Protein Structure: Motifs, Folds, and Domains The classic definition of a protein domain is that a polypeptide chain comprising the domain remains highly stable such that it retains its three-dimensional structure and biological function independent of the rest of the larger protein (Richardson, 1981...
and pattern, which recognizes a specific part of DNA and can bind with the single or double-stranded DNA (Rudnick & Bruinsma, 1999). Hence, theprotein domainsor motifs and the specific part of DNA are crucial to recognizing the binding between DNA and protein. Therefore predicting and ...
First, we investigated TATA-binding proteins (TBPs), which bind to TATA-box motifs in eukaryotic promoters26. Many DNA viruses target human TBP to promote viral gene expression or modulate host gene expression27,28. So far, three families of large dsDNA viruses have been found to encode viral...
3b shows a high similarity and conservation of the main protein motifs and domains among these three DRG1 homologs. The main difference can be found in the conserved G-binding domain (G5 motif) where 274Ser-His-Gln in SceRBG1 is replaced with the Ala-His-His sequence in human and sponge...
and fills in domain superfamily and functional site information, as well as structural motifs, for each region of the sequence. It then re-sorts the hits and calculates a set of nonredundant representative hits. The result is presented in a tab-delimited flat file and can be looked at ...
Table 2 Properties and motifs of maize SUN-domain protiens. Full size table Conservation of Two Classes of SUN-domain Proteins in Plants We next carried out a phylogenetic analysis of CCSD and PM3-type SUN-domain protein sequences from maize, sorghum, rice,Arabidopsis, and moss (Physcomitrella...
These motifs coincide with the recognition sites for antibodies, as the epitopes of four monoclonal antibodies and two polyclonal antibodies were shown to overlap with the UPMs. Most of the UPMs were found to correlate well with the potential antigenic regions predicted by PROTEAN. Furthermore, an...
Other members of the PDI family differ substantially in terms of the a/b-domains configurations and other important motifs (Fig.1A). Phylogenetic analysis that is based on sequence similarities of PDI reveals the existence of multiple subfamilies, markedly the AGR (TXNDC12, AGR2, AGR3), TMX...
(2003) Domains, motifs, and clusters in the protein universe. Curr. Opin. Chem. Biol., 7, 5-11.Liu J, Rost B (2003) Domains, motifs, and clusters in the protein universe. Current Opinion in Chemical Biology 7: 5-11. PMID: 12547420...
. Our analysis result (Supplementary Fig.1) indicated that the relatively large prediction errors under two clustering settings may result from certain protein families, domains, and organisms (e.g., histone and GPCR for the protein families, trypsin and kringle for the domains, and bovine for ...