SNOSite: Exploiting Maximal Dependence Decomposition to Identify Cysteine S-Nitrosylation with Substrate Site Specificity

S-nitrosylation, the covalent attachment of a nitric oxide to (NO) the sulfur atom of cysteine, is a selective and reversible protein post-translational modification (PTM) that regulates protein activity, localization, and stability. Despite its implication in the regulation of protein functions and cell signaling, the substrate specificity of cysteine S-nitrosylation remains unknown. Based on a total of 586 experimentally identified S-nitrosylation sites from SNAP/L-cysteine-stimulated mouse endothelial cells, this work presents an informatics investigation on S-nitrosylation sites including structural factors such as the flanking amino acids composition, the accessible surface area (ASA) and physicochemical properties, i.e. positive charge and side chain interaction parameter. Due to the difficulty to obtain the conserved motifs by conventional motif analysis, maximal dependence decomposition (MDD) has been applied to obtain statistically significant conserved motifs. Support vector machine (SVM) is applied to generate predictive model for each MDD-clustered motif. According to five-fold cross-validation, the MDD-clustered SVMs could achieve an accuracy of 0.902, and provides a promising performance in an independent test set. The effectiveness of the model was demonstrated on the correct identification of previously reported S-nitrosylation sites of Bos taurus dimethylarginine dimethylaminohydrolase 1 (DDAH1) and human hemoglobin subunit beta (HBB). Finally, the MDD-clustered model was adopted to construct an effective web-based tool, named SNOSite (http://csb.cse.yzu.edu.tw/SNOSite/), for identifying S-nitrosylation sites on the uncharacterized protein sequences

Characteristics of eddy structures generated by a self-aspirating impeller

Na podstawie pomiarów wykonanych przy użyciu anemometru laserowego w mieszalniku z samozasysającym mieszadłem tarczowym wykonano obliczenia wielkości skal długości, czasu i prędkości dla wirów z zakresu Kolmogurtncu, Taylora i Brodkcy'a.Based on measurements carried out using a laser anemometer in an agitator with a self-aspirating impeller the calculations of'length. time and velocity scales for eddies in the Kolmtigorov, Taylor and Brodkey range were made

Method of convective velocity determination from dissipative range of energy spectrum

In the study a new proposal of convective velocity determination necessary for eddy size determination from the dissipative range in a turbulent flow in a mixer was made. The proposed quantity depends on all the mean and fluctuating velocity components. By applying convective velocity one may determine the distribution of time and linear Taylor microscale in a stirred vessel