Non-Protein Amino Acids in the Design of Secondary Structure Scaffolds

The use of stereochemically constrained amino acids permits the design of short peptides as models for protein secondary structures. Amino acid residues that are restrained to a limited range of backbone torsion angles (ϕ-ψ) may be used as folding nuclei in the design of helices and β-hairpins. α-Amino-isobutyric acid (Aib) and related Cαα dialkylated residues are strong promoters of helix formation, as exemplified by a large body of experimentally determined structures of helical peptides. DPro-Xxx sequences strongly favor type II’ turn conformations, which serve to nucleate registered β-hairpin formation. Appropriately positioned DPro-Xxx segments may be used to nucleate the formation of multistranded antiparallel β-sheet structures. Mixed (α/β) secondary structures can be generated by linking rigid modules of helices and β-hairpins. The approach of using stereochemically constrained residues promotes folding by limiting the local structural space at specific residues. Several aspects of secondary structure design are outlined in this chapter, along with commonly used methods of spectroscopic characterization.

Synthesis, Structure, Spirocyclization Mechanism, and Glutathione Peroxidase-like Antioxidant Activity of Stable Spirodiazaselenurane and Spirodiazatellurane

The first examples of stable spirodiazaselenurane and spirodiazatellurane were synthesized by oxidative spirocyclization of the corresponding diaryl selenide and telluride and were structurally characterized. X-ray crystal structures of the spirodiazaselenurane and spirodiazatellurane suggest that the structures are distorted trigonal bipyramidal (TBP) with the electronegative nitrogen atoms occupying the apical positions and two carbon atoms and the lone pair of Se/Te occupying the equatorial positions. Interestingly, the spirodiazatellurane underwent spontaneous chiral resolution during crystallization, and the absolute configurations of its enantiomers were confirmed by single-crystal X-ray analyses. A detailed mechanistic study indicates that the cyclization to spirodiazaselenurane and spirodiazatellurane occurs via selenoxide and telluroxide intermediates. The chalcogenoxides cyclize to the corresponding spiro compounds in a stepwise manner via the involvement of hydroxyl chalcogenurane intermediates, and the activation energy for them spirocyclization reaction decreases in the order S > Se > Te. In addition to the synthesis, characterization, and mechanism of cyclization, the glutathione peroxidase (GPx) mimetic activity of the newly synthesized compounds was evaluated. These studies suggest that the tellurium compounds are more effective as GPx mimics than their selenium counterparts due to the fast oxidation of the tellurium center in the presence of peroxide and the involvement of an efficient redox cycle between the telluride and telluroxide intermediate.

Crystal structure of dimeric FabZ of Plasmodium falciparum reveals conformational switching to active hexamers by peptide flips

The crystal structure of beta-hydroxyacyl acyl carrier protein dehydratase of Plasmodium falciparum (PfFabZ) has been determined at a resolution of 2.4 angstrom. PfFabZ has been found to exist as a homodimer (d-PfFabZ) in the crystals of the present study in contrast to the reported hexameric form (h-PfFabZ) which is a trimer of dimers crystallized in a different condition. The catalytic sites of this enzyme are located in deep narrow tunnel-shaped pockets formed at the dimer interface. A histidine residue from one subunit of the dimer and a glutamate residue from the other subunit lining the tunnel form the catalytic dyad in the reported crystal structures. While the position of glutamate remains unaltered in the crystal structure of d-PffabZ compared to that in b-PfFabZ, the histidine residue takes up an entirely different conformation and moves away from the tunnel leading to a His-Phe cis-trans peptide flip at the histidine residue. In addition, a loop in the vicinity has been observed to undergo a similar flip at a Tyr-Pro peptide bond. These alterations not only prevent the formation of a hexamer but also distort the active site geometry resulting in a dimeric form of FabZ that is incapable of substrate binding. The dimeric state and an altered catalytic site architecture make d-PfFabZ distinctly different from the FabZ structures described so far. Dynamic light scattering and size exclusion chromatographic studies clearly indicate a pH-related switching of the dimers to active hexamers. (c) 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserv.

Structure and optical properties of Cd-substituted ZnO (Zn1-xCdxO) nanostructures synthesized by the high-pressure solution route

We report the synthesis of Cd-substituted ZnO nanostructures (Zn1-xCdxO with x up to approximate to 0.09) by the high-pressure solution growth method. The synthesized nanostructures comprise nanocrystals that are both particles (similar to 10-15 nm) and rods which grow along the [002] direction as established by transmission electron microscope (TEM) and x-ray diffraction (XRD) analysis. Rietveld analysis of the XRD data shows a monotonic increase of the unit cell volume with the increase of Cd concentration. The optical absorption, as well as the photoluminescence (PL), shows a red shift on Cd substitution. The line width of the PL spectrum is related to the strain inhomogeneity and it peaks in the region where the CdO phase separates from the Zn1-xCdxO nanostructures. The time-resolved photoemission showed a long-lived (similar to 10 ns) component. We propose that the PL behaviour of the Zn1-xCdxO is dominated by strain in the sample with the red shift of the PL linked to the expansion of the unit cell volume on Cd substitution.

