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Sequence analysis of an artificial family of RNA‐binding peptides
Author(s) -
Barrick Jeffrey E.,
Roberts Richard W.
Publication year - 2002
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.0208902
Subject(s) - peptide sequence , context (archaeology) , consensus sequence , biology , computational biology , genetics , gene , paleontology
Diverse peptide sequences recognizing the λ boxB RNA hairpin were previously isolated from a library encoding the 22‐residue λ N peptide with random amino acids at positions 13–22 using mRNA display. We have statistically analyzed amino acid distributions in 65 unique sequences from rounds 11 and 12 of this selection and evaluated the resulting structural and functional predictions by alanine‐scanning mutagenesis and circular dichroism spectrometry. This artificial sequence family has a consensus structure that continues the bent α helix of λ N up to position 17 when bound to λ boxB. A charge pair (E 14 R 15 ) and hydrophobic patch (A 21 L 22 or V 21 L 22 ) have important functional roles in this context. Notably, amino acid covariance reveals six specific pairs of random region positions with >95% significant linkage and strong overall helical (i+1, i+3, and i+4) couplings. The covariance analysis suggests that (1) the sequence context of every residue in each insert has been optimized, (2) selected sequences are local optima on a rugged fitness landscape, and (3) it is possible to detect more subtle structural features with artificial protein sequence families than natural homologs. Our results provide a framework for investigating the structures of in vitro selected proteins by functional minimization, reselection, and covariance analysis.