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Published September 16, 1997 | Published
Journal Article Open

Probing the role of packing specificity in protein design


By using a protein-design algorithm that quantitatively considers side-chain packing, the effect of specific steric constraints on protein design was assessed in the core of the streptococcal protein G beta 1 domain. The strength of packing constraints used in the design was varied, resulting in core sequences that reflected differing amounts of packing specificity. The structural flexibility and stability of several of the designed proteins were experimentally determined and showed a trend from well-ordered to highly mobile structures as the degree of packing specificity in the design decreased. This trend both demonstrates that the inclusion of specific packing interactions is necessary for the design of native-like proteins and defines a useful range of packing specificity for the design algorithm. In addition, an analysis of the modeled protein structures suggested that penalizing for exposed hydrophobic surface area can improve design performance.

Additional Information

© 1997 by The National Academy of Sciences Communicated by William A. Goddard III, California Institute of Technology, Pasadena, CA, June 24, 1997 (received for review March 7, 1997) We thank D. B. Gordon for helpful discussions, S. Ross for assistance with the NMR spectroscopy, and G. Hathaway for mass spectra. This work was supported by 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 National Institutes of Health Training Grant GM 08346. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

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