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Jingyuan He – One of the best experts on this subject based on the ideXlab platform.
supersecondary structure prediction using chou s pseudo Amino Acid compositionJournal of Computational Chemistry, 2011Co-Authors: Zhongshi He, Jingyuan HeAbstract:
Supersecondary structures (SSSs) are the building blocks of protein 3D structures. Accurate prediction of SSSs can be one important step toward building a tertiary structure from the specified secondary structure. How to improve the accuracy of prediction of SSSs by effectively incorporating the sequence order effects is an important and challenging problem. Based on a different form of Chou’s pseudo Amino Acid composition, a novel approach for feature representation of SSSs is proposed. Amino Acid basic compositions, dipeptide components, and Amino Acid composition distribution are incorporated to represent the compositional features of proteins. Each supersecondary structural motif is characterized as a vector of 36 dimensions. In addition, we propose a novel prediction system by using SVM and IDQD algorithm as classifiers. Our method is trained and tested on ArchDB40 dataset containing 3088 proteins. The highest overall accuracy for the training dataset and the independent testing dataset are 77.7 and 69.4%, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
L Gullo – One of the best experts on this subject based on the ideXlab platform.
effect of pancreatic polypeptide thyrotropin releasing hormone and glucagon on plasma Amino Acid uptake by human pancreasGastroenterology, 1991Co-Authors: L GulloAbstract:
Abstract The effects of pancreatic polypeptide, thyrotropin-releasing hormone, and glucagon on plasma Amino Acid uptake by the exocrine pancreas were studied in 12 healthy volunteers aged 22–31 years. Pancreatic Amino Acid uptake was determined by measuring free plasma Amino Acid concentration before and during pancreatic stimulation with cerulein (50 ng/kg · h). The administration of this peptide caused a significant decrease (by 14%–20%) in plasma Amino Acid concentration. Pancreatic polypeptide and thyrotropin-releasing hormone, given at respective doses of 195 pmol/kg · h and 2 μg/kg · h, significantly prevented this decrease by 79.3% and 55.8%, respectively. Glucagon, administered at a dose of 7.5 μg/kg · h, significantly augmented (by 68.8%) the decreasing effect of cerulein on plasma Amino Acid concentration. In 2 patients with severe exocrine pancreatic insufficiency, cerulein had no effect on the concentration of plasma Amino Acids, whereas the addition of glucagon caused a marked decrease. The results indicate that pancreatic polypeptide and thyrotropin-releasing hormone are able to inhibit plasma Amino Acid uptake by pancreatic acinar cells; this inhibitory effect could be a mechanism by which these peptides decrease pancreatic enzyme secretion. Glucagon does not seem to affect pancreatic Amino Acid uptake, at least not under the experimental conditions of this study. The decrease in plasma Amino Acid concentration following glucagon administration was likely the result of the stimulation of Amino Acid uptake by extrapancreatic tissues by this peptide.
Ken Nishikawa – One of the best experts on this subject based on the ideXlab platform.
protein surface Amino Acid compositions distinctively differ between thermophilic and mesophilic bacteriaJournal of Molecular Biology, 2001Co-Authors: Satoshi Fukuchi, Ken NishikawaAbstract:
Abstract One of the well-known observations of proteins from thermophilic bacteria is the bias of the Amino Acid composition in which charged residues are present in large numbers, and polar residues are scarce. On the other hand, it has been reported that the molecular surfaces of proteins are adapted to their subcellular locations, in terms of the Amino Acid composition. Thus, it would be reasonable to expect that the differences in the Amino Acid compositions between proteins of thermophilic and mesophilic bacteria would be much greater on the protein surface than in the interior. We performed systematic comparisons between proteins from thermophilic bacteria and mesophilic bacteria, in terms of the Amino Acid composition of the protein surface and the interior, as well as the entire Amino Acid chains, by using sequence information from the genome projects. The biased Amino Acid composition of thermophilic proteins was confirmed, and the differences from those of mesophilic proteins were most obvious in the compositions of the protein surface. In contrast to the surface composition, the interior composition was not distinctive between the thermophilic and mesophilic proteins. The frequency of the Amino Acid pairs that are closely located in the space was also analyzed to show the same trend of the single Amino Acid compositions. Interestingly, extracellular proteins from mesophilic bacteria showed an inverse trend against thermophilic proteins (i.e. a reduced number of charged residues and rich in polar residues). Nuclear proteins from eukaryotes, which are known to be abundant in positive charges, showed different compositions as a whole from the thermophiles. These results suggest that the bias of the Amino Acid composition of thermophilic proteins is due to the residues on the protein surfaces, which may be constrained by the extreme environment.