Student Theses and Dissertations


Chi-Hon Lee

Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)

RU Laboratory

Kuriyan Laboratory


The peptide-recognition domains playa key role in Eukaryotic signal transduction by mediating sequence-specific interactions with their protein/peptide ligands. In this thesis, I illustrate in molecular detail the recognition mechanisms utilized by three peptide-recognition domains: SH2 (Src homology 2) domains, PTB (phosphotyrosine binding) domains, and SH3 (Src homology 3) domains. The SH2 domains recognize tyrosylphosphorylated peptides using a binding mode that is conserved among the SH2 family members. In particular, the structure of the SH-PTP2 SH2 domain (described in this thesis) has revealed that sequence specificity can extend across the five residues immediately C-terminal to the phosphotyrosine. On the other hand, the PTB domains interact with peptide residues that are Nterminal to the phosphotyrosine in the sequence context, NPxY*. Although phosphorylation on tyrosine residue of ligand is absolutely required for interacting with the SH2 domains, some PTB domains (such as the XlI PTB domain described in this thesis) are able to mediate phosphorylationindependent interaction. The three-dimensional structure of the XlI PTB/peptide complex has revealed a general mechanism utilized for recognizing both phosphorylated and nonphosphorylated peptide ligands. In combination with in vitro binding study, the structural findings suggest that the PTB domains should be regarded as peptide recognition modules rather than phosphotyrosine binding module (as for the SH2 domain). While local sequences in the peptide ligands appear to determine the specificity in binding to the SH2 and PTB domains, SH3/peptide interactions are in general of low specificity and low affinity. As demonstrated by my biochemical study of HIV-l Nef/SH3 domain interaction, regions of intact SH3 binding proteins outside the PxxP motif can enhance both affinity and specificity by targeting the highly divergent RT-loop of the SH3 domains. The crystal structure of Nef in complex with a Src-family SH3 domain has provided the first example of high affinity SH3-protein interaction and revealed a novel mechanism by which SH3-mediated interaction achieves high affinity and specificity by the presentation of the PxxP motif on the tertiary structure of Nef. Furthermore, the structure of HIV-l Nef suggests that Nef functions as an adaptor to subvert cellular signaling processes for the benefit of the invading virus.


A thesis presented to the faculty of The Rockefeller University in partial fulfillment of the requirements of the degree of Doctor of Philosophy

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