DOI: 10.1110/ps.0208902. Sequence analysis of an artificial family of RNA‐binding peptides

Sequence analysis of an artificial family of RNA‐binding peptides

10.1110/ps.0208902

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractDiverse 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 (E14R15) and hydrophobic patch (A21L22or V21L22) 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.

Bibliography

Barrick, J. E., & Roberts, R. W. (2002). Sequence analysis of an artificial family of RNAâbinding peptides. Protein Science, 11(11), 2688â2696. Portico.

Authors 2

Jeffrey E. Barrick (first)
Richard W. Roberts (additional)

References 35 Referenced 16

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Dates

Type	When
Created	22 years, 10 months ago (Oct. 15, 2002, 3:21 p.m.)
Deposited	1 year, 7 months ago (Jan. 7, 2024, 4 a.m.)
Indexed	1 year, 7 months ago (Jan. 7, 2024, 7:06 p.m.)
Issued	22 years, 9 months ago (Nov. 1, 2002)
Published	22 years, 9 months ago (Nov. 1, 2002)
Published Online	16 years, 4 months ago (April 13, 2009)
Published Print	22 years, 9 months ago (Nov. 1, 2002)

Funders 0

None

BibTeX

@article{Barrick_2002, title={Sequence analysis of an artificial family of RNA‐binding peptides}, volume={11}, ISSN={1469-896X}, url={http://dx.doi.org/10.1110/ps.0208902}, DOI={10.1110/ps.0208902}, number={11}, journal={Protein Science}, publisher={Wiley}, author={Barrick, Jeffrey E. and Roberts, Richard W.}, year={2002}, month=nov, pages={2688–2696} }

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