Stability and peptide binding affinity of an SH3 domain from the Caenorhabditis elegans signaling protein Sem‐5

We have determined the thermodynamic stability and peptide binding affinity of the carboxy‐terminal Src homology 3 (SH3) domain from the Caenorhabditis elegans signal‐transduction protein Sem‐5. Despite its small size (62 residues) and lack of disulfide bonds, this domain is highly stable to thermal denaturation — at pH 7.3, the protein has a Tm of 73.1 °C. Interestingly, the protein is not maximally stable at neutral pH, but reaches a maximum at around pH 4.7 (Tm ≅ 80 °C). Increasing ionic strength also stabilizes the protein, suggesting that 1 or more car‐boxylate ions are involved in a destabilizing electrostatic interaction. By guanidine hydrochloride denaturation, the protein is calculated to have a free energy of unfolding of 4.1 kcal/mol at 25 °C. We have also characterized binding of the domain to 2 different length proline‐rich peptides from the guanine nucleotide exchange factor, Sos, one of Sem‐5′s likely physiological ligands in cytoplasmic signal transduction. Upon binding, these peptides cause about a 2‐fold increase in fluorescence intensity. Both bind with only modest affinities (Kd ≅ 30 μM), lower than some previous estimates for SH3 domains. By fluorescence, the domain also appears to associate with the homopolymer poly‐L‐proline in a similar fashion.

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