Design of a phosphorylatable PDZ domain with peptide-specific affinity changes

Colin A Smith; Catherine A Shi; Matthew K Chroust; Thomas E Bliska; Mark J S Kelly; Matthew P Jacobson; Tanja Kortemme

doi:10.1016/j.str.2012.10.007

Design of a phosphorylatable PDZ domain with peptide-specific affinity changes

Structure. 2013 Jan 8;21(1):54-64. doi: 10.1016/j.str.2012.10.007. Epub 2012 Nov 15.

Authors

Colin A Smith¹, Catherine A Shi², Matthew K Chroust³, Thomas E Bliska⁴, Mark J S Kelly⁵, Matthew P Jacobson⁶, Tanja Kortemme⁷

Affiliations

¹ Graduate Program in Biological and Medical Informatics, University of California San Francisco, 1700 4(th) Street, San Francisco, CA 94158, USA. Electronic address: [email protected].
² Graduate Group in Biophysics, University of California San Francisco, 1700 4(th) Street, San Francisco, CA 94158, USA.
³ School of Dentistry, University of California San Francisco, 1700 4(th) Street, San Francisco, CA 94158, USA.
⁴ Williams College, 880 Main Street, Williamstown, MA 01267, USA.
⁵ Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4(th) Street, San Francisco, CA 94158, USA.
⁶ 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.
⁷ 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: [email protected].

PMID: 23159126
DOI: 10.1016/j.str.2012.10.007

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.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Adaptor Proteins, Signal Transducing / chemistry
Amino Acid Motifs
Amino Acid Sequence
Cyclic AMP-Dependent Protein Kinases / chemistry
Humans
Models, Molecular
Molecular Sequence Data
PDZ Domains
Peptide Fragments / chemistry*
Phosphoproteins / chemistry*
Phosphorylation
Protein Binding
Protein Engineering
Protein Processing, Post-Translational
Protein Stability
Protein Structure, Secondary
Substrate Specificity
Transition Temperature

Substances

Adaptor Proteins, Signal Transducing
ERBIN protein, human
Peptide Fragments
Phosphoproteins
Cyclic AMP-Dependent Protein Kinases