Structure determination and biochemical studies on Bacillus stearothermophilus E53Q serine hydroxymethyltransferase and its complexes provide insights on function and enzyme memory

Serine hydroxymethyltransferase (SHMT) belongs to the alpha-family of pyridoxal 5'-phosphate-dependent enzymes and catalyzes the reversible conversion of L-Ser and etrahydrofolate to Gly and 5,10-methylene tetrahydrofolate. 5,10-Methylene tetrahydrofolate serves as a source of one-carbon fragment in many biological processes. SHMT also catalyzes the tetrahydrofolate-independent conversion of L-allo-Thr to Gly and acetaldehyde. The crystal structure of Bacillus stearothermophilus SHMT (bsSHMT) suggested that E53 interacts with the substrate, L-Ser and etrahydrofolate. To elucidate the role of E53, it was mutated to Q and structural and biochemical studies were carried out with the mutant enzyme. The internal aldimine structure of E53QbsSHMT was similar to that of the except for significant changes at Q53, Y60 and Y61. The wild-type enzyme, carboxyl of Gly and side chain of L-Ser were in two conformations in the respective external aldimine structures. The mutant enzyme was completely inactive for tetrahydrofolate-depen dent cleavage of L-Ser, whereas there was a 1.5-fold increase in the rate of tetrahydrofolate-independent reaction with L-allo-Thr. The results obtained from these studies suggest that E53 plays an essential role in tetrahydrofolate/5-formyl tetrahydrofolate binding and in the proper positioning of C beta of L-Ser for direct attack by N5 of tetrahydrofolate. Most interestingly, the structure of the complex obtained by cocrystallization of E53QbsSHMT with Gly and 5-formyl tetrahydrofolate revealed the gem-diamine form of pyridoxal 5'-phosphate bound to Gly and active site Lys. However, density for 5-formyl tetrahydrofolate was not observed. Gly carboxylate was in a single conformation, whereas pyridoxal 5'-phosphate had two distinct conformations. The differences between the structures of this complex and Gly external aldimine suggest that the changes induced by initial binding of 5-formyl tetrahydrofolate are retained even though 5-formyl tetrahydrofolate is absent in the final structure. Spectral studies carried out with this mutant enzyme also suggest that 5-formyl tetrahydrofolate binds to the E53QbsSHMT-Gly complex forming a quinonoid intermediate and falls off within 4 h of dialysis, leaving behind the mutant enzyme in the gemdiamine form. This is the first report to provide direct evidence for enzyme memory based on the crystal structure of enzyme complexes.

Crystal structure of peanut lectin, a protein with an unusual quaternary structure

The x-ray crystal structure of the tetrameric T-antigen-binding lectin from peanut, M(r) 110,000, has been determined by using the multiple isomorphous replacement method and refined to an R value of 0.218 for 22,155 reflections within the 10- to 2.95-A resolution range. Each subunit has essentially the same characteristic tertiary fold that is found in other legume lectins. The structure, however, exhibits an unusual quaternary arrangement of subunits. Unlike other well-characterized tetrameric proteins with identical subunits, peanut lectin has neither 222 (D2) nor fourfold (C4) symmetry. A noncrystallographic twofold axis relates two halves of the molecule. The two monomers in each half are related by a local twofold axis. The mutual disposition of the axes is such that they do not lead to a closed point group. Furthermore, the structure of peanut lectin demonstrates that differences in subunit arrangement in legume lectins could be due to factors intrinsic to the protein molecule and, contrary to earlier suggestions, are not necessarily caused by interactions involving covalently linked sugar. The structure provides a useful framework for exploring the structural basis and the functional implications of the variability in the subunit arrangement in legume lectins despite all of them having nearly the same subunit structure, and also for investigating the general problem of "open" quaternary assembly in oligomeric proteins.

Phonetic tone signals quantity and word structure

Many languages exploit suprasegmental devices in signaling word meaning. Tone languages exploit fundamental frequency whereas quantity languages rely on segmental durations to distinguish otherwise similar words. Traditionally, duration and tone have been taken as mutually exclusive. However, some evidence suggests that, in addition to durational cues, phonological quantity is associated with and co-signaled by changes in fundamental frequency in quantity languages such as Finnish, Estonian, and Serbo-Croat. The results from the present experiment show that the structure of disyllabic word stems in Finnish are indeed signaled tonally and that the phonological length of the stressed syllable is further tonally distinguished within the disyllabic sequence. The results further indicate that the observed association of tone and duration in perception is systematically exploited in speech production in Finnish.

