Extent of Structural Asymmetry in Homodimeric Proteins: Prevalence and Relevance

Most homodimeric proteins have symmetric structure. Although symmetry is known to confer structural and functional advantage, asymmetric organization is also observed. Using a non-redundant dataset of 223 high-resolution crystal structures of biologically relevant homodimers, we address questions on the prevalence and significance of asymmetry. We used two measures to quantify global and interface asymmetry, and assess the correlation of several molecular and structural parameters with asymmetry. We have identified rare cases (11/223) of biologically relevant homodimers with pronounced global asymmetry. Asymmetry serves as a means to bring about 2:1 binding between the homodimer and another molecule; it also enables cellular signalling arising from asymmetric macromolecular ligands such as DNA. Analysis of these cases reveals two possible mechanisms by which possible infinite array formation is prevented. In case of homodimers associating via non-topologically equivalent surfaces in their tertiary structures, ligand-dependent mechanisms are used. For stable dimers binding via large surfaces, ligand-dependent structural change regulates polymerisation/depolymerisation; for unstable dimers binding via smaller surfaces that are not evolutionarily well conserved, dimerisation occurs only in the presence of the ligand. In case of homodimers associating via interaction surfaces with parts of the surfaces topologically equivalent in the tertiary structures, steric hindrance serves as the preventive mechanism of infinite array. We also find that homodimers exhibiting grossly symmetric organization rarely exhibit either perfect local symmetry or high local asymmetry. Binding of small ligands at the interface does not cause any significant variation in interface asymmetry. However, identification of biologically relevant interface asymmetry in grossly symmetric homodimers is confounded by the presence of similar small magnitude changes caused due to artefacts of crystallisation. Our study provides new insights regarding accommodation of asymmetry in homodimers.

Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase

Salmonella typhimurium DCyD (StDCyD) is a fold type II pyridoxal 5' phosphate (PLP)-dependent enzyme that catalyzes the degradation of D-Cys to H2S and pyruvate. It also efficiently degrades beta-chloro-D-alanine (beta CDA). D-Ser is a poor substrate while the enzyme is inactive with respect to L-Ser and 1-amino-1-carboxy cyclopropane (ACC). Here, we report the X-ray crystal structures of StDCyD and of crystals obtained in the presence of D-Cys, beta CDA, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS) at resolutions ranging from 1.7 to 2.6 angstrom. The polypeptide fold of StDCyD consisting of a small domain (residues 48-161) and a large domain (residues 1-47 and 162-328) resembles other fold type II PLP dependent enzymes. The structures obtained in the presence of D-Cys and beta CDA show the product, pyruvate, bound at a site 4.0-6.0 angstrom away from the active site. ACC forms an external aldimine complex while D- and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at C alpha proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggest formation of PMP by the hydrolysis of cycloserines. Mutational studies suggest that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for C alpha proton abstraction from D-Cys. Based on these studies, a probable mechanism for the degradation of D-Cys by StDCyD is proposed.

Structural and phase dependent thermo and photoluminescent properties of Dy(OH)(3) and Dy2O3 nanorods

Hexagonal Dy(OH)(3) and cubic Dy2O3 nanorods were prepared by hydrothermal method. Dy(OH)(3) nanorods was directly obtained at 180 degrees C for 20 h after hydrothermal treatment whereas subsequently heat treatment at 750 degrees C for 2 h gives pure cubic Dy2O3. SEM micrographs reveal that needle shaped rods with different sizes were observed in both the phases. TEM results also confirm this. The TL response of hexagonal Dy(OH)(3) and cubic Dy2O3 nanorods have been analyzed for gamma-irradiation over a wide range of exposures (1-5 kGy). TL glow peak intensity increases with gamma dose in both the phases. The activation energy (E), order of kinetics (6), and frequency factor (s) for both the phases have been determined using Chen's peak shape method. The simple glow curve shape, structure and linear response to gamma-irradiation over a large span of exposures makes the cubic Dy2O3 as a useful dosimetric material to estimate high exposures of gamma-rays. (c) 2012 Elsevier Ltd. All rights reserved.

Structural, EPR, optical and Raman studies of Nd2O3:Cu2+ nanophosphors

Nanocrystalline Nd2O3:Cu2+ (2 mol %) phosphors have been prepared by a low temperature solution combustion technique. Powder X-ray diffraction (PXRD) results confirm that hexagonal A-type Nd2O3 (900 degrees C, 3 h) and the lattice parameters have been evaluated by Rietveld refinement. Surface morphology of as-formed and Cu2+ doped Nd2O3 phosphors show that the particles are irregular in shape and porous in nature. TEM results also confirm the nature and size of the particles. The EPR spectrum exhibits two resonance signals with effective g values at g(parallel to) approximate to 2.12 and g(perpendicular to) approximate to 2.04. The g values indicate that the site symmetry of Cu2+ ions is octahedral symmetry with elongated tetragonal distortion. Raman studies show major peaks, which are assigned, to F-g and combination of A(g) + E-g modes. It is observed that the Raman peaks and intensity have been reduced in Cu2+ doped samples. UV-Visible absorption spectra exhibit a strong and broad absorption band at similar to 240 nm. Further, the absorption peak shifts to similar to 14 nm in Cu2+ doped samples. The optical band gap is estimated to be 5.28 eV for Cu doped Nd2O3 nanoparticles which are higher than the bulk Nd2O3 (4.7 eV). This can be attributed to the quantum confinement effect of the nanoparticles. (C) 2012 Elsevier B.V. All rights reserved.