An integrative approach unveils a distal encounter site for rPTPε and phospho-Src complex formation.

Nadendla EswarKumar, Cheng-Han Yang, Sunilkumar Tewary, Wen-Hsin Peng, Guang-Chao Chen, Yi-Qi Yeh, Hsiao-Ching Yang, Meng-Chiao Ho

Journal: Structure (London, England : 1993) 2023;31(12):1567-1577.e5

PMID: 37794594

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Abstract

The structure determination of protein tyrosine phosphatase (PTP): phospho-protein complexes, which is essential to understand how specificity is achieved at the amino acid level, remains a significant challenge for protein crystallography and cryoEM due to the transient nature of binding interactions. Using rPTPεD1 and phospho-SrcKD as a model system, we have established an integrative workflow to address this problem, by means of which we generate a protein:phospho-protein complex model using predetermined protein structures, SAXS and pTyr-tailored MD simulations. Our model reveals transient protein-protein interactions between rPTPεD1 and phospho-SrcKD and is supported by three independent experimental validations. Measurements of the association rate between rPTPεD1 and phospho-SrcKD showed that mutations on the rPTPεD1: SrcKD complex interface disrupts these transient interactions, resulting in a reduction in protein-protein association rate and, eventually, phosphatase activity. This integrative approach is applicable to other PTP: phospho-protein complexes and the characterization of transient protein-protein interface interactions.

Address: Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.; Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan.; Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan.; National Synchrotron Radiation Research Center, Hsin-Chu 300, Taiwan.; Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan. Electronic address: [email protected].; Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan. Electronic address: [email protected].

DOI: 10.1016/j.str.2023.09.004

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MeSH Terms: Scattering, Small Angle, X-Ray Diffraction, Proteins, Phosphorylation