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Published August 1997 | public
Journal Article

Coupling backbone flexibility and amino acid sequence selection in protein design


Using a protein design algorithm that considers side-chain packing quantitatively, the effect of explicit backbone motion on the selection of amino acids in protein design was assessed in the core of the streptococcal protein G β1 domain (Gβ1). Concerted backbone motion was introduced by varying Gβ1's supersecondary structure parameter values. The stability and structural flexibility of seven of the redesigned proteins were determined experimentally and showed that core variants containing as many as 6 of 10 possible mutations retain native-like properties. This result demonstrates that backbone flexibility can be combined explicitly with amino acid side-chain selection and that the selection algorithm is sufficiently robust to tolerate perturbations as large as 15% of Gβ1's native supersecondary structure parameter values.

Additional Information

© 1997 The Protein Society. Received January 27, 1997; Accepted March 21, 1997. Article first published online: 31 Dec. 2008. We thank M. Ary, S. Malakauskas, and S. Ross for technical assistance, G. Hathaway of the Caltech Protein and Peptide Microanalytical Facility for mass spectra, the Caltech DNA Sequencing Core Facility for DNA sequencing, and the Caltech Center for Advanced Computing Research for use of the Intel Delta. This work was supported by the Rita Allen Foundation, the David and Lucile Packard Foundation, and the Searle Scholars Program/The Chicago Community Trust.

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