Nucleotide sequences of genome segments $8, encoding a capsid
... being folded to give capsomeres of the same dimensions, which would make the three viruses indistinguishable in electron microscopy. The high scores (70 to 75%) obtained for chemically similar amino acids (Dayhoff et al., 1972) would also support the supposition that the spatial conformations of the ...
... being folded to give capsomeres of the same dimensions, which would make the three viruses indistinguishable in electron microscopy. The high scores (70 to 75%) obtained for chemically similar amino acids (Dayhoff et al., 1972) would also support the supposition that the spatial conformations of the ...
Nucleotide sequences of genome segments $8, encoding a capsid
... being folded to give capsomeres of the same dimensions, which would make the three viruses indistinguishable in electron microscopy. The high scores (70 to 75%) obtained for chemically similar amino acids (Dayhoff et al., 1972) would also support the supposition that the spatial conformations of the ...
... being folded to give capsomeres of the same dimensions, which would make the three viruses indistinguishable in electron microscopy. The high scores (70 to 75%) obtained for chemically similar amino acids (Dayhoff et al., 1972) would also support the supposition that the spatial conformations of the ...
View/Open - Oregon State University
... and the codon of the mRNA. A sequence known as the Shine-Dalgarno sequence in the mRNA (in prokaryotes only) helps the ribosome to properly align the mRNA in the ribosome. The Shine-Dalgarno sequence forms a base paired region with the 16S rRNA of the 30S subunit of the ribosome. 4. Elongation of tr ...
... and the codon of the mRNA. A sequence known as the Shine-Dalgarno sequence in the mRNA (in prokaryotes only) helps the ribosome to properly align the mRNA in the ribosome. The Shine-Dalgarno sequence forms a base paired region with the 16S rRNA of the 30S subunit of the ribosome. 4. Elongation of tr ...
Based Method for Identification of Horizontal Gene Transfer in Bacteria
... 1-Letter Code A R N D C Q E G H I L K M F P S T W Y V ...
... 1-Letter Code A R N D C Q E G H I L K M F P S T W Y V ...
Sequence-based prediction of protein interaction
... genomics, the amount of protein structures, determined by timeconsuming and expensive experimental technologies, is significantly smaller than those of protein sequences produced by large-scale DNA sequencing methods. For example, by July 29, 2008, there are 392 667 identified protein sequences in U ...
... genomics, the amount of protein structures, determined by timeconsuming and expensive experimental technologies, is significantly smaller than those of protein sequences produced by large-scale DNA sequencing methods. For example, by July 29, 2008, there are 392 667 identified protein sequences in U ...
Determination of the Binding Site-Size of the Protein
... Binding mode is not always the same for several DNA-binding proteins. For example, differences in the binding condition, such as the ionic strength, pH and some small molecules included in the reaction mixture, can affect the binding mode of SSB (8). These factors also influence the stability of the ...
... Binding mode is not always the same for several DNA-binding proteins. For example, differences in the binding condition, such as the ionic strength, pH and some small molecules included in the reaction mixture, can affect the binding mode of SSB (8). These factors also influence the stability of the ...
Orthologs, paralogs and homology inference Where are we now?
... – identify genes in reference genomes that may have the same or similar functions, so that comprehensive curation can be done simultaneously ...
... – identify genes in reference genomes that may have the same or similar functions, so that comprehensive curation can be done simultaneously ...
Discovery of a novel ligand that modulates the
... Encouraged by the fact that clear changes could be observed in the presence of Liddean, we next used it as a tool to examine Liddean-induced changes on the global peptide-binding space of reptin. ...
... Encouraged by the fact that clear changes could be observed in the presence of Liddean, we next used it as a tool to examine Liddean-induced changes on the global peptide-binding space of reptin. ...
Engineering and Identifying Supercharged Proteins
... Most medicines are small molecules, chemical compounds containing less than 100 atoms. For many diseases, however, small-molecule-based therapies have not been found. Recent efforts to discover bioactive molecules including human therapeutics have increasingly focused on macromolecules—for the purp ...
... Most medicines are small molecules, chemical compounds containing less than 100 atoms. For many diseases, however, small-molecule-based therapies have not been found. Recent efforts to discover bioactive molecules including human therapeutics have increasingly focused on macromolecules—for the purp ...
Nuclear Factor-90 of Activated T-Cells: A Double
... DNA-binding activity and transcriptional activation to the immunosuppressant drugs cyclosporin A and FK506 (31, 32). Both subunits of the heterodimeric complex have been cloned and found to consist of subunits of Mr ) 45 000 (NF45) and Mr ) 90 000 (NF90). The phosphorylation state of this ARRE-2 bin ...
