title: Affinity Enhancement by Ligand Clustering Effect Inspired by Peptide Dendrimers-Shank PDZ Proteins Interactions.
abstract: High-affinity binders are desirable tools to probe the function that specific protein-protein interactions play in cell. In the process of seeking a general strategy to design high-affinity binders, we found a clue from the βPIX (p21-activated kinase interacting exchange factor)-Shank PDZ interaction in synaptic assembly: three PDZ-binding sites are clustered by a parallel coiled-coil trimer but bind to Shank PDZ protein with 1:1 stoichiometry (1 trimer/1 PDZ). Inspired by this architecture, we proposed that peptide dendrimer, mimicking the ligand clustering in βPIX, will also show enhanced binding affinity, yet with 1:1 stoichiometry. This postulation has been proven here, as we synthesized a set of monomeric, dimeric and trimeric peptides and measured their binding affinity and stoichiometry with Shank PDZ domains by isothermal titration calorimetry, native mass spectrometry and surface plasmon resonance. This affinity enhancement, best explained by proximity effect, will be useful to guide the design of high-affinity blockers for protein-protein interactions.
authors.affiliation: Department of Chemistry, Centre of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
authors.forename: Jiahui
authors.initials: J
authors.lastname: Liu
authors.affiliation: Department of Chemistry, Centre of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
authors.forename: Miao
authors.initials: M
authors.lastname: Liu
authors.affiliation: Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Zheng
authors.affiliation: Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China.
authors.forename: Zhongping
authors.initials: Z
authors.lastname: Yao
authors.affiliation: Department of Chemistry, Centre of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Xia
mesh_terms: D000595:Amino Acid Sequence; D050091:Dendrimers / Q000737:chemistry*; D019281:Dimerization; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000378:metabolism*; D054731:PDZ Domains; D057786:Peptidomimetics / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D064067:Rho Guanine Nucleotide Exchange Factors / Q000378:metabolism
chemical_list: D050091:Dendrimers; D008024:Ligands; D009419:Nerve Tissue Proteins; D057786:Peptidomimetics; D064067:Rho Guanine Nucleotide Exchange Factors