title: Targeting Self-Binding Peptides as a Novel Strategy To Regulate Protein Activity and Function: A Case Study on the Proto-oncogene Tyrosine Protein Kinase c-Src.
abstract: Previously, we have reported a new biomolecular phenomenon spanning between protein folding and binding, termed as self-binding peptides (SBPs), where a short peptide segment in monomeric protein functions as a molecular switch by dynamically binding to/unbinding from its cognate domain in the monomer (Yang et al. J. Chem. Inf.
  
  
  
  2015, 55, 329-342). Here, we attempt to raise the SBP as a new class of druggable targets to regulate the biological activity and function of proteins. A case study was performed on the proto-oncogene nonreceptor tyrosine kinase, c-Src, which contains two SBPs that bind separately to SH3 and SH2 domains of the kinase. State-of-the-art molecular dynamics (MD) simulations and post binding energetics analysis revealed that disrupting the kinase-intramolecular interactions of SH3 and SH2 domains with their cognate SBP ligands can result in totally different effects on the structural dynamics of c-Src kinase architecture; targeting the SH2 domain unlocks the autoinhibitory form of the kinase-this is very similar to the pTyr527 dephosphorylation that functionally activates the kinase, whereas targeting the SH3 domain can only release the domain from the tightly packed kinase but has a moderate effect on the kinase activity. Subsequently, based on the cognate SBP sequence we computationally designed a number of SH2-binding phosphopeptides using a motif grafting strategy. Fluorescence polarization (FP) assay observed that most of the designed phosphopeptides have higher binding affinity to SH2 domain as compared to the native SBP segment (Kd= 53 nM). Kinase assay identified a typical dose-response relationship of phosphopeptides against kinase activation, substantiating that disruption of SH2-SBP interaction can mimic c-Src dephosphorylation and activate the kinase. Two rationally designed phosphopeptides, namely EPQpYEEIEN and EPQpYEELEN, were determined as strong binders of SH2 domain (Kd= 8.3 and 15 nM, respectively) and potent activators of c-Src kinase (EC50= 3.2 and 41 μM, respectively).
authors.affiliation: Center for Informational Biology, School of Life Science and Technology, ‡Center for Information in BioMedicine, and §Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China (UESTC) , Chengdu 610054, China.
authors.forename: Zhengya
authors.initials: Z
authors.lastname: Bai
authors.affiliation: Center for Informational Biology, School of Life Science and Technology, ‡Center for Information in BioMedicine, and §Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China (UESTC) , Chengdu 610054, China.
authors.forename: Shasha
authors.initials: S
authors.lastname: Hou
authors.affiliation: Center for Informational Biology, School of Life Science and Technology, ‡Center for Information in BioMedicine, and §Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China (UESTC) , Chengdu 610054, China.
authors.forename: Shilei
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Center for Informational Biology, School of Life Science and Technology, ‡Center for Information in BioMedicine, and §Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China (UESTC) , Chengdu 610054, China.
authors.forename: Zhongyan
authors.initials: Z
authors.lastname: Li
authors.affiliation: Center for Informational Biology, School of Life Science and Technology, ‡Center for Information in BioMedicine, and §Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China (UESTC) , Chengdu 610054, China.
authors.forename: Peng
authors.identifier: 0000-0001-5681-9937
authors.initials: P
authors.lastname: Zhou
mesh_terms: D000595:Amino Acid Sequence; D000081247:CSK Tyrosine-Protein Kinase; D006801:Humans; D056004:Molecular Dynamics Simulation; D058990:Molecular Targeted Therapy; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism*; D010766:Phosphorylation; D011485:Protein Binding; D000090063:Proto-Oncogene Mas; D018909:src Homology Domains; D019061:src-Family Kinases / Q000737:chemistry* / Q000378:metabolism*
chemical_list: C000715470:MAS1 protein, human; D010446:Peptide Fragments; D000090063:Proto-Oncogene Mas; D000081247:CSK Tyrosine-Protein Kinase; D019061:src-Family Kinases; C000631346:CSK protein, human