References
1. Songyang Z, Fanning AS, Fu C, Xu J, Marfatia
SM, Chishti AH, Crompton A, Chan AC,
Anderson JM, Cantley LC (1997) Recognition
of unique carboxyl-terminal motifs by distinct
PDZ domains. Science 275:73–77
2. Stricker NL, Christopherson KS, Yi BA, Schatz
PJ, Raab RW, Dawes G, Bassett DE Jr, Bredt
DS, Li M (1997) PDZ domain of neuronal
nitric oxide synthase recognizes novel
C-terminal peptide sequences. Nat Biotechnol
15:336–342
3. Tonikian R, Zhang Y, Sazinsky SL, Currell B,
Yeh JH, Reva B, Held HA, Appleton BA,
Evangelista M, Wu Y, Xin X, Chan AC,
Seshagiri S, Lasky LA, Sander C, Boone C,
Bader GD, Sidhu SS (2008) A specificity map
for the PDZ domain family. PLoS Biol 6:e239
4. Kim J, Kim I, Yang JS, Shin YE, Hwang J,
Park S, Choi YS, Kim S (2012) Rewiring of
PDZ domain-ligand interaction network contributed to eukaryotic evolution. PLoS Genet
8:e1002510
5. Ernst A, Appleton BA, Ivarsson Y, Zhang Y,
Gfeller D, Wiesmann C, Sidhu SS (2014) A
structural portrait of the PDZ domain family.
J Mol Biol 426:3509–3519
6. Zhang Y, Appleton BA, Wiesmann C, Lau T,
Costa M, Hannoush RN, Sidhu SS (2009)
Inhibition of Wnt signaling by Dishevelled
PDZ peptides. Nat Chem Biol 5:217–219
7. Luck K, Trave G (2011) Phage display can
select over-hydrophobic sequences that may
impair prediction of natural domain-peptide
interactions. Bioinformatics 27:899–902
8. Ivarsson Y, Arnold R, McLaughlin M, Nim S,
Joshi R, Ray D, Liu B, Teyra J, Pawson T,
Moffat J, Li SS, Sidhu SS, Kim PM (2014)
Large-scale interaction profiling of PDZ
domains through proteomic peptide-phage
display using human and viral phage peptidomes. Proc Natl Acad Sci U S A
111:2542–2547
9. Garrido-Urbani S, Garg P, Ghossoub R,
Arnold R, Lembo F, Sundell GN, Kim PM,
Lopez M, Zimmermann P, Sidhu SS, Ivarsson
Y (2016) Proteomic peptide phage display
uncovers novel interactions of the PDZ1-2supramodule of syntenin. FEBS Lett 590:3–12
10. Sundell
GN,
Arnold
R,
Ali
M,
Naksukpaiboon P, Orts J, Guntert P, Chi CN,
Ivarsson Y (2018) Proteome-wide analysis of
phospho-regulated PDZ domain interactions.
Mol Syst Biol 14:e8129
11. Rajan S, Sidhu SS (2012) Simplified synthetic
antibody
libraries.
Methods
Enzymol
502:3–23
12. Held HA, Sidhu SS (2004) Comprehensive
mutational analysis of the M13 major coat protein: improved scaffolds for C-terminal phage
display. J Mol Biol 340:587–597
13. Kunkel TA (1985) Rapid and efficient sitespecific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A 82:488–492
14. Huang H, Sidhu SS (2011) Studying binding
specificities of peptide recognition modules by
high-throughput phage display selections.
Methods Mol Biol 781:87–97
15. McLaughlin ME, Sidhu SS (2013) Engineering and analysis of peptide-recognition domain
specificities by phage display and deep sequencing. Methods Enzymol 523:327–349
16. Ali M, Simonetti L, Ivarsson Y (2020) Screening intrinsically disordered regions for short
linear binding motifs. Methods Mol Biol
2141:529–552
60
Susanne Lu ¨ chow et al.
1. Songyang Z, Fanning AS, Fu C, Xu J, Marfatia
SM, Chishti AH, Crompton A, Chan AC,
Anderson JM, Cantley LC (1997) Recognition
of unique carboxyl-terminal motifs by distinct
PDZ domains. Science 275:73–77
2. Stricker NL, Christopherson KS, Yi BA, Schatz
PJ, Raab RW, Dawes G, Bassett DE Jr, Bredt
DS, Li M (1997) PDZ domain of neuronal
nitric oxide synthase recognizes novel
C-terminal peptide sequences. Nat Biotechnol
15:336–342
3. Tonikian R, Zhang Y, Sazinsky SL, Currell B,
Yeh JH, Reva B, Held HA, Appleton BA,
Evangelista M, Wu Y, Xin X, Chan AC,
Seshagiri S, Lasky LA, Sander C, Boone C,
Bader GD, Sidhu SS (2008) A specificity map
for the PDZ domain family. PLoS Biol 6:e239
4. Kim J, Kim I, Yang JS, Shin YE, Hwang J,
Park S, Choi YS, Kim S (2012) Rewiring of
PDZ domain-ligand interaction network contributed to eukaryotic evolution. PLoS Genet
8:e1002510
5. Ernst A, Appleton BA, Ivarsson Y, Zhang Y,
Gfeller D, Wiesmann C, Sidhu SS (2014) A
structural portrait of the PDZ domain family.
J Mol Biol 426:3509–3519
6. Zhang Y, Appleton BA, Wiesmann C, Lau T,
Costa M, Hannoush RN, Sidhu SS (2009)
Inhibition of Wnt signaling by Dishevelled
PDZ peptides. Nat Chem Biol 5:217–219
7. Luck K, Trave G (2011) Phage display can
select over-hydrophobic sequences that may
impair prediction of natural domain-peptide
interactions. Bioinformatics 27:899–902
8. Ivarsson Y, Arnold R, McLaughlin M, Nim S,
Joshi R, Ray D, Liu B, Teyra J, Pawson T,
Moffat J, Li SS, Sidhu SS, Kim PM (2014)
Large-scale interaction profiling of PDZ
domains through proteomic peptide-phage
display using human and viral phage peptidomes. Proc Natl Acad Sci U S A
111:2542–2547
9. Garrido-Urbani S, Garg P, Ghossoub R,
Arnold R, Lembo F, Sundell GN, Kim PM,
Lopez M, Zimmermann P, Sidhu SS, Ivarsson
Y (2016) Proteomic peptide phage display
uncovers novel interactions of the PDZ1-2supramodule of syntenin. FEBS Lett 590:3–12
10. Sundell
GN,
Arnold
R,
Ali
M,
Naksukpaiboon P, Orts J, Guntert P, Chi CN,
Ivarsson Y (2018) Proteome-wide analysis of
phospho-regulated PDZ domain interactions.
Mol Syst Biol 14:e8129
11. Rajan S, Sidhu SS (2012) Simplified synthetic
antibody
libraries.
Methods
Enzymol
502:3–23
12. Held HA, Sidhu SS (2004) Comprehensive
mutational analysis of the M13 major coat protein: improved scaffolds for C-terminal phage
display. J Mol Biol 340:587–597
13. Kunkel TA (1985) Rapid and efficient sitespecific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A 82:488–492
14. Huang H, Sidhu SS (2011) Studying binding
specificities of peptide recognition modules by
high-throughput phage display selections.
Methods Mol Biol 781:87–97
15. McLaughlin ME, Sidhu SS (2013) Engineering and analysis of peptide-recognition domain
specificities by phage display and deep sequencing. Methods Enzymol 523:327–349
16. Ali M, Simonetti L, Ivarsson Y (2020) Screening intrinsically disordered regions for short
linear binding motifs. Methods Mol Biol
2141:529–552
60
Susanne Lu ¨ chow et al.