The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein

Yu Wen Huang, Chih Min Chang, Chi Wen Lee, Jenn-Kang Hwang

Research output: Contribution to journalArticle

6 Scopus citations

Abstract

The conservation profile of a protein is a curve of the conservation levels of amino acids along the sequence. Biologists are usually more interested in individual points on the curve (namely, the conserved amino acids) than the overall shape of the curve. Here, we show that the conservation curves of proteins bear the imprints of molecules that are evolutionarily coupled to the proteins. Our method is based on recent studies that a sequence conservation profile is quantitatively linked to its structural packing profile. We find that the conservation profiles of nucleic acid (NA) binding proteins are better correlated with the packing profiles of the protein-NA complexes than those of the proteins alone. This indicates that a nucleic acid binding protein evolves to accommodate the nucleic acid in such a way that the residues involved in binding have their conservation levels closely coupled with the specific nucleotides. Proteins 2015; 83:1407-1413. (c) 2015 Wiley Periodicals, Inc.
Original languageEnglish
Pages (from-to)1407-1413
Number of pages7
JournalProteins: Structure, Function and Genetics
Volume83
Issue number8
DOIs
StatePublished - Aug 2015

Keywords

  • protein structure; structural packing; sequence conservation; weighted contact number; nucleic acid binding protein
  • VON-WILLEBRAND-FACTOR; PACKING DENSITY; SEQUENCE; FLEXIBILITY; INFORMATION; CONSURF; DNA

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