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AMP-activated protein kinase (AMPK) is a metabolite- sensed protein kinase in various eukaryotes. The activated AMPK regulates important proteins which cause diabetes, obesity, metabolic aberrant, and also breast cancer. In this study, the yeast AMPK structure was used as a template to model the human AMPK structure. By homology modeling, the reliable AMPK structure was built, and the active binding...
Myf5 plays a major role in determining myogenic cell fate at the onset of skeletal muscle formation in the embryo and maintenance of its phenotype. we cloned the total coding region of duck Myf5 gene in this study. The total CDS region of duck Myf5 gene consists of 768 nucleotides and codes for 255 AA, including the bHLH domain. The similarity between duck and chicken is 90.5% at nucleotide level...
The Human Genome is essentially complete, and yet the impact on how we understand physiological processes such as cellular force transduction has been minimal in part because of our inability to work from known sequence to structure, i.e. the Foldome. In order to specifically identify cytoskeletal proteins that change conformation or assembly in stressed versus static cells, in situ labeling of sterically-shielded...
The wild boar OPN cDNA in size of 909bp was cloned by RT-PCR and analyzed by bioinformatics. The result showed that wild boar OPN contains 1) a potential calcium phosphate apatite binding region of eight consecutive Asp residues beginning at amino acid 86, 2) a cell-attachment Gly-Arg-Gly- Asp-Ser (GRGDS) sequence (residues 153-157), 3) a thrombin RS cleavage site (residues 163 and 164). The phylogenetic...
The menin is a tumour suppressor protein, whose deficiency is the cause of familial multiple endocrine neoplasia type I (MEN1). To understand its mutation pattern is very helpful for managing its clinical manifest and outcome. The amino-acid pair predictability is used to transfer the symbolized human menin and its 99 missense point mutants to scalar data and classify the amino-acid pairs as predictable...
Autism is one of the major disorders associated with brain development that presents early in life, as early as the fetal development phases to the early stages post birth. About 1 in 150 eight-year-old children in multiple areas of the United States had an autism spectrum disorder (ASD). Environmental agents and genetics are likely players but no specific target or cure has yet been identified. In...
Protein cleavage by a caspase enzyme is observed in many pathways including apoptosis pathway, which induces protein modifications such as N-myristoylation. By exhaustive search of NCBI GenBank database based on the information in PeptideCutter website, we have identified a protein very likely to control apoptosis after N-myristoylation which is caused by the cleavage by caspase-8. To find more rules...
Codon usage bias is well established in different species from bacteria to mammals. A number of models have been proposed to show this bias as a balance between mutation and selection. Most of these models emphasize controlling the speed of protein translation from the mRNA and increasing the accuracy where this bias is dependent on the abundance and properties of the available tRNA. In this work,...
Opioid is provided with the characteristics of antalgic and addiction, its primary target is opioid receptor. As for novel drug design, it is of great significance to study the structures and functions of opioid receptors by using bioinformatics methods, and it will contribute to defending and abstaining from opioid drug addiction. Bioinformatics methods such as sequence alignment, evolution analysis...
Human mitochondrial proteins are involved in fundamental biological process including apoptosis, energy production and many metabolic pathways, prediction of mitochondrial proteins is a major challenge in genome annotation. In this study, we implemented a machine learning approach and developed reliable neural network and SVM based methods to classify human mitochondria proteins with high confidence...
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