Detecting protein dissimilarities in multiple alignments using Bayesian variable selection

Sinae Kim, Jerry Tsai, Ioannis Kagiampakis, Patricia LiWang, Marina Vannucci

Research output: Contribution to journalArticle

Abstract

Motivation: We present an application of Bayesian variable selection to the novel detection of sequence elements that confer negative design to protein structure and function. As an illustration, we analyze the different dimer interfaces between the CXCL8 chemokine family with the CCL4 and CCL2 chemokine families to discover the changes that disfavor CXCL8 of quaternary structure. Results: In comparison with known experimental results, our method identifies evolutionarily conserved sequence changes in the CC families that inhibit CXCL8 quaternary structure. Therefore, we find positive selection of negative design elements. Furthermore, our approach predicts that a two-residue deletion conserved in the CCL4 chemokine family disfavors CXCL8 dimerization.

Original languageEnglish (US)
Pages (from-to)245-246
Number of pages2
JournalBioinformatics
Volume23
Issue number2
DOIs
StatePublished - Feb 6 2007

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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