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De novo protein design: towards fully automated sequence selection

Dahiyat, Bassil I. and Sarisky, Catherine A. and Mayo, Stephen L. (1997) De novo protein design: towards fully automated sequence selection. Journal of Molecular Biology, 273 (4). pp. 789-796. ISSN 0022-2836. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160423493

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Abstract

Several groups have applied and experimentally tested systematic, quantitative methods to protein design with the goal of developing general design algorithms. We have sought to expand the range of computational protein design by developing quantitative design methods for residues of all parts of a protein: the buried core, the solvent exposed surface, and the boundary between core and surface. Our goal is an objective, quantitative design algorithm that is based on the physical properties that determine protein structure and stability and which is not limited to specific folds or motifs. We chose the ββα motif typified by the zinc finger DNA binding module to test our design methodology. Using previously published sequence scoring functions developed with a combined experimental and computational approach and the Dead-End Elimination theorem to search for the optimal sequence, we designed 20 out of 28 positions in the test motif. The resulting sequence has less than 40% homology to any known sequence and does not contain any metal binding sites or cysteine residues. The resulting peptide, pda8d, is highly soluble and monomeric and circular dichroism measurements showed it to be folded with a weakly cooperative thermal unfolding transition. The NMR solution structure of pda8d was solved and shows that it is well-defined with a backbone ensemble rms deviation of 0.55 Å. Pda8d folds into the desired betabetaalpha motif with well-defined elements of secondary structure and tertiary organization. Superposition of the pda8d backbone to the design target is excellent, with an atomic rms deviation of 1.04 Å.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1006/jmbi.1997.1341DOIUNSPECIFIED
http://www.sciencedirect.com/science/article/pii/S0022283697913413PublisherUNSPECIFIED
Additional Information:© 1997 Academic Press Limited. Received 22 April 1997; received in revised form 7 August 1997; accepted 7 August 1997. Available online 22 April 2002. We thank Scott Ross for assistance with NMR studies, Pak Poon of the UCLA Molecular Biology Institute for sedimentation equilibrium studies, and Gary Hathaway of the Caltech Protein and Peptide Microanalytical Laboratory for mass spectra. We acknowledge financial support from the Rita Allen Foundation, the David and Lucile Packard Foundation and the Searle Scholars Program/ The Chicago Community Trust. B.I.D. is partially supported by NIH Training Grant GM 08346.
Funders:
Funding AgencyGrant Number
Rita Allen FoundationUNSPECIFIED
David and Lucile Packard FoundationUNSPECIFIED
Searle Scholars Program/Chicago Community TrustUNSPECIFIED
National Institutes of Health Training GM 08346
Subject Keywords:Protein Engineering; Algorithms; Amino Acid Sequence; Zinc Fingers; Drug Design; Magnetic Resonance Spectroscopy; Circular Dichroism; Protein Conformation; Models: Molecular; Molecular Sequence Data; protein design; NMR; force field; sequence optimization; dead-end elimination
Record Number:CaltechAUTHORS:20110620-160423493
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20110620-160423493
Official Citation:Bassil I Dahiyat, Catherine A Sarisky, Stephen L Mayo, De Novo protein design: towards fully automated sequence selection, Journal of Molecular Biology, Volume 273, Issue 4, 7 November 1997, Pages 789-796, ISSN 0022-2836, 10.1006/jmbi.1997.1341.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:24078
Collection:CaltechAUTHORS
Deposited By: Marie Ary
Deposited On:03 Oct 2011 22:42
Last Modified:03 Oct 2011 22:42

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