Autoinhibitory mechanism and activity-related structural changes in a mycobacterial adenylyl cyclase

An adenylyl cyclase from Mycobacterium avium, Mal 120, is a functional orthologue of a pseudogene Rv1120c from Mycobacterium tuberculosis. We report the crystal structure of Mal 120 in a monomeric form and its truncated construct as a dimer. Mal 120 exists as a monomer in solution and crystallized as a monomer in the absence of substrate or inhibitor. An additional alpha-helix present at the N-terminus of the monomeric structure blocks the active site by interacting with the substrate binding residues and occupying the dimer interface region. However, the enzyme has been found to be active in solution, indicating the movement of the helix away from the interface to facilitate the formation of active dimers in conditions favourable for catalysis. Thus, the N-terminal helix of Ma1120 keeps the enzyme in an autoinhibited state when it is not active. Deletion of this helix enabled us to crystallize the molecule as an active homodimer in the presence of a P-site inhibitor 2',5'-dideoxy-3'-ATP, or pyrophosphate along with metal ions. The substrate specifying lysine residue plays a dual role of interacting with the substrate and stabilizing the dimer. The dimerization loop region harbouring the second substrate specifying residue, an aspartate, shows significant differences in conformation and position between the monomeric and dimeric structures. Thus, this study has not only revealed that significant structural transitions are required for the interconversion of the inactive and the active forms of the enzyme, but also provided precise nature of these transitions. (C) 2015 Elsevier Inc. All rights reserved.

Donut-Shaped Fingerprint In Homologous Polypeptide Relationships-A Topological Feature Related To Pathogenic Structural Changes In Conformational Disease

Features of homologous relationship of proteins can provide us a general picture of protein universe, assist protein design and analysis, and further our comprehension of the evolution of organisms. Here we carried Out a Study of the evolution Of protein molecules by investigating homologous relationships among residue segments. The motive was to identify detailed topological features of homologous relationships for short residue segments in the whole protein universe. Based on the data of a large number of non-redundant Proteins, the universe of non-membrane polypeptide was analyzed by considering both residue mutations and structural conservation. By connecting homologous segments with edges, we obtained a homologous relationship network of the whole universe of short residue segments, which we named the graph of polypeptide relationships (GPR). Since the network is extremely complicated for topological transitions, to obtain an in-depth understanding, only subgraphs composed of vital nodes of the GPR were analyzed. Such analysis of vital subgraphs of the GPR revealed a donut-shaped fingerprint. Utilization of this topological feature revealed the switch sites (where the beginning of exposure Of previously hidden "hot spots" of fibril-forming happens, in consequence a further opportunity for protein aggregation is Provided; 188-202) of the conformational conversion of the normal alpha-helix-rich prion protein PrPC to the beta-sheet-rich PrPSc that is thought to be responsible for a group of fatal neurodegenerative diseases, transmissible spongiform encephalopathies. Efforts in analyzing other proteins related to various conformational diseases are also introduced. (C) 2009 Elsevier Ltd. All rights reserved.

Special effects of YbF3 on the structural changes for fluorophosphate glass

From Raman and IR spectra, obvious differences of the glass structure were observed in non-Yb3+-doped and Yb3+ -doped fluorophosphate glasses. Results showed that Yb3+ ions can induce, in a better glass, polymerization and network uniformity. Compared with the monophosphate-mastered Yb3+-free glass, Yb3+-doped glass has a pyrophosphate environment. The main building blocks in Yb3+ -doped samples are metaphosphate groups, pyrophosphate groups (P-2(O,F)(7),PO3F), Al[F-6]+Al[O,F](6) and F3Al-O-AlF3 while those of the Yb3+ -free glasses are monophosphate groups P(O,F)(4), little pyrophosphate groups, Al[F-4]+Al[F-6]+Al[O,F](4)+Al[O,F](6) and F3Al-O-AlF3. The DSC analysis also showed a slight increase in crystallization stability. (c) 2005 Elsevier B.V. All rights reserved.