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of mn K-edge XANES data

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K-edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3. The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K-edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

Local structure of Sr(2)FeMoxW1-xO(6) double perovskites studied by EXAFS

Sr2FeMoO6 double perovskits display low field MR at a relatively high temperature and unusual ferromagnetic properties. These compounds depicts metal to insulator transition increasing x above x(c) similar to 0.25. A comparative analysis of the near edge regions (XANES) suggests that iron is Fe3+ in the metallic range. Checking the end compounds, we found that the doped samples can be viewn as inhomogeneous distributions of the end compounds. This could help to distinguish between the two scenarios proposed to explain the metal to insulator transition. Moreover, the local atomic structure of Sr2FeMoxW1-xO6 as a function of composition (0 <= x <= 1) has been investigated by Extended X-ray absorption spectroscopy (EXAFS) a the Fe, Mo, Sr K-edges andW L-III-edge.

Structure of Ferroverdin

FERROVERDIN, a green iron-containing pigment, was isolated in 1955 by Chain, Tonolo and Carilli1 from an unidentified species of Streptomyces. It was at first assigned the formula C30H24O8N2Fe and the iron was shown by measurements of magnetic susceptibility to be in the ferrous state2. Later the ligand present was proved to be the p-vinyl phenyl ester of 3-nitroso-4-hydroxy-benzoic acid3,4. X-ray crystallographic measurements were undertaken to find the atomic arrangement in this unusual complex; they show, in two different crystal structures, that each iron atom is attached to three nitrosophenyl ligands and that the charge is balanced by sodium ions.

Family of Mixed-Valence Oxovanadium(IV/V) Dinuclear Entities Incorporating N4O3-Coordinating Heptadentate Ligands: Synthesis, Structure, and EPR Spectra

Dinuclear ((VVV)-V-IV) oxophenoxovanadates of general formula [V2O3L] have been synthesized in excellent yields by reacting bis(acetylacetonato)oxovanadium(IV) with H3L in a 2:1 ratio in acetone under an N-2 atmosphere. Here L3- is the deprotonated form of 2,6-bis[{{(2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L1), 2,6-bis[{{(5-methyl-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L2) 2,6-bis[ {{(5-tert-butyl-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenoI (H3L3), 2,6-bis[{{(5-chloro-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L4) , 2,6-bis[{{(5-bromo-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L5), or 2,6-bis[{{(5-methoxy-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L6). In [V2O3L1], both the metal atoms have distorted octahedral geometry. The relative disposition of two terminal V=O groups in the complex is essentially cis. The O=V...V=O torsion angle is 24.6(2)degrees. The V-O-oxo-V and V-O-phenoxo-V angles are 117.5(4) and 93.4(3)degrees, respectively. The V...V bond distance is 3.173(5) Angstrom. X-ray crystallography, IR, UV-vis, and H-1 and V-51 NMR measurements show that the mixed-valence complexes contain two indistinguishable vanadium atoms (type 111). The thermal ellipsoids of O2, O4, C10, C14, and C15 also suggests a type III complex in the solid state. EPR spectra of solid complexes at 77 K display a single line indicating the localization of the odd electron (3d(xy)(1)). Valence localization at 77 K is also consistent with the V-51 hyperfine structure of the axial EPR spectra (3d(xy)(1) ground state) of the complexes in frozen (77 K) dichloromethane solution: S = 1/2, g(parallel to) similar to 1.94, g(perpendicular to) similar to 1.98, A(parallel to) similar to 166 x 10(-4) cm(-1), and A(perpendicular to) similar to 68 x 10(-4) cm(-1). In contrast isotropic room-temperature solution spectra of the family have 15 hyperfine lines (g(iso) similar to 1.974 and A(iso) similar to 50 x 10(-4) cm(-1)) revealing that the unpaired electron is delocalized between the metal centers. Crystal data for the [V2O3L1].CH2Cl2 complex are as follows: chemical formula, C32H43O6N4C12V2; crystal system, monoclinic; space group, C2/c; a = 18.461(4), b = 17.230(3), c = 13.700(3) Angstrom; beta = 117.88(3)degrees; Z = 8.

Approximate solutions for the structure of shock waves

Approximate solutions of the B-G-K model equation are obtained for the structure of a plane shock, using various moment methods and a least squares technique. Comparison with available exact solution shows that while none of the methods is uniformly satisfactory, some of them can provide accurate values for the density slope shock thickness delta n . A detailed error analysis provides explanations for this result. An asymptotic analysis of delta n for largeMach numbers shows that it scales with theMaxwell mean free path on the hot side of the shock, and that their ratio is relatively insensitive to the viscosity law for the gas.