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The ββα fold: explorations in sequence space

Sarisky, Catherine A. and Mayo, Stephen L. (2001) The ββα fold: explorations in sequence space. Journal of Molecular Biology, 307 (5). pp. 1411-1418. ISSN 0022-2836. doi:10.1006/jmbi.2000.4345.

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The computational redesign of the second zinc finger of Zif268 to produce a 28 residue peptide (FSD-1) that assumes a ββα fold without metal binding was recently reported. In order to explore the tolerance of this metal-free fold towards sequence variability, six additional peptides resulting from the ORBIT computational protein design process were synthesized and characterized. The experimental stabilities of five of these peptides are strongly correlated with the energies calculated by ORBIT. However, when a peptide with a mutation in the β-turn is examined, the calculated stability does not accurately predict the experimentally determined stability. The NMR solution structure of a peptide incorporating this mutation (FSD-EY) reveals that the register between the β-strands is different from the model structure used to select and score the sequences. FSD-EY has a type I' turn instead of the target EbaaagbE turn (rubredoxin knuckle). Two additional peptides that have improved side-chain to backbone hydrogen bonding and turn propensity for the target turn were characterized. Both are of stability comparable to that of FSD-1. These results demonstrate the robustness of the ORBIT protein design methods and underscore the need for continued improvements in negative design.

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Mayo, Stephen L.0000-0002-9785-5018
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Additional Information:© 2001 Academic Press. Received 23 August 2000; revised 14 November 2000; Accepted 15 November 2000. Available online 26 February 2002. We thank Scott Ross for assistance with NMR data collection and helpful discussions regarding the FSD-EY solution structure. Shannon Marshall, Chantal Morgan, Bassil Dahiyat, and Alyce Su provided insights into peptide synthesis, purification, and characterization by CD. This work was supported by the Howard Hughes Medical Institute (S. L. M.) and the National Science Foundation (C. A. S.).
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Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Subject Keywords:Software; Amino Acid Sequence; Protein Engineering; Magnetic Resonance Spectroscopy; Solutions; Transcription Factors; Thermodynamics; Zinc Fingers; Molecular Sequence Data; Algorithms; DNA-Binding Proteins; Circular Dichroism; Protein Folding; Mutation; Peptides; Computer Simulation; Models: Molecular; Rubredoxins; Hydrogen Bonding; Protein Structure: Secondary; protein design; negative design; zinc finger; ORBIT
Issue or Number:5
Record Number:CaltechAUTHORS:20111003-155045528
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Official Citation:Catherine A Sarisky, Stephen L Mayo, The ββα fold: explorations in sequence space, Journal of Molecular Biology, Volume 307, Issue 5, 13 April 2001, Pages 1411-1418, ISSN 0022-2836, 10.1006/jmbi.2000.4345.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:25533
Deposited By: Tony Diaz
Deposited On:04 Oct 2011 14:09
Last Modified:09 Nov 2021 16:34

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