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Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification

Ross, Scott A. and Sarisky, Catherine A. and Su, Alyce and Mayo, Stephen L. (2001) Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification. Protein Science, 10 (2). pp. 450-454. ISSN 0961-8368. http://resolver.caltech.edu/CaltechAUTHORS:20110621-075054655

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Abstract

The solution structures of two computationally designed core variants of the β1 domain of streptococcal protein G (Gβ1) were solved by ^1H NMR methods to assess the robustness of amino acid sequence selection by the ORBIT protein design package under changes in protein backbone specification. One variant has mutations at three of 10 core positions and corresponds to minimal perturbations of the native Gβ1 backbone. The other, with mutations at six of 10 positions, was calculated for a backbone in which the separation between Gβ1's α-helix and β-sheet was increased by 15% relative to native Gβ1. Exchange broadening of some resonances and the complete absence of others in spectra of the sixfold mutant bespeak conformational heterogeneity in this protein. The NMR data were sufficiently abundant, however, to generate structures of similar, moderately high quality for both variants. Both proteins adopt backbone structures similar to their target folds. Moreover, the sequence selection algorithm successfully predicted all core χ(1) angles in both variants, five of six χ_2 angles in the threefold mutant and four of seven χ_2 angles in the sixfold mutant. We conclude that ORBIT calculates sequences that fold specifically to a geometry close to the template, even when the template is moderately perturbed relative to a naturally occurring structure. There are apparently limits to the size of acceptable perturbations: In this study, the larger perturbation led to undesired dynamic behavior.


Item Type:Article
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http://dx.doi.org/10.1110/ps.32501DOIUNSPECIFIED
http://onlinelibrary.wiley.com/doi/10.1110/ps.32501/abstractPublisherUNSPECIFIED
Additional Information:© 2001 The Protein Society. Published by Cold Spring Harbor Laboratory Press. Received August 1, 2000; Final Revision November 6, 2000; Accepted November 6, 2000. Article first published online: 31 Dec. 2008. We thank Monica Breckow for assistance with molecular biology protocols. This work was supported by the Howard Hughes Medical Institute (S.L.M.). C.A.S. is partially supported by an NSF graduate research fellowship. Coordinates and NMR restraints have been deposited in the Protein Data Bank. Accession numbers for the coordinates are 1fd6 and 1fc1 for Δ0 and Δ1.5, respectively. The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.
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Funding AgencyGrant Number
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
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Subject Keywords:Thermodynamics, Software, Mutation, Models: Molecular, Protein Structure: Tertiary, Protein Conformation, Bacterial Proteins, Magnetic Resonance Spectroscopy
Non-Subject Keywords:protein design; backbone design; core sidechain packing; dead-end elimination; ORBIT
Record Number:CaltechAUTHORS:20110621-075054655
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20110621-075054655
Official Citation:Ross, S. A., Sarisky, C. A., Su, A. and Mayo, S. L. (2001), Designed protein G core variants fold to native-like structures: Sequence selection by ORBIT tolerates variation in backbone specification. Protein Science, 10: 450–454. doi: 10.1110/ps.32501
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:24143
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:21 Jun 2011 14:58
Last Modified:22 Jun 2011 14:36

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