Bacterial protein structures reveal phylum dependent divergence

Matthew D. Shortridge, Thomas Triplet, Peter Revesz, Mark A Griep, Robert Powers

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Protein sequence space is vast compared to protein fold space. This raises important questions about how structures adapt to evolutionary changes in protein sequences. A growing trend is to regard protein fold space as a continuum rather than a series of discrete structures. From this perspective, homologous protein structures within the same functional classification should reveal a constant rate of structural drift relative to sequence changes. The clusters of orthologous groups (COG) classification system was used to annotate homologous bacterial protein structures in the Protein Data Bank (PDB). The structures and sequences of proteins within each COG were compared against each other to establish their relatedness. As expected, the analysis demonstrates a sharp structural divergence between the bacterial phyla Firmicutes and Proteobacteria. Additionally, each COG had a distinct sequence/structure relationship, indicating that different evolutionary pressures affect the degree of structural divergence. However, our analysis also shows the relative drift rate between sequence identity and structure divergence remains constant.

Original languageEnglish (US)
Pages (from-to)24-33
Number of pages10
JournalComputational Biology and Chemistry
Volume35
Issue number1
DOIs
StatePublished - Feb 1 2011

Fingerprint

Bacterial Structures
Bacterial Proteins
Protein Structure
Divergence
Proteins
Dependent
Protein
Protein Sequence
Fold
Group Classification
Sequence Space
Rate Constant
Proteobacteria
Continuum
Distinct
Series
Databases
Pressure
Demonstrate

Keywords

  • Evolution
  • Function
  • Proteins
  • Sequence
  • Structure

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Organic Chemistry
  • Computational Mathematics

Cite this

Bacterial protein structures reveal phylum dependent divergence. / Shortridge, Matthew D.; Triplet, Thomas; Revesz, Peter; Griep, Mark A; Powers, Robert.

In: Computational Biology and Chemistry, Vol. 35, No. 1, 01.02.2011, p. 24-33.

Research output: Contribution to journalArticle

Shortridge, Matthew D. ; Triplet, Thomas ; Revesz, Peter ; Griep, Mark A ; Powers, Robert. / Bacterial protein structures reveal phylum dependent divergence. In: Computational Biology and Chemistry. 2011 ; Vol. 35, No. 1. pp. 24-33.
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