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Nanocarriers as an Emerging Platform for Cancer Therapy
Published in Lajos P. Balogh, Nano-Enabled Medical Applications, 2020
Dan Peer, Jeffrey M. Karp, Seungpyo Hong, Omid C. Farokhzad, Rimona Margalit, Robert Langer
It is also possible to increase binding affinity and selectivity to cell surface targets by engineering proteins that detect a specific conformation of a target receptor. In a recent in vivo study using a fusion protein consisting of an scFv antibody fragment to target and deliver small interfering RNA (siRNA) to lymphocytes—a type of white blood cell—a 10,000-fold increased affinity for the target receptor, integrin LFA-1, was observed [18]. Integrin LFA-1 is usually present in a low-affinity non-adhesive form on na¨ıve leukocytes (white blood cells that are not activated by cancer cells or pathogens that enter the body), but converts to the high-affinity adhesive form through conformational changes on activation of the immune system. Therefore, targeting the high-affinity form of LFA-1 enables drugs to be selectively delivered to the activated and adhesive leukocytes. New classes of targeting molecules can be engineered to target specific conformations. These include small protein domains, known as affibodies, that can be engineered to bind specifically to different target proteins in a conformational-sensitive manner. Other small proteins that act like antibodies—called avimers—are used to bind selectively to target receptors through multivalent effects. Nanobodies, which are heavy-chain antibodies engineered to one tenth of the size of an intact antibody with a missing light chain, have been used to bind to carcinoembryonic antigen (CEA), a protein used as a tumour marker [38–40] (Fig. 2.2b).
Cellular and Viral Oncogenes
Published in Pimentel Enrique, Oncogenes, 2020
Cellular oncogenes, as all genes, are subjected to continuous evolutionary changes and data obtained from studies at either the DNA or the protein levels may contribute to delineate the phylogeny of oncogenes and to define the functional properties of the respective protein products. The protein domains which are more highly conserved in evolution are probably those which have a more crucial role for preservation of the essential functional properties of the protein in different species. Such domains may be recognized by comparative studies of either the nucleotide or amino acid sequences from the gene or the protein, respectively. A discussion of this subject has been published.32
Disease Prediction and Drug Development
Published in Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam, Introduction to Computational Health Informatics, 2019
Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam
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.
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).
Genetic engineering strategies for construction of multivalent chimeric VLPs vaccines
Published in Expert Review of Vaccines, 2020
Xinnuo Lei, Xiong Cai, Yi Yang
Protein domains are units of evolution [95,96]. Nature is a tinkerer and not an inventor, and often brings several domains together to form multi-domain and multifunctional proteins [97–99]. Each domain structure is able to fold, function, and exist independently of the rest of the protein domain(s) so that they can be ‘swapped’ by genetic engineering to make chimeric proteins [100]. In a same way, domains of viral structural proteins can be appropriately manipulated to make chimeric proteins and form chi–VLP.