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.

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.

STUDIES ON RADIATION EFFECTS OF PTFE .2. RADIATION-INDUCED STRUCTURAL-CHANGES AND THE TEMPERATURE EFFECT

In this work PTFE sheets irradiated with gamma-rays at 150-degrees-C and 200-degrees-C were studied using x-ray photoelectron spectroscopy (XPS). The main structural changes in PTFE due to radiation are the formation of CF3 and CF groups. An irradiation temperature dependence of the relative content of the three kinds of groups in irradiated PTFE was observed. The CF3 groups, especially when irradiation is carried out a lower temperatures, can defluorinate in the same manner as previosly reported for CF2 groups. The CF groups, on the other hand, are observed to increase with increasing irradiation dose and irradiation temperature; the latter was explained as due to an increase in branching structures.

Structural and optical changes in GaAs/InAs/GaAs structure induced by thermal annealing

Self-organized InAs quantum; dots sheets are grown on GaAs(100) substrate and tapped by 80nm GaAs layer with molecular beam epitaxy. Samples were annealed and characterized with Raman spectra, transmission electron microscopy (TEM) and photolumincscence (PL). The Raman spectra indicates arsenic clusters in the GaAs capping layer. The TEM analysis revealed the relaxation of strain in some InAs islands with the introduction of the network of 90 dislocations. In addition, the structural changes also lead to the changes of the PL spectra from me InAs islands. Their correlation was discussed, Our results suggest:est that annealing may be used to intentionally modify me properties of self-organized InAs islands on GaAs.

Switch Region for Pathogenic Structural Change in Conformational Disease and Its Prediction

Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs) and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1) influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1) it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2) it provides an ideal target for clinical treatment.

Structural evolution of mechanically alloyed nanocrystalline FeAl intermetallics

Nanostructured FeAl intermetallics were prepared directly by mechanical alloying (MA) in a high-energy planetary ball-mill. The phase transformations and structural changes occurring in the studied material during mechanical alloying were investigated by X-ray diffraction (XRD). Transmission electron microscopy (TEM) was employed to examine the morphology of the powders. Thermal behavior of the milled powders was examined by differential scanning calorimetry (DSC). Disordered Fe(Al) solid solution was formed at the early stage. After 30 h of milling, Fe(Al) solid solution transformed into an ordered FeAl phase. The average crystallite size reduction down to about 12 nm was accompanied by the introduction of the average lattice strain up to 1.7%. The TEM picture showed that the size of milled powders was less than 30 nm. (c) 2007 Elsevier B.V. All rights reserved.

Structural properties of ne implanted GaN

We report a study on the micro-structural changes in GaN due to neon ion implantation using the x-ray diffraction and Raman scattering techniques. An implantation dose of 10(14) cm(-2) was found unable to produce lattice deformation observable by Raman measurements. For higher doses of implantation several disorder activated Raman scattering centers were observed which corroborate the literature. A new dose dependent feature has been recorded at 1595 cm(-1) for higher implantation doses which is suggested to be the vibrational mode of microcavities produced in the lattice.