30. Structural Genomics Consortium, China
Structural Genomics Consortium, Northeast
Structural Genomics Consortium, Gr€ aslund S,
Nordlund P, Weigelt J, Hallberg BM, Bray J,
Gileadi O, Knapp S, Oppermann U,
Arrowsmith
C,
Hui
R,
Ming
J,
Dhe-Paganon S, Park H, Savchenko A, Yee A,
Edwards A, Vincentelli R, Cambillau C, Kim R,
Kim S-H, Rao Z, Shi Y, Terwilliger TC, Kim
C-Y, Hung L-W, Waldo GS, Peleg Y, Albeck S,
Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A,
Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M,
Burley SK, Emtage JS, Sauder JM,
Thompson D, Bain K, Luz J, Gheyi T,
Zhang F, Atwell S, Almo SC, Bonanno JB,
Fiser A, Swaminathan S, Studier FW, Chance
MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC,
Hunt JF, Tong L, Cunningham K, Inouye M,
Anderson S, Janjua H, Shastry R, Ho CK,
Wang D, Wang H, Jiang M, Montelione GT,
Stuart DI, Owens RJ, Daenke S, Schu ¨tz A,
Heinemann U, Yokoyama S, Bu ¨ssow K, Gunsalus KC (2008) Protein production and purification. Nat Methods 5:135–146. https://doi.
org/10.1038/nmeth.f.202
31. Dupeux F, Ro ¨wer M, Seroul G, Blot D, Ma ´rquez JA (2011) A thermal stability assay can
help to estimate the crystallization likelihood of
biological samples. Acta Crystallogr D Biol
Crystallogr 67:915–919. https://doi.org/10.
1107/S0907444911036225
32. Bruce D, Cardew E, Freitag-Pohl S, Pohl E
(2019) How to stabilize protein: stability
screens for thermal shift assays and nano differential scanning fluorimetry in the virus-X project. J Vis Exp. https://doi.org/10.3791/
58666
33. Boivin S, Kozak S, Meijers R (2013) Optimization of protein purification and characterization using Thermofluor screens. Protein Expr
Purif 91:192–206. https://doi.org/10.1016/
j.pep.2013.08.002
34. Genera M, Samson D, Raynal B, Haouz A,
Baron B, Simenel C, Guerois R, Wolff N,
Caillet-Saguy C (2019) Structural and functional characterization of the PDZ domain of
the human phosphatase PTPN3 and its interaction with the human papillomavirus E6
oncoprotein. Sci Rep 9:7438. https://doi.
org/10.1038/s41598-019-43932-x
35. Monsellier E, Bedouelle H (2005) Quantitative measurement of protein stability from
unfolding equilibria monitored with the fluorescence maximum wavelength. Protein Eng
Des Sel 18:445–456. https://doi.org/10.
1093/protein/gzi046
36. Terrien E, Chaffotte A, Lafage M, Khan Z,
Pre ´haud C, Cordier F, Simenel C,
Delepierre M, Buc H, Lafon M, Wolff N
(2012) Interference with the PTEN-MAST2
interaction by a viral protein leads to cellular
relocalization of PTEN. Sci Signal 5:ra58.
https://doi.org/10.1126/scisignal.2002941
37. Rath A, Glibowicka M, Nadeau VG, Chen G,
Deber CM (2009) Detergent binding explains
anomalous SDS-PAGE migration of membrane proteins. Proc Natl Acad Sci U S A
106:1760–1765. https://doi.org/10.1073/
pnas.0813167106
38. Shirai A, Matsuyama A, Yashiroda Y,
Hashimoto A, Kawamura Y, Arai R,
Komatsu Y, Horinouchi S, Yoshida M (2008)
Global analysis of gel mobility of proteins and
its use in target identification. J Biol Chem
283:10745–10752.
https://doi.org/10.
1074/jbc.M709211200
39. Duhoo Y, Girault V, Turchetto J, Ramond L,
Durbesson F, Fourquet P, Nomine ´ Y,
Cardoso V, Sequeira AF, Bra ´s JLA, Fontes
CMGA, Trave ´ G, Wolff N, Vincentelli R
(2019) High-throughput production of a new
library of human single and tandem PDZ
domains allows quantitative PDZ-peptide
interaction
screening
through
highthroughput holdup assay. Methods Mol Biol
2025:439–476.