Degeneration of postovulatory follicles in the Iberian sardine Sardina pilchardus: structural changes and factors affecting resorption

Inaccuracy in the aging of postovulatory follicles (POFs) and in estimating the effect of temperature on the resorption rate of POFs may introduce bias in the determination of the daily spawning age classes with the daily egg production method (DEPM). To explore the above two bias problems with f ield-collected European pilchard (Sardina pilchardus, known regionally as the Iberian sardine), a method was developed in which the time elapsed from spawning (POF age) was estimated from the size of POFs (i.e., from the cross-sectional area in histological sections). The potential effect of the preservative type and embedding material on POF size and the effect of ambient water temperature on POF resorption rate are taken into account with this method. A highly significant loglinear relationship was found between POF area and age; POF area shrank by approximately 50% per day. POFs were also shown to shrink faster at higher temperatures (approximately 3% per degree), but this temperature effect is unlikely to be an important source of bias in the assignment of females to daily spawning classes. The embedding material was also shown to influence the size of POFs, the latter being significantly larger in resin than in paraffin sections. In conclusion, the size of POFs provides an indirect, reliable estimation of the time elapsed from spawning and may thus be used to test both the validity of POF staging criteria for identifying daily classes of spawners and the effect of other factors (such as temperature and laboratory processing) in applications of the DEPM to S. pilchardus and other fish species.

Real-Time Study of Genomic DNA Structural Changes upon Interaction with Small Molecules Using Dual-Polarization Interferometry

The structural changes of genomic DNA upon interaction with small molecules have been studied in real time using dual-polarization interferometry (DPI). Native or thermally denatured DNA was immobilized on the silicon oxynitride surface via a preadsorbed poly(ethylenimine) (PEI) layer. The mass loading was similar for both types of DNA, however, native DNA formed a looser and thicker layer due to its rigidity, unlike the more flexible denatured DNA, which mixed with PEI to form a denser and thinner layer. Ethidium bromide (EtBr), a classical intercalator, induced the large thickness decrease and density increase of native DNA (double-stranded), but a slight increase in both the thickness and density of denatured DNA (partial single-stranded).

Probing structural changes of spin-coated polystyrene film after swelling and precipitation by synchrotron GIUSAXS and AFM

Polystyrenc film of about 50 nm in thickness on silicon wafer was obtained by spin-coating in tetrahydrofuran solution.The film exhibits a rough surface as shown by atomic force microscopy images and ellipsometry data.

Structural changes of TiO2 gel using Eu3+ ion as the fluorescence probe

Because of the extremely sensitivity to the local environment of the D-5(0) --> F-7(2) transition of Eu3+ ion, the fluorescence of Eu3+ ions was Studied by introducing Eu3+ ions to TiO2 gel by the sol-gel method, from which the structural changes of TiO2 gel were characterized. The results showed that the intensity of D-5(0) --> F-7(2) transition increased with the increasement of heat treatment temperature, which indicated the evaporation of molecular water and the completeness of the condensation reaction. Because of the quenching of the fluorescence induced by the cluster of Eu3+ ions, the addition of Al3+ ions greatly enhanced the emission intensity of Eu3+ ion.

XPS STUDIES OF RADIATION-INDUCED STRUCTURAL-CHANGES IN POLYVINYLIDENE FLUORIDE

In this work the radiation-induced structural changes in PVDF were studied using XPS. It was found that for PVDF irradiated at 150-degrees-C, double bonds were formed mainly through the further dehydrofluorination of crosslinked and/or branched molecules, whereas for samples irradiated at 20-degrees-C the dehydrofluorination of macromolecular radicals to form stable polyene radicals is the main source of unsaturated structures.

XPS STUDIES ON RADIATION-INDUCED STRUCTURAL-CHANGES IN THE COPOLYMER OF TETRAFLUOROETHYLENE AND ETHYLENE

In this work, the radiation-induced structural changes in the copolymer of tetrafluoroethylene and ethylene (F-40) were studied by X-ray photoelectron spectroscopy (XPS). During irradiation, some CF2 groups in the polymer were found to have been converted into carbon structures that bonded indirectly with fluorine atoms.