Stereochemical preferences modulate affinity and selectivity among five PDZ domains that bind CFTR: comparative structural and sequence analyses

Jeanine F Amacher; Patrick R Cushing; Lionel Brooks 3rd; Prisca Boisguerin; Dean R Madden

doi:10.1016/j.str.2013.09.019

Stereochemical preferences modulate affinity and selectivity among five PDZ domains that bind CFTR: comparative structural and sequence analyses

Structure. 2014 Jan 7;22(1):82-93. doi: 10.1016/j.str.2013.09.019. Epub 2013 Nov 7.

Authors

Jeanine F Amacher¹, Patrick R Cushing¹, Lionel Brooks 3rd², Prisca Boisguerin³, Dean R Madden⁴

Affiliations

¹ Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
² Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
³ Institute of Medical Immunology, Charité, 10115 Berlin, Germany; Centre de Recherches de Biochimie Macromoleculaire, CRBM-CNRS, UMR-5237, UM1-UM2, University of Montpellier, Department of Molecular Biophysics and Therapeutics, 34293 Montpellier, France.
⁴ Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. Electronic address: drm0001@dartmouth.edu.

Abstract

PDZ domain interactions are involved in signaling and trafficking pathways that coordinate crucial cellular processes. Alignment-based PDZ binding motifs identify the few most favorable residues at certain positions along the peptide backbone. However, sequences that bind the CAL (CFTR-associated ligand) PDZ domain reveal only a degenerate motif that overpredicts the true number of high-affinity interactors. Here, we combine extended peptide-array motif analysis with biochemical techniques to show that non-motif "modulator" residues influence CAL binding. The crystallographic structures of 13 CAL:peptide complexes reveal defined, but accommodating stereochemical environments at non-motif positions, which are reflected in modulator preferences uncovered by multisequence substitutional arrays. These preferences facilitate the identification of high-affinity CAL binding sequences and differentially affect CAL and NHERF PDZ binding. As a result, they also help determine the specificity of a PDZ domain network that regulates the trafficking of CFTR at the apical membrane.

Publication types

Comparative Study
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Adaptor Proteins, Signal Transducing
Amino Acid Sequence
Binding Sites
Carrier Proteins / chemistry*
Carrier Proteins / genetics
Carrier Proteins / metabolism
Crystallography, X-Ray
Cystic Fibrosis Transmembrane Conductance Regulator / chemistry*
Cystic Fibrosis Transmembrane Conductance Regulator / genetics
Cystic Fibrosis Transmembrane Conductance Regulator / metabolism
Gene Expression Regulation
Golgi Matrix Proteins
Humans
Membrane Proteins / chemistry*
Membrane Proteins / genetics
Membrane Proteins / metabolism
Membrane Transport Proteins
Models, Molecular
Molecular Sequence Data
PDZ Domains / genetics*
Protein Array Analysis
Protein Binding
Recombinant Proteins / chemistry
Recombinant Proteins / genetics
Recombinant Proteins / metabolism
Sequence Alignment
Signal Transduction
Stereoisomerism
Structure-Activity Relationship
Thermodynamics

Substances

Adaptor Proteins, Signal Transducing
CFTR protein, human
Carrier Proteins
GOPC protein, human
Golgi Matrix Proteins
Membrane Proteins
Membrane Transport Proteins
Recombinant Proteins
Cystic Fibrosis Transmembrane Conductance Regulator

Abstract

Publication types

MeSH terms

Substances

Grants and funding