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.

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.

Influences of Structural Damping and Buoyancy-Weight Ratio on Dynamic Responses of Submerged Floating Tunnel

The recent progress of submerged floating tunnel (SFT) investigation and SFT prototype (SFTP) project in Qiandao Lake (Zhejiang Province, P.R. China) is the background of this research. Structural damping effect is brought into present computation model in terms of Rayleigh damping. Based on the FEM computational results of SFTPs as a function of buoyancy-weight ratio (BWR) under hydrodynamic loads, the effect of BWR on the dynamic response of SFT is illustrated. In addition, human comfort index is adopted to discuss the comfort status of the SFTP.

Thermal, structural and optical properties of NiOx thin films deposited by reactive dc-magnetron sputtering

The NiOx thin films were deposited by reactive dc-magnetron sputtering from a nickel metal target in Ar + O-2 with the relative O-2 content 5%. The as-deposited NiOx, thin films could represent a two-component system comprising crystalline NiO particles dispersed in an amorphous Ni2O3. Decomposition temperature of the as-deposited NiO, thin films was at about 263 degrees C. After annealed at 400 degrees C for 30 min in air, the surface morphology of the films became very rough due to the decomposition of the Ni2O3, leading to the changes of the optical properties of the NiO, thin films. The reflectivity of the films annealed at 400 degrees C was lower than that of the as-deposited one and the optical contrast was 52% at 405 nm. (c) 2006 Elsevier B.V. All rights reserved.

Structural change of laser-irradiated Ge2Sb2Te5 films studied by electrical property measurement

Sheet resistance of laser-irradiated Ge2Sb2Te5 thin films prepared by magnetron sputtering was measured by the four-point probe method. With increasing laser power the sheet resistance undergoes an abrupt drop from 10(7) to 10(3) Omega/square at about 580 mW. The abrupt drop in resistance is due to the structural change from amorphous to crystalline state as revealed by X-ray diffraction (XRD) study of the samples around the abrupt change point. Crystallized dots were also formed in the amorphous Ge2Sb2Te5 films by focused short pulse laser-irradiated, the resistivities at the crystallized dots and the non-crystallized area are 3.375 x 10(-3) and 2.725 Omega m, sheet resistance is 3.37 x 10(4) and 2.725 x 10(7) Omega/square respectively, deduced from the I-V Curves that is obtained by conductive atomic force microscope (C-AFM). (C) 2008 Elsevier B.V. All rights reserved.