Disease Prediction and Drug Development
Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam in Introduction to Computational Health Informatics, 2019
Genome analysis tools play a major role in understanding the structure and function of genes, gene-variations, pathway variations and facilitate identifying possible causes of genetic diseases. The tools include: 1) identifying the sequence of nucleotides making a genome; 2) identifying gene-sequences in a genome sequence; 3) identifying the coregulated genes in gene-groups called operons; 4) predict three-dimensional folding-structure of proteins; 5) identifying protein-domains and their properties; 6) identifying the protein-DNA binding patterns; 7) identifying the protein-protein binding patterns; 8) deriving metabolic pathways in newly sequenced genomes; 9) deriving cell signaling pathways using a combination of artificial intelligence technique such as clustering and microarray analysis; 10) simulation of metabolic flux using partial differential equations; 11) derivation of microRNAs and 12) analysis of variations of genes using multiple techniques such as SNP (Single-Nucleotide Polymorphism), GWAS (Genome-Wide Association Studies), SAGE (Serial Analysis of Gene Expressions), etc.
Plant Lectins in Cancer Treatment: The Case of Viscum album L.
Spyridon E. Kintzios, Maria G. Barberaki, Evangelia A. Flampouri in Plants That Fight Cancer, 2019
Advances in analytical techniques generate significant progress in lectinology, highlighting the insufficiency of existing classification systems to explain and describe new data. The traditional classifications are being supplanted by homology-based systems that incorporate sequence and structural homology plus evolutionary relations in order to categorize the plant lectins (De Hoff et al. 2009). A vast number of plant lectins have been identified and genome-transcriptome analyses revealed that groups are particularly widespread; thus many proteins contain one or more carbohydrate-binding domains, forming complex structures. Thorough analyses of the lectin sequences distinguish 12 different, evolutionary and structurally related carbohydrate-binding domains identified in plants. Every protein domain is characterized by unique folding with highly specific sugar binding sites. The domains are Agaricus bisporus agglutinin homologs, amaranthins, class V chitinase homologs, cyanovirin family, Euonymus europaeus agglutinin family, Galanthus nivalis agglutinin family, proteins with hevein domains, jacalins, proteins with a legume lectin domain, LysM domains, Nicotiana tabacum agglutinin family, and ricin-B family (Van Damme et al. 2008). Representative lectins from each family are listed in Table 8.1.
The Stress Response and Stress Proteins
John J. Lemasters, Constance Oliver in Cell Biology of Trauma, 2020
Many weak forces help stabilize the native structures of proteins, but the hydrophobic effect is generally considered the dominant force driving folding. In the cell, hydrophobic side chains cause surrounding water molecules to adopt an ordered, lattice-like structure that is entropically very unfavorable. Protein domains begin folding with the collapse of hydrophobic side chains into the “core” of the molecule. This collapse, which occurs on a millisecond time scale, allows these side chains to interact with each other and shields them from the surrounding aqueous environment. On the same time scale, units of secondary structure form, primarily α helices and β sheets. At this stage, the protein has a compact structure, but lacks stable tertiary interactions and is thought to resemble the “molten globule” state observed in some proteins under very specific, mild denaturation conditions. The transition from this structure to the final native structure generally requires 50 ms to a few minutes.23
TMT-Based proteomics analysis of LPS-induced acute lung injury
Published in Experimental Lung Research, 2021
Shengsong Chen, Yi Zhang, Qingyuan Zhan
Proteins are composed of structural domains that control function and provide insight into protein evolution. The study of protein domains is of great importance for understanding the biological functions and evolution of proteins. InterPro is a database that combines information on protein families, domains, and functional sites. We used this database to analyze the annotation and enrichment of the functional domains of the DEPs and list the top 10 items that were significantly enriched with the smallest P value. The results (Figure 4C) showed enrichment of the DEPs in the following sites, proteins, families, and functions: minichromosome maintenance proteins, minichromosome maintenance, conserved sites, the MCM N-terminal domain, the MCM OB domain, the MCM domain, peptidase S1A, the chymotrypsin family, serine proteases, the trypsin domain, the DAPIN domain, peptidase S1, the PA clan, and the serpin domain.
Quantitative analysis of the global proteome in lung from mice with blast injury
Published in Experimental Lung Research, 2020
Ying Liu, Yunen Liu, Changci Tong, Peifang Cong, Xiuyun Shi, Lin Shi, Mingxiao Hou, Hongxu Jin, Yongli Bao
In order to find out whether the differentially expressed proteins had significant enrichment trends in some functional types, enrichment analysis of GO classification, KEGG pathway and protein domain were conducted. 20 of the most significant enrichment classifications are presented in the bubble chart (Figure 4). In the biological process category, the regulated proteins were highly enriched in terms such as positive regulation of cytokine production, regulation of carbohydrate metabolic process, and acute-phase response. The enrichment analysis of the cellular component category showed that proteins related to extracellular space, mitochondrial protein complex, and mitochondrial membrane part. According to the molecular function enrichment results, we found they are take part in NADH dehydrogenase (ubiquinone) activity, peptidase inhibitor activity, cyclic-nucleotide phosphodiesterase activity, and serine-type endopeptidase inhibitor activity (Additional file 6). KEGG pathway enrichment, which is an information network that connects known intermolecular interactions, was further conducted to elucidate the biological functions of proteins. We found the changes of vitamin digestion and absorption, asthma, and oxidative phosphorylation (Additional file 7). In addition, protein domain, which refers to some components that occur repeatedly in different protein molecules were shown (Additional file 8).
Identification of the protective effect of Polygonatum sibiricum polysaccharide on d -galactose-induced brain ageing in mice by the systematic characterization of a circular RNA-associated ceRNA network
Published in Pharmaceutical Biology, 2021
Zheyu Zhang, Bo Yang, Jianhua Huang, Wenqun Li, Pengji Yi, Min Yi, Weijun Peng
GO analysis of 679 PSP-related mRNAs identified several GO terms that were highly enriched (Figure 2(E)). The most enriched terms with regards to biological processes were positive regulation of dendritic spine development, cellular component organization, and localization. As for cellular components, the most enriched terms were the intracellular part, organelle part, and cell cortex. The most enriched molecular function terms were protein binding, binding, and protein domain–specific binding. As shown in Figure 2(E), KEGG analysis demonstrated that O-glycan biosynthesis, sulphur metabolism, and adherens junctions, may be closely associated with the ameliorative effect of PSP on cognitive impairment and brain ageing.