title: Design of a phosphorylatable PDZ domain with peptide-specific affinity changes.
abstract: Phosphorylation is one of the most common posttranslational modifications controlling cellular protein activity. Here, we describe a combined computational and experimental strategy to design new phosphorylation sites into globular proteins to regulate their functions. We target a peptide recognition protein, the Erbin PDZ domain, to be phosphorylated by cAMP-dependent protein kinase. Comparing the five successful designs to the unsuccessful cases, we find a trade-off between protein stability and the ability to be modified by phosphorylation. In two designs, Erbin's peptide binding function is modified by phosphorylation, where the presence of the phosphate group destabilizes peptide binding. One of these showed an additional switch in specificity by introducing favorable interactions between a designed arginine in the peptide and phosphoserine on the PDZ domain. Because of the diversity of PDZ domains, this opens avenues for the design of related phosphoswitchable domains to create a repertoire of regulatable interaction parts for synthetic biology.
authors.affiliation: Graduate Program in Biological and Medical Informatics, University of California San Francisco, 1700 4(th) Street, San Francisco, CA 94158, USA. Electronic address: colin.smith@mpibpc.mpg.de.
authors.forename: Colin A
authors.initials: CA
authors.lastname: Smith
authors.affiliation: Graduate Group in Biophysics, University of California San Francisco, 1700 4(th) Street, San Francisco, CA 94158, USA.
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Shi
authors.affiliation: School of Dentistry, University of California San Francisco, 1700 4(th) Street, San Francisco, CA 94158, USA.
authors.forename: Matthew K
authors.initials: MK
authors.lastname: Chroust
authors.affiliation: Williams College, 880 Main Street, Williamstown, MA 01267, USA.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Bliska
authors.affiliation: Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4(th) Street, San Francisco, CA 94158, USA.
authors.forename: Mark J S
authors.initials: MJS
authors.lastname: Kelly
authors.affiliation: Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4(th) Street, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, 1700 4(th) Street, San Francisco, CA 94158, USA.
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Jacobson
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4(th) Street, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, 1700 4(th) Street, San Francisco, CA 94158, USA. Electronic address: kortemme@cgl.ucsf.edu.
authors.forename: Tanja
authors.initials: T
authors.lastname: Kortemme
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000737:chemistry; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017868:Cyclic AMP-Dependent Protein Kinases / Q000737:chemistry; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D054731:PDZ Domains; D010446:Peptide Fragments / Q000737:chemistry*; D010750:Phosphoproteins / Q000737:chemistry*; D010766:Phosphorylation; D011485:Protein Binding; D015202:Protein Engineering; D011499:Protein Processing, Post-Translational; D055550:Protein Stability; D017433:Protein Structure, Secondary; D013379:Substrate Specificity; D044366:Transition Temperature
chemical_list: D048868:Adaptor Proteins, Signal Transducing; C413364:ERBIN protein, human; D010446:Peptide Fragments; D010750:Phosphoproteins; D017868:Cyclic AMP-Dependent Protein Kinases