Globally, unrelated protein sequences appear random.

Bioinformatics
Daniel T Lavelle, William R Pearson

Abstract

To test whether protein folding constraints and secondary structure sequence preferences significantly reduce the space of amino acid words in proteins, we compared the frequencies of four- and five-amino acid word clumps (independent words) in proteins to the frequencies predicted by four random sequence models. While the human proteome has many overrepresented word clumps, these words come from large protein families with biased compositions (e.g. Zn-fingers). In contrast, in a non-redundant sample of Pfam-AB, only 1% of four-amino acid word clumps (4.7% of 5mer words) are 2-fold overrepresented compared with our simplest random model [MC(0)], and 0.1% (4mers) to 0.5% (5mers) are 2-fold overrepresented compared with a window-shuffled random model. Using a false discovery rate q-value analysis, the number of exceptional four- or five-letter words in real proteins is similar to the number found when comparing words from one random model to another. Consensus overrepresented words are not enriched in conserved regions of proteins, but four-letter words are enriched 1.18- to 1.56-fold in alpha-helical secondary structures (but not beta-strands). Five-residue consensus exceptional words are enriched for alpha-helix 1.43- to 1.61-f...Continue Reading

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Citations

Jan 24, 2016·Cellular and Molecular Life Sciences : CMLS·Jia-Feng YuYaoqi Zhou
Apr 26, 2011·Current Opinion in Structural Biology·Avner SchlessingerBurkhard Rost
May 26, 2016·PloS One·Guangyu WangZhang Zhang
Oct 13, 2018·Scientific Reports·Jarosław PoznańskiMarcin Grynberg
May 4, 2018·F1000Research·Wolfram HöpsAlex Bateman
Sep 22, 2018·The Journal of Physical Chemistry. B·Pablo Turjanski, Diego U Ferreiro

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