https://doi.org/10.1007/
978-1-4939-9624-7_21
40. Ivarsson Y, Wawrzyniak AM, Kashyap R,
Polanowska J, Betzi S, Lembo F,
Vermeiren E, Chiheb D, Lenfant N,
Morelli X, Borg J-P, Reboul J, Zimmermann
P (2013) Prevalence, specificity and determinants of lipid-interacting PDZ domains from
an in-cell screen and in vitro binding experiments. PLoS One 8:e54581. https://doi.org/
10.1371/journal.pone.0054581
41. Wawrzyniak AM, Kashyap R, Zimmermann P
(2013) Phosphoinositides and PDZ domain
scaffolds. Adv Exp Med Biol 991:41–57.
https://doi.org/10.1007/978-94-007-63319_4
42. Layne E (1957) Spectrophotometric and turbidimetric methods for measuring proteins.
Methods Enzymol 3:447–454
43. Lees JG, Miles AJ, Wien F, Wallace BA (2006)
A reference database for circular dichroism
spectroscopy covering fold and secondary
structure
space.
Bioinformatics
22:1955–1962. https://doi.org/10.1093/bio
informatics/btl327
44. Page R, Peti W, Wilson IA, Stevens RC,
Wu ¨thrich K (2005) NMR screening and crystal
quality of bacterially expressed prokaryotic and
PDZ Sample Quality Assessment
123
Structural Genomics Consortium, Northeast
Structural Genomics Consortium, Gr€ aslund S,
Nordlund P, Weigelt J, Hallberg BM, Bray J,
Gileadi O, Knapp S, Oppermann U,
Arrowsmith
C,
Hui
R,
Ming
J,
Dhe-Paganon S, Park H, Savchenko A, Yee A,
Edwards A, Vincentelli R, Cambillau C, Kim R,
Kim S-H, Rao Z, Shi Y, Terwilliger TC, Kim
C-Y, Hung L-W, Waldo GS, Peleg Y, Albeck S,
Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A,
Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M,
Burley SK, Emtage JS, Sauder JM,
Thompson D, Bain K, Luz J, Gheyi T,
Zhang F, Atwell S, Almo SC, Bonanno JB,
Fiser A, Swaminathan S, Studier FW, Chance
MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC,
Hunt JF, Tong L, Cunningham K, Inouye M,
Anderson S, Janjua H, Shastry R, Ho CK,
Wang D, Wang H, Jiang M, Montelione GT,
Stuart DI, Owens RJ, Daenke S, Schu ¨tz A,
Heinemann U, Yokoyama S, Bu ¨ssow K, Gunsalus KC (2008) Protein production and purification. Nat Methods 5:135–146. https://doi.
org/10.1038/nmeth.f.202
31. Dupeux F, Ro ¨wer M, Seroul G, Blot D, Ma ´rquez JA (2011) A thermal stability assay can
help to estimate the crystallization likelihood of
biological samples. Acta Crystallogr D Biol
Crystallogr 67:915–919. https://doi.org/10.
1107/S0907444911036225
32. Bruce D, Cardew E, Freitag-Pohl S, Pohl E
(2019) How to stabilize protein: stability
screens for thermal shift assays and nano differential scanning fluorimetry in the virus-X project. J Vis Exp. https://doi.org/10.3791/
58666
33. Boivin S, Kozak S, Meijers R (2013) Optimization of protein purification and characterization using Thermofluor screens. Protein Expr
Purif 91:192–206. https://doi.org/10.1016/
j.pep.2013.08.002
34. Genera M, Samson D, Raynal B, Haouz A,
Baron B, Simenel C, Guerois R, Wolff N,
Caillet-Saguy C (2019) Structural and functional characterization of the PDZ domain of
the human phosphatase PTPN3 and its interaction with the human papillomavirus E6
oncoprotein. Sci Rep 9:7438. https://doi.
org/10.1038/s41598-019-43932-x
35. Monsellier E, Bedouelle H (2005) Quantitative measurement of protein stability from
unfolding equilibria monitored with the fluorescence maximum wavelength. Protein Eng
Des Sel 18:445–456. https://doi.org/10.
1093/protein/gzi046
36. Terrien E, Chaffotte A, Lafage M, Khan Z,
Pre ´haud C, Cordier F, Simenel C,
Delepierre M, Buc H, Lafon M, Wolff N
(2012) Interference with the PTEN-MAST2
interaction by a viral protein leads to cellular
relocalization of PTEN. Sci Signal 5:ra58.
https://doi.org/10.1126/scisignal.2002941
37. Rath A, Glibowicka M, Nadeau VG, Chen G,
Deber CM (2009) Detergent binding explains
anomalous SDS-PAGE migration of membrane proