Evolutionary information hidden in a single protein structure

Chien Hua Shih, Chih Min Chang, Yeong-Shin Lin, Wei-Cheng Lo, Jenn Kang Hwang*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


The knowledge of conserved sequences in proteins is valuable in identifying functionally or structurally important residues. Generating the conservation profile of a sequence requires aligning families of homologous sequences and having knowledge of their evolutionary relationships. Here, we report that the conservation profile at the residue level can be quantitatively derived from a single protein structure with only backbone information. We found that the reciprocal packing density profiles of protein structures closely resemble their sequence conservation profiles. For a set of 554 nonhomologous enzymes, 74% (408/554) of the proteins have a correlation coefficient > 0.5 between these two profiles. Our results indicate that the three-dimensional structure, instead of being a mere scaffold for positioning amino acid residues, exerts such strong evolutionary constraints on the residues of the protein that its profile of sequence conservation essentially reflects that of its structural characteristics.

Original languageEnglish
Pages (from-to)1647-1657
Number of pages11
JournalProteins: Structure, Function and Bioinformatics
Issue number6
StatePublished - 1 Jun 2012


  • B-factors
  • Contact number
  • Evolution
  • Protein structure
  • Sequence conservation

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