18. Columns are usually stored in 20% (v/v) ethanol. Therefore,
the column must first be washed extensively with water (at least
2 column volumes) as ethanol may precipitate salts from the
buffer.
19. The buffer should be stable over time as any change, such as
oxidation, will lead to a drift in the baseline of the refractometer. The software baseline correction can compensate negligible drift.
20. High concentrations of chloride ions absorb at wavelengths
lower than 215 nm and limit the use of the spectrum below
that wavelengths. To avoid scattering, buffer and sample
should be filtered and degassed.
21. Chloride ions absorb strongly in the far-UV so low concentrations of NaCl and KCl in CD buffer are recommended. The
best way would be to prepare a phosphate buffer by mixing diand monosodium phosphates. In addition, DTT, detergents,
glycerol, or imidazole that absorb in the far-UV should be
removed.
Acknowledgments
The authors acknowledge Florence Cordier for technical support in
NMR. The authors thank the molecular biophysics facility at Institut Pasteur for providing cutting-edge instruments.
References
1. Weatheritt RJ, Luck K, Petsalaki E, Davey NE,
Gibson TJ (2012) The identification of short
linear motif-mediated interfaces within the
human
interactome.
Bioinformatics
28:976–982. https://doi.org/10.1093/bioin
formatics/bts072
2. Caillet-Saguy
C,
Maisonneuve
P,
Delhommel F, Terrien E, Babault N,
Lafon M, Cordier F, Wolff N (2015) Strategies
to interfere with PDZ-mediated interactions in
neurons: what we can learn from the rabies
virus. Prog Biophys Mol Biol 119:53–59.
https://doi.org/10.1016/j.pbiomolbio.
2015.02.007
3. Luck K, Charbonnier S, Trave ´ G (2012) The
emerging contribution of sequence context to
the specificity of protein interactions mediated
by PDZ domains. FEBS Lett 586:2648–2661.
https://doi.org/10.1016/j.febslet.2012.03.
056
4. Ye F, Zhang M (2013) Structures and target
recognition modes of PDZ domains: recurring
themes and emerging pictures. Biochem J
455:1–14.
https://doi.org/10.1042/
BJ20130783
5. Wang CK, Pan L, Chen J, Zhang M (2010)
Extensions of PDZ domains as important
structural and functional elements. Protein
Cell 1:737–751. https://doi.org/10.1007/
s13238-010-0099-6
6. Delhommel F, Cordier F, Bardiaux B,
Bouvier G, Colcombet-Cazenave B, Brier S,
Raynal B, Nouaille S, Bahloul A, ChamotRooke J, Nilges M, Petit C, Wolff N (2017)
Structural characterization of whirlin reveals an
unexpected and dynamic supramodule conformation of its PDZ tandem. Structure
25:1645–1656.e5. https://doi.org/10.1016/
j.str.2017.08.013
7. Long J, Wei Z, Feng W, Yu C, Zhao Y, Zhang
M (2008) Supramodular nature of GRIP1
revealed by the structure of its PDZ12 tandem
in complex with the carboxyl tail of Fras1. J
Mol Biol 375:1457–1468. https://doi.org/
10.1016/j.jmb.2007.11.088
PDZ Sample Quality Assessment
121
the column must first be washed extensively with water (at least
2 column volumes) as ethanol may precipitate salts from the
buffer.
19. The buffer should be stable over time as any change, such as
oxidation, will lead to a drift in the baseline of the refractometer. The software baseline correction can compensate negligible drift.
20. High concentrations of chloride ions absorb at wavelengths
lower than 215 nm and limit the use of the spectrum below
that wavelengths. To avoid scattering, buffer and sample
should be filtered and degassed.
21. Chloride ions absorb strongly in the far-UV so low concentrations of NaCl and KCl in CD buffer are recommended. The
best way would be to prepare a phosphate buffer by mixing diand monosodium phosphates. In addition, DTT, detergents,
glycerol, or imidazole that absorb in the far-UV should be
removed.
Acknowledgments
The authors acknowledge Florence Cordier for technical support in
NMR. The authors thank the molecular biophysics facility at Institut Pasteur for providing cutting-edge instruments.
References
1. Weatheritt RJ, Luck K, Petsalaki E, Davey NE,
Gibson TJ (2012) The identification of short
linear motif-mediated interfaces within the
human
interactome.
Bioinformatics
28:976–982. https://doi.org/10.1093/bioin
formatics/bts072
2. Caillet-Saguy
C,
Maisonneuve
P,
Delhommel F, Terrien E, Babault N,
Lafon M, Cordier F, Wolff N (2015) Strategies
to interfere with PDZ-mediated interactions in
neurons: what we can learn from the rabies
virus. Prog Biophys Mol Biol 119:53–59.
https://doi.org/10.1016/j.pbiomolbio.
2015.02.007
3. Luck K, Charbonnier S, Trave ´ G (2012) The
emerging contribution of sequence context to
the specificity of protein interactions mediated
by PDZ domains. FEBS Lett 586:2648–2661.
https://doi.org/10.1016/j.febslet.2012.03.
056
4. Ye F, Zhang M (2013) Structures and target
recognition modes of PDZ domains: recurring
themes and emerging pictures. Biochem J
455:1–14.
https://doi.org/10.1042/
BJ20130783
5. Wang CK, Pan L, Chen J, Zhang M (2010)
Extensions of PDZ domains as important
structural and functional elements. Protein
Cell 1:737–751. https://doi.org/10.1007/
s13238-010-0099-6
6. Delhommel F, Cordier F, Bardiaux B,
Bouvier G, Colcombet-Cazenave B, Brier S,
Raynal B, Nouaille S, Bahloul A, ChamotRooke J, Nilges M, Petit C, Wolff N (2017)
Structural characterization of whirlin reveals an
unexpected and dynamic supramodule conformation of its PDZ tandem. Structure
25:1645–1656.e5. https://doi.org/10.1016/
j.str.2017.08.013
7. Long J, Wei Z, Feng W, Yu C, Zhao Y, Zhang
M (2008) Supramodular nature of GRIP1
revealed by the structure of its PDZ12 tandem
in complex with the carboxyl tail of Fras1. J
Mol Biol 375:1457–1468. https://doi.org/
10.1016/j.jmb.2007.11.088
PDZ Sample Quality Assessment
121