Word decoding of protein amino Acid sequences with availability analysis: a linguistic approach.

The amino acid sequences of proteins determine their three-dimensional structures and functions. However, how sequence information is related to structures and functions is still enigmatic. In this study, we show that at least a part of the sequence information can be extracted by treating amino aci...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Kenta Motomura, Tomohiro Fujita, Motosuke Tsutsumi, Satsuki Kikuzato, Morikazu Nakamura, Joji M Otaki
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/69640475a7e64675a31d1c645d27b861
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:69640475a7e64675a31d1c645d27b861
record_format	dspace
spelling	oai:doaj.org-article:69640475a7e64675a31d1c645d27b8612021-11-18T08:07:48ZWord decoding of protein amino Acid sequences with availability analysis: a linguistic approach.1932-620310.1371/journal.pone.0050039https://doaj.org/article/69640475a7e64675a31d1c645d27b8612012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23185527/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The amino acid sequences of proteins determine their three-dimensional structures and functions. However, how sequence information is related to structures and functions is still enigmatic. In this study, we show that at least a part of the sequence information can be extracted by treating amino acid sequences of proteins as a collection of English words, based on a working hypothesis that amino acid sequences of proteins are composed of short constituent amino acid sequences (SCSs) or "words". We first confirmed that the English language highly likely follows Zipf's law, a special case of power law. We found that the rank-frequency plot of SCSs in proteins exhibits a similar distribution when low-rank tails are excluded. In comparison with natural English and "compressed" English without spaces between words, amino acid sequences of proteins show larger linear ranges and smaller exponents with heavier low-rank tails, demonstrating that the SCS distribution in proteins is largely scale-free. A distribution pattern of SCSs in proteins is similar among species, but species-specific features are also present. Based on the availability scores of SCSs, we found that sequence motifs are enriched in high-availability sites (i.e., "key words") and vice versa. In fact, the highest availability peak within a given protein sequence often directly corresponds to a sequence motif. The amino acid composition of high-availability sites within motifs is different from that of entire motifs and all protein sequences, suggesting the possible functional importance of specific SCSs and their compositional amino acids within motifs. We anticipate that our availability-based word decoding approach is complementary to sequence alignment approaches in predicting functionally important sites of unknown proteins from their amino acid sequences.Kenta MotomuraTomohiro FujitaMotosuke TsutsumiSatsuki KikuzatoMorikazu NakamuraJoji M OtakiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 11, p e50039 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kenta Motomura Tomohiro Fujita Motosuke Tsutsumi Satsuki Kikuzato Morikazu Nakamura Joji M Otaki Word decoding of protein amino Acid sequences with availability analysis: a linguistic approach.
description	The amino acid sequences of proteins determine their three-dimensional structures and functions. However, how sequence information is related to structures and functions is still enigmatic. In this study, we show that at least a part of the sequence information can be extracted by treating amino acid sequences of proteins as a collection of English words, based on a working hypothesis that amino acid sequences of proteins are composed of short constituent amino acid sequences (SCSs) or "words". We first confirmed that the English language highly likely follows Zipf's law, a special case of power law. We found that the rank-frequency plot of SCSs in proteins exhibits a similar distribution when low-rank tails are excluded. In comparison with natural English and "compressed" English without spaces between words, amino acid sequences of proteins show larger linear ranges and smaller exponents with heavier low-rank tails, demonstrating that the SCS distribution in proteins is largely scale-free. A distribution pattern of SCSs in proteins is similar among species, but species-specific features are also present. Based on the availability scores of SCSs, we found that sequence motifs are enriched in high-availability sites (i.e., "key words") and vice versa. In fact, the highest availability peak within a given protein sequence often directly corresponds to a sequence motif. The amino acid composition of high-availability sites within motifs is different from that of entire motifs and all protein sequences, suggesting the possible functional importance of specific SCSs and their compositional amino acids within motifs. We anticipate that our availability-based word decoding approach is complementary to sequence alignment approaches in predicting functionally important sites of unknown proteins from their amino acid sequences.
format	article
author	Kenta Motomura Tomohiro Fujita Motosuke Tsutsumi Satsuki Kikuzato Morikazu Nakamura Joji M Otaki
author_facet	Kenta Motomura Tomohiro Fujita Motosuke Tsutsumi Satsuki Kikuzato Morikazu Nakamura Joji M Otaki
author_sort	Kenta Motomura
title	Word decoding of protein amino Acid sequences with availability analysis: a linguistic approach.
title_short	Word decoding of protein amino Acid sequences with availability analysis: a linguistic approach.
title_full	Word decoding of protein amino Acid sequences with availability analysis: a linguistic approach.
title_fullStr	Word decoding of protein amino Acid sequences with availability analysis: a linguistic approach.
title_full_unstemmed	Word decoding of protein amino Acid sequences with availability analysis: a linguistic approach.
title_sort	word decoding of protein amino acid sequences with availability analysis: a linguistic approach.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/69640475a7e64675a31d1c645d27b861
work_keys_str_mv	AT kentamotomura worddecodingofproteinaminoacidsequenceswithavailabilityanalysisalinguisticapproach AT tomohirofujita worddecodingofproteinaminoacidsequenceswithavailabilityanalysisalinguisticapproach AT motosuketsutsumi worddecodingofproteinaminoacidsequenceswithavailabilityanalysisalinguisticapproach AT satsukikikuzato worddecodingofproteinaminoacidsequenceswithavailabilityanalysisalinguisticapproach AT morikazunakamura worddecodingofproteinaminoacidsequenceswithavailabilityanalysisalinguisticapproach AT jojimotaki worddecodingofproteinaminoacidsequenceswithavailabilityanalysisalinguisticapproach
_version_	1718422172326690816

Word decoding of protein amino Acid sequences with availability analysis: a linguistic approach.

Ejemplares similares