TY - JOUR
T1 - Alteration of the C-terminal ligand specificity of the Erbin PDZ domain by allosteric mutational effects
AU - Murciano-Calles, Javier
AU - McLaughlin, Megan E.
AU - Erijman, Ariel
AU - Hooda, Yogesh
AU - Chakravorty, Nishant
AU - Martinez, Jose C.
AU - Shifman, Julia M.
AU - Sidhu, Sachdev S.
N1 - Publisher Copyright:
© 2014 Elsevier Ltd.
PY - 2014/10/23
Y1 - 2014/10/23
N2 - Modulation of protein binding specificity is important for basic biology and for applied science. Here we explore how binding specificity is conveyed in PDZ (postsynaptic density protein-95/discs large/zonula occludens-1) domains, small interaction modules that recognize various proteins by binding to an extended C terminus. Our goal was to engineer variants of the Erbin PDZ domain with altered specificity for the most C-terminal position (position 0) where a Val is strongly preferred by the wild-type domain. We constructed a library of PDZ domains by randomizing residues in direct contact with position 0 and in a loop that is close to but does not contact position 0. We used phage display to select for PDZ variants that bind to 19 peptide ligands differing only at position 0. To verify that each obtained PDZ domain exhibited the correct binding specificity, we selected peptide ligands for each domain. Despite intensive efforts, we were only able to evolve Erbin PDZ domain variants with selectivity for the aliphatic C-terminal side chains Val, Ile and Leu. Interestingly, many PDZ domains with these three distinct specificities contained identical amino acids at positions that directly contact position 0 but differed in the loop that does not contact position 0. Computational modeling of the selected PDZ domains shows how slight conformational changes in the loop region propagate to the binding site and result in different binding specificities. Our results demonstrate that second-sphere residues could be crucial in determining protein binding specificity.
AB - Modulation of protein binding specificity is important for basic biology and for applied science. Here we explore how binding specificity is conveyed in PDZ (postsynaptic density protein-95/discs large/zonula occludens-1) domains, small interaction modules that recognize various proteins by binding to an extended C terminus. Our goal was to engineer variants of the Erbin PDZ domain with altered specificity for the most C-terminal position (position 0) where a Val is strongly preferred by the wild-type domain. We constructed a library of PDZ domains by randomizing residues in direct contact with position 0 and in a loop that is close to but does not contact position 0. We used phage display to select for PDZ variants that bind to 19 peptide ligands differing only at position 0. To verify that each obtained PDZ domain exhibited the correct binding specificity, we selected peptide ligands for each domain. Despite intensive efforts, we were only able to evolve Erbin PDZ domain variants with selectivity for the aliphatic C-terminal side chains Val, Ile and Leu. Interestingly, many PDZ domains with these three distinct specificities contained identical amino acids at positions that directly contact position 0 but differed in the loop that does not contact position 0. Computational modeling of the selected PDZ domains shows how slight conformational changes in the loop region propagate to the binding site and result in different binding specificities. Our results demonstrate that second-sphere residues could be crucial in determining protein binding specificity.
KW - binding cooperativity
KW - computational modeling
KW - phage display
KW - protein engineering
KW - protein interaction domains
UR - http://www.scopus.com/inward/record.url?scp=84907809712&partnerID=8YFLogxK
U2 - 10.1016/j.jmb.2014.05.003
DO - 10.1016/j.jmb.2014.05.003
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C2 - 24813123
AN - SCOPUS:84907809712
SN - 0022-2836
VL - 426
SP - 3500
EP - 3508
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
IS - 21
ER -