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There are emerging interests in understanding higher order assemblies of biopolymers within and between cells, such as protein-protein and protein-RNA biomolecular condensates. These biomolecular condensates are thought to assemble/disassemble via multivalent interactions, including those mediated particularly by unique repeated amino acid motifs (URM). We asked how common are proteins with such URMs, their incidence and abundance, by exhaustively enumerating repeating motifs of length 3-10 in the human proteome. We found that URMs are very common and widely distributed across the human proteome. Moreover, the number of repetitions and intervals between them do not correlate with their lengths, which suggests that the number of repeats among proteins in the proteome is independent of length, contrary to the notion that short motifs are more abundant then long motifs. Finally, we describe two examples of URMs in proteins known to form higher order biopolymer assemblies: multi-PDZ domain-containing proteins and the FUS family of RNA binding proteins. For the FUS family, we predicted a known sequence 'grammar', specific motifs and interval sequence compositions that are essential to phase separation and material properties of condensates formed by this family of proteins. In PDZ domain-containing proteins we found a novel repeated motif that was surprisingly both within and between individual PDZ domains. We speculate that these motifs could be binding sites for multivalent interactions, a residual result of the mechanism by which PDZ-domain duplications occurred or that the linker sequences between PDZ domains may encode cryptic PDZ domains.
This article was published in the following journal.
Name: Current opinion in structural biology
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SNARE proteins where the central amino acid residue of the SNARE motif is an ARGININE. They are classified separately from the Q-SNARE PROTEINS where the central amino acid residue of the SNARE motif is a GLUTAMINE. This subfamily contains the vesicle associated membrane proteins (VAMPs) based on similarity to the prototype for the R-SNAREs, VAMP2 (synaptobrevin 2).
SNARE proteins in which the central amino acid residue of the SNARE motif is a GLUTAMINE. They are classified separately from the R-SNARE PROTEINS where the central amino acid residue of the SNARE motif is an ARGININE. Subfamilies, the QA-SNARES; QB-SNARES; and QC-SNARES are grouped by the position of their SNARE motif-containing-domains in the SNARE complex and by their sequence similarities.
A helix-turn-helix motif characterized by three alpha-helices and four-stranded beta-sheets arranged in the order alpha1-beta1-beta2-alpha2-alpha3-beta3-beta4. The third alpha-helix contacts the major groove of DNA. The ETS motif and the flanking amino acid sequences of Ets proteins influence the binding affinity, and the alteration of a single amino acid in the Ets domain can change its DNA binding specificity.
A conserved AMINO ACID SEQUENCE located in the intracellular domains of a family of transmembrane proteins that negatively regulate the signal transduction processes emanating from transmembrane proteins containing IMMUNORECEPTOR TYROSINE-BASED ACTIVATION MOTIFS. The CONSENSUS SEQUENCE of this motif is I(or V)LXYXXL(or V) (where X denotes any amino acid). Also known as ITIM motifs.
Protein interaction motifs of approximately 40 amino acids that usually terminate in TRYPTOPHAN and ASPARTIC ACID. They form characteristic beta-propeller structures and occur in many eukaryotic proteins that function in a variety of cellular processes. Proteins that contain WD40 repeats often function as assembly platforms for MULTIPROTEIN COMPLEXES.
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