{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T06:11:30Z","timestamp":1790662290213,"version":"4.1.0"},"reference-count":58,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2020,10,2]],"date-time":"2020-10-02T00:00:00Z","timestamp":1601596800000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>\n                    The proteome of the malaria parasite\n                    <jats:italic>Plasmodium falciparum<\/jats:italic>\n                    is notable for the pervasive occurrence of homopeptides or low-complexity regions (i.e., regions that are made from a small subset of amino-acid residue types). The most prevalent of these are made from residues encoded by adenine\/thymidine (AT)-rich codons, in particular asparagine. We examined homopeptide occurrences within protein domains in\n                    <jats:italic>P. falciparum<\/jats:italic>\n                    . Homopeptide enrichments occur for hydrophobic (e.g., valine), or small residues (alanine or glycine) in short spans (&lt;5 residues), but these enrichments disappear for longer lengths. We observe that short asparagine homopeptides (&lt;10 residues long) have a dramatic relative depletion inside protein domains, indicating some selective constraint to keep them from forming. We surmise that this is possibly linked to co-translational protein folding, although there are specific protein domains that are enriched in longer asparagine homopeptides (\u226510 residues) indicating a functional linkage for specific poly-asparagine tracts. Top gene ontology functional category enrichments for homopeptides associated with diverse protein domains include \u201cvesicle-mediated transport\u201d, and \u201cDNA-directed 5\u2032-3\u2032 RNA polymerase activity\u201d, with various categories linked to \u201cbinding\u201d evidencing significant homopeptide depletions. Also, in general homopeptides are substantially enriched in the parts of protein domains that are near\/in IDRs. The implications of these findings are discussed.\n                  <\/jats:p>","DOI":"10.7717\/peerj.9940","type":"journal-article","created":{"date-parts":[[2020,10,2]],"date-time":"2020-10-02T04:47:23Z","timestamp":1601614043000},"page":"e9940","source":"Crossref","is-referenced-by-count":2,"title":["The relationship between protein domains and homopeptides in the\n                    <i>Plasmodium falciparum<\/i>\n                    proteome"],"prefix":"10.7717","volume":"8","author":[{"given":"Yue","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsin Jou","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul 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