... DNA-binding activity and transcriptional activation to the immunosuppressant drugs cyclosporin A and FK506 (31, 32). Both subunits of the heterodimeric complex have been cloned and found to consist of subunits of Mr ) 45 000 (NF45) and Mr ) 90 000 (NF90). The phosphorylation state of this ARRE-2 bin ...
Lecture 12
... Labeling protocol – alkylation (well-developed); Affinity isolation: simplified peptide mixtures; presence and # of Cys aids identification (constraint) The only commercially available method selective for a specific residue (Cys); enrichment allows proteomic studies on a much wider dynamic range th ...
... Labeling protocol – alkylation (well-developed); Affinity isolation: simplified peptide mixtures; presence and # of Cys aids identification (constraint) The only commercially available method selective for a specific residue (Cys); enrichment allows proteomic studies on a much wider dynamic range th ...
A quantitative atlas of mitotic phosphorylation
... either G1 or M-phase arrested cells grown in conventional media (‘‘light’’) and lysed in 8 M urea (Fig. 1). The mixed whole-cell extracts were directly proteolyzed with trypsin. The resultant peptides were desalted by solid-phase extraction and then separated by strong cation exchange (SCX) chromato ...
... either G1 or M-phase arrested cells grown in conventional media (‘‘light’’) and lysed in 8 M urea (Fig. 1). The mixed whole-cell extracts were directly proteolyzed with trypsin. The resultant peptides were desalted by solid-phase extraction and then separated by strong cation exchange (SCX) chromato ...
Free amino acids and proteins dynamics in somatic embryogenesis
... 2006). However, some specific analyzes should be done to determine the roles of specific amino acids. In fact, studies have shown that certain amino acids may be more efficient than others in this process (Garin et al., 2000; Booz et al., 2009). There are several studies on the biosynthesis and accu ...
... 2006). However, some specific analyzes should be done to determine the roles of specific amino acids. In fact, studies have shown that certain amino acids may be more efficient than others in this process (Garin et al., 2000; Booz et al., 2009). There are several studies on the biosynthesis and accu ...
Production of final product
... Some enzyme reactions produce light and this can be measured to detect product ...
... Some enzyme reactions produce light and this can be measured to detect product ...
Protein conformational changes induced by adsorption onto material
... unfolded. The biological role of nonfolded protein domains is also the focus of considerable work in structural biology [25]. The classic view of Langmuir isotherm for protein adsorption on material surfaces assumes that some interaction energy is reversibly available to form a protein-material comp ...
... unfolded. The biological role of nonfolded protein domains is also the focus of considerable work in structural biology [25]. The classic view of Langmuir isotherm for protein adsorption on material surfaces assumes that some interaction energy is reversibly available to form a protein-material comp ...
Topological characterization of the essential Escherichia coli cell
... To generate L-lactamase fusions we followed the method described by [17]. Various truncated forms of the ftsW gene (at the 3P end) were ampli¢ed by PCR from the E. coli chromosomal DNA using as primers oligonucleotides generating a KpnI site. The oligonucleotide A60 (5P-CGTACCAGGTACCGCCTGTGCCAGCAGTA ...
... To generate L-lactamase fusions we followed the method described by [17]. Various truncated forms of the ftsW gene (at the 3P end) were ampli¢ed by PCR from the E. coli chromosomal DNA using as primers oligonucleotides generating a KpnI site. The oligonucleotide A60 (5P-CGTACCAGGTACCGCCTGTGCCAGCAGTA ...
Intricacies and surprises of nuclear–mitochondrial co
... mammalian mt protein synthesis machinery, including mt EF-Tu and SerRS proteins, may have simply been able to cope with the tRNASer D-arm truncation. The D-armless tRNASer seems to still function suboptimally in mt protein synthesis, as inferred from results obtained in a mammalian mt in vitro trans ...
... mammalian mt protein synthesis machinery, including mt EF-Tu and SerRS proteins, may have simply been able to cope with the tRNASer D-arm truncation. The D-armless tRNASer seems to still function suboptimally in mt protein synthesis, as inferred from results obtained in a mammalian mt in vitro trans ...
Supplementary data Expression and purification of
... These recombinant plasmids were transformed into E. coli Rosetta™ and induced the production for 3h, overnight, respectively. The Rosetta™ cell line helps to alleviate codon bias and enhance expression of heterologous proteins. The 10-20% gradient SDS-PAGE gel analysis suggests that fusion peptides ...
... These recombinant plasmids were transformed into E. coli Rosetta™ and induced the production for 3h, overnight, respectively. The Rosetta™ cell line helps to alleviate codon bias and enhance expression of heterologous proteins. The 10-20% gradient SDS-PAGE gel analysis suggests that fusion peptides ...
Holbert, Daniel: Detecting motifs with EMOTIF-MAKER and MASIA: A critical comparison of two tools for finding protein motifs
... ways to create motifs that match a given multiple alignment. The most intuitive motif, perhaps, is the one in which each position contains the smallest group that can represent all of the amino acids observed at that position in the multiple alignment. However, if one of the proteins has a sequencin ...
... ways to create motifs that match a given multiple alignment. The most intuitive motif, perhaps, is the one in which each position contains the smallest group that can represent all of the amino acids observed at that position in the multiple alignment. However, if one of the proteins has a sequencin ...
Protein Interactions Techniques and Challenges
... There are some types of residues (amonoacids) that have a preference to bind, while other types prefer not to bind. Binding Site Prediction is the task to identify specific regions on a protein surface that have a binding preference (hot spots) Binding Site Prediction can improve docking since it co ...
... There are some types of residues (amonoacids) that have a preference to bind, while other types prefer not to bind. Binding Site Prediction is the task to identify specific regions on a protein surface that have a binding preference (hot spots) Binding Site Prediction can improve docking since it co ...
File - Tay
... (2) What domain are found in the related proteins located at the lysosome? - Are Glycoside hydrolase family 20, catalytic domain found in those protein? Method: Using the SMART database to find the domains of the related proteins that are located in the lysosome. ...
... (2) What domain are found in the related proteins located at the lysosome? - Are Glycoside hydrolase family 20, catalytic domain found in those protein? Method: Using the SMART database to find the domains of the related proteins that are located in the lysosome. ...
Gene Section SS18 (synovial sarcoma translocation, chromosome 18) Atlas of Genetics and Cytogenetics
... 418 amino acids. 2 domains; the SHN domain (the SYT N-terminal homology domain) that is found in proteins from a wide variety of species ranging from plants to human, and the QPGY domain at the C-terminal part, rich in glutamine, proline, glycine and tyrosine. Four putative src-homology binding doma ...
... 418 amino acids. 2 domains; the SHN domain (the SYT N-terminal homology domain) that is found in proteins from a wide variety of species ranging from plants to human, and the QPGY domain at the C-terminal part, rich in glutamine, proline, glycine and tyrosine. Four putative src-homology binding doma ...
File - Tay
... (2) What domain are found in the related proteins located at the lysosome? - Are Glycoside hydrolase family 20, catalytic domain found in those protein? Method: Using the SMART database to find the domains of the related proteins that are located in the lysosome. ...
... (2) What domain are found in the related proteins located at the lysosome? - Are Glycoside hydrolase family 20, catalytic domain found in those protein? Method: Using the SMART database to find the domains of the related proteins that are located in the lysosome. ...
TissueNet database of human tissue protein–protein interactions
... Here, we focus on the human PPIs. Unlike unicellular organisms such as yeast, the human body is composed of many tissues, each expressing a distinct set of proteins [e.g. (8,9)]. Consequently, many proteins have varying PPI partners across tissues (10,11). A tissue-sensitive view of PPIs is therefor ...
... Here, we focus on the human PPIs. Unlike unicellular organisms such as yeast, the human body is composed of many tissues, each expressing a distinct set of proteins [e.g. (8,9)]. Consequently, many proteins have varying PPI partners across tissues (10,11). A tissue-sensitive view of PPIs is therefor ...
Intrinsically disordered proteins
An intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure. IDPs cover a spectrum of states from fully unstructured to partially structured and include random coils, (pre-)molten globules, and large multi-domain proteins connected by flexible linkers. They constitute one of the main types of protein (alongside globular, fibrous and membrane proteins).The discovery of IDPs has challenged the traditional protein structure paradigm, that protein function depends on a fixed three-dimensional structure. This dogma has been challenged over the last decades by increasing evidence from various branches of structural biology, suggesting that protein dynamics may be highly relevant for such systems. Despite their lack of stable structure, IDPs are a very large and functionally important class of proteins. In some cases, IDPs can adopt a fixed three-dimensional structure after binding to other macromolecules.