 and 749 cm−1 are assigned to the ν3 (VO3) antisymmetric stretching vibrations; those at 814 cm−1 to the ν3 (VOV) antisymmetric vibrations; that at 508 cm−1 to the ν1 (VOV) symmetric stretching vibration and those at 442 and 476 cm−1 and 347 and 308 cm−1 to the ν4 (VO3) and ν2 (VO3) bending vibrations, respectively. The spectra of vésigniéite and volborthite are similar, especially in the region of skeletal vibrations, even though their crystal structures differ.

Loss-of-function fibroblast growth factor receptor-2 mutations in melanoma

We report that 10% of melanoma tumors and cell lines harbor mutations in the fibroblast growth factor receptor 2 (FGFR2) gene. These novel mutations include three truncating mutations and 20 missense mutations occurring at evolutionary conserved residues in FGFR2 as well as among all four FGFRs. The mutation spectrum is characteristic of those induced by UV radiation. Mapping of these mutations onto the known crystal structures of FGFR2 followed by in vitro and in vivo studies show that these mutations result in receptor loss of function through several distinct mechanisms, including loss of ligand binding affinity, impaired receptor dimerization, destabilization of the extracellular domains, and reduced kinase activity. To our knowledge, this is the first demonstration of loss-of-function mutations in a class IV receptor tyrosine kinase in cancer. Taken into account with our recent discovery of activating FGFR2 mutations in endometrial cancer, we suggest that FGFR2 may join the list of genes that play context-dependent opposing roles in cancer.