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Protein Science (2003), 12:776-783.
Copyright © 2003 The Protein Society

Structural and kinetic characterization of the simplified SH3 domain FP1

Qian Yi1, Ponni Rajagopal1, Rachel E. Klevit1 and David Baker1,2

1 Department of Biochemistry and
2 Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA

Reprint requests to: David Baker, Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195, USA; e-mail: dabaker{at}u.washington.edu; fax: (206) 685-1792.

The simplified SH3 domain sequence, FP1, obtained in phage display selection experiments has an amino acid composition that is 95% Ile, Lys, Glu, Ala, Gly. Here we use NMR to investigate the tertiary structure of FP1. We find that the overall topology of FP1 resembles that of the src SH3 domain, the hydrogen-deuterium exchange and chemical shift perturbation profiles are similar to those of naturally occurring SH3 domains, and the 15N relaxation rates are in the range of naturally occurring small proteins. Guided by the structure, we further simplify the FP1 sequence and compare the effects on folding kinetics of point mutations in FP1 and the wild-type src SH3 domain. The results suggest that the folding transition state of FP1 is similar to but somewhat less polarized than that of the wild-type src SH3 domain.

Keywords: FP1; simplified SH3; folding kinetics; NMR structure


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