8. Delhommel F, Chaffotte A, Terrien E,
Raynal B, Buc H, Delepierre M, Cordier F,
Wolff N (2015) Deciphering the unconventional peptide binding to the PDZ domain of
MAST2. Biochem J 469:159–168. https://
doi.org/10.1042/BJ20141198
9. Wu J, Yang Y, Zhang J, Ji P, Du W, Jiang P,
Xie D, Huang H, Wu M, Zhang G, Wu J, Shi Y
(2007) Domain-swapped dimerization of the
second PDZ domain of ZO2 may provide a
structural basis for the polymerization of claudins. J Biol Chem 282:35988–35999. https://
doi.org/10.1074/jbc.M703826200
10. Chang BH, Gujral TS, Karp ES, BuKhalid R,
Grantcharova VP, MacBeath G (2011) A systematic family-wide investigation reveals that
$30% of mammalian PDZ domains engage in
PDZ-PDZ
interactions.
Chem
Biol
18:1143–1152. https://doi.org/10.1016/j.
chembiol.2011.06.013
11. Laemmli UK (1970) Cleavage of structural
proteins during the assembly of the head of
bacteriophage T4. Nature 227:680–685.
https://doi.org/10.1038/227680a0
12. Gasteiger E, Hoogland C, Gattiker A,
Duvaud S, Wilkins M, Appel RD, Bairoch AM
(2005) Protein identification and analysis tools
on the ExPASy server. In: Walker JM (ed) The
proteomics protocols handbook. Humana
Press, pp 571–607
13. Noble JE (2014) Quantification of protein
concentration using UV absorbance and Coomassie dyes. Methods Enzymol 536:17–26.
https://doi.org/10.1016/B978-0-12420070-8.00002-7
14. Glasel JA (1995) Validity of nucleic acid purities monitored by 260nm/280nm absorbance
ratios. BioTechniques 18:62–63
15. Pace CN, Vajdos F, Fee L, Grimsley G, Gray T
(1995) How to measure and predict the molar
absorption coefficient of a protein. Protein Sci
4:2411–2423. https://doi.org/10.1002/pro.
5560041120
16. Karas M, Hillenkamp F (1988) Laser desorption ionization of proteins with molecular
masses exceeding 10,000 daltons. Anal Chem
60:2299–2301.
https://doi.org/10.1021/
ac00171a028
17. Suckau
D,
Resemann
A
(2003)
T3-sequencing: targeted characterization of
the N- and C-termini of undigested proteins
by
mass
spectrometry.
Anal
Chem
75:5817–5824.
https://doi.org/10.1021/
ac034362b
18. Philo JS (2006) Is any measurement method
optimal for all aggregate sizes and types? AAPS
J 8:E564–E571. https://doi.org/10.1208/
aapsj080365
19. Nobbmann U, Connah M, Fish B, Varley P,
Gee C, Mulot S, Chen J, Zhou L, Lu Y, Shen F,
Yi J, Harding SE (2007) Dynamic light scattering as a relative tool for assessing the molecular
integrity and stability of monoclonal antibodies. Biotechnol Genet Eng Rev 24:117–128
20. Raynal B, Lenormand P, Baron B, Hoos S,
England P (2010) Quality assessment and optimization of purified protein samples: why and
how? Microb Cell Factories 13. https://doi.
org/10.1186/s12934-014-0180-6
21. Fekete S, Beck A, Veuthey J-L, Guillarme D
(2014) Theory and practice of size exclusion
chromatography for the analysis of protein
aggregates.
J
Pharm
Biomed
Anal
101:161–173.
https://doi.org/10.1016/j.
jpba.2014.04.011
22. Sahin E, Roberts CJ (2012) Size-exclusion
chromatography with multi-angle light scattering for elucidating protein aggregation
mechanisms.
Methods
Mol
Biol
899:403–423.
https://doi.org/10.1007/
978-1-61779-921-1_25
23. Daviter T, Chmel N, Rodger A (2013) Circular
and linear dichroism spectroscopy for the study
of protein-ligand interactions. Methods Mol
Biol 1008:211–241
24. Schuck P (2003) On the analysis of protein
self-association by sedimentation velocity analytical ultracentrifugation. Anal Biochem
320:104–124.
https://doi.org/10.1016/
S0003-2697(03)00289-6
25. Demeler B (2010) Methods for the design and
analysis of sedimentation velocity and sedimentation equilibrium experiments with proteins.
Curr Protoc Protein Sci:1–24. https://doi.
org/10.1002/0471140864.ps0713s60
26. Balbo A, Zhao H, Brown PH, Schuck P (2009)
Assembly, loading, and alignment of an analytical ultracentrifuge sample cell. J Vis Exp:
e1530. https://doi.org/10.3791/1530
27. Schuck P (2000) Size-distribution analysis of
macromolecules by sedimentation velocity
ultracentrifugation and lamm equation modeling. Biophys J 78:1606–1619. https://doi.
org/10.1016/S0006-3495(00)76713-0
28. Micsonai A, Wien F, Bulya ´ki E ´ , Kun J, Moussong E ´ , Lee Y-H, Goto Y, Re ´fre ´giers M, Kardos J (2018) BeStSel: a web server for accurate
protein secondary structure prediction and fold
recognition from the circular dichroism spectra. Nucleic Acids Res 46:W315–W322.
https://doi.org/10.1093/nar/gky497
29. Medrano G, Dolan MC, Condori J, Radin DN,
Cramer CL (2012) Quality assessment of
recombinant proteins produced in plants.
Methods Mol Biol 824:535–564. https://doi.
org/10.1007/978-1-61779-433-9_29
122
Ce ´ lia Caillet-Saguy et al.
Raynal B, Buc H, Delepierre M, Cordier F,
Wolff N (2015) Deciphering the unconventional peptide binding to the PDZ domain of
MAST2. Biochem J 469:159–168. https://
doi.org/10.1042/BJ20141198
9. Wu J, Yang Y, Zhang J, Ji P, Du W, Jiang P,
Xie D, Huang H, Wu M, Zhang G, Wu J, Shi Y
(2007) Domain-swapped dimerization of the
second PDZ domain of ZO2 may provide a
structural basis for the polymerization of claudins. J Biol Chem 282:35988–35999. https://
doi.org/10.1074/jbc.M703826200
10. Chang BH, Gujral TS, Karp ES, BuKhalid R,
Grantcharova VP, MacBeath G (2011) A systematic family-wide investigation reveals that
$30% of mammalian PDZ domains engage in
PDZ-PDZ
interactions.
Chem
Biol
18:1143–1152. https://doi.org/10.1016/j.
chembiol.2011.06.013
11. Laemmli UK (1970) Cleavage of structural
proteins during the assembly of the head of
bacteriophage T4. Nature 227:680–685.
https://doi.org/10.1038/227680a0
12. Gasteiger E, Hoogland C, Gattiker A,
Duvaud S, Wilkins M, Appel RD, Bairoch AM
(2005) Protein identification and analysis tools
on the ExPASy server. In: Walker JM (ed) The
proteomics protocols handbook. Humana
Press, pp 571–607
13. Noble JE (2014) Quantification of protein
concentration using UV absorbance and Coomassie dyes. Methods Enzymol 536:17–26.
https://doi.org/10.1016/B978-0-12420070-8.00002-7
14. Glasel JA (1995) Validity of nucleic acid purities monitored by 260nm/280nm absorbance
ratios. BioTechniques 18:62–63
15. Pace CN, Vajdos F, Fee L, Grimsley G, Gray T
(1995) How to measure and predict the molar
absorption coefficient of a protein. Protein Sci
4:2411–2423. https://doi.org/10.1002/pro.
5560041120
16. Karas M, Hillenkamp F (1988) Laser desorption ionization of proteins with molecular
masses exceeding 10,000 daltons. Anal Chem
60:2299–2301.
https://doi.org/10.1021/
ac00171a028
17. Suckau
D,
Resemann
A
(2003)
T3-sequencing: targeted characterization of
the N- and C-termini of undigested proteins
by
mass
spectrometry.
Anal
Chem
75:5817–5824.
https://doi.org/10.1021/
ac034362b
18. Philo JS (2006) Is any measurement method
optimal for all aggregate sizes and types? AAPS
J 8:E564–E571. https://doi.org/10.1208/
aapsj080365
19. Nobbmann U, Connah M, Fish B, Varley P,
Gee C, Mulot S, Chen J, Zhou L, Lu Y, Shen F,
Yi J, Harding SE (2007) Dynamic light scattering as a relative tool for assessing the molecular
integrity and stability of monoclonal antibodies. Biotechnol Genet Eng Rev 24:117–128
20. Raynal B, Lenormand P, Baron B, Hoos S,
England P (2010) Quality assessment and optimization of purified protein samples: why and
how? Microb Cell Factories 13. https://doi.
org/10.1186/s12934-014-0180-6
21. Fekete S, Beck A, Veuthey J-L, Guillarme D
(2014) Theory and practice of size exclusion
chromatography for the analysis of protein
aggregates.
J
Pharm
Biomed
Anal
101:161–173.
https://doi.org/10.1016/j.
jpba.2014.04.011
22. Sahin E, Roberts CJ (2012) Size-exclusion
chromatography with multi-angle light scattering for elucidating protein aggregation
mechanisms.
Methods
Mol
Biol
899:403–423.
https://doi.org/10.1007/
978-1-61779-921-1_25
23. Daviter T, Chmel N, Rodger A (2013) Circular
and linear dichroism spectroscopy for the study
of protein-ligand interactions. Methods Mol
Biol 1008:211–241
24. Schuck P (2003) On the analysis of protein
self-association by sedimentation velocity analytical ultracentrifugation. Anal Biochem
320:104–124.
https://doi.org/10.1016/
S0003-2697(03)00289-6
25. Demeler B (2010) Methods for the design and
analysis of sedimentation velocity and sedimentation equilibrium experiments with proteins.
Curr Protoc Protein Sci:1–24. https://doi.
org/10.1002/0471140864.ps0713s60
26. Balbo A, Zhao H, Brown PH, Schuck P (2009)
Assembly, loading, and alignment of an analytical ultracentrifuge sample cell. J Vis Exp:
e1530. https://doi.org/10.3791/1530
27. Schuck P (2000) Size-distribution analysis of
macromolecules by sedimentation velocity
ultracentrifugation and lamm equation modeling. Biophys J 78:1606–1619. https://doi.
org/10.1016/S0006-3495(00)76713-0
28. Micsonai A, Wien F, Bulya ´ki E ´ , Kun J, Moussong E ´ , Lee Y-H, Goto Y, Re ´fre ´giers M, Kardos J (2018) BeStSel: a web server for accurate
protein secondary structure prediction and fold
recognition from the circular dichroism spectra. Nucleic Acids Res 46:W315–W322.
https://doi.org/10.1093/nar/gky497
29. Medrano G, Dolan MC, Condori J, Radin DN,
Cramer CL (2012) Quality assessment of
recombinant proteins produced in plants.
Methods Mol Biol 824:535–564. https://doi.
org/10.1007/978-1-61779-433-9_29
122
Ce ´ lia Caillet-Saguy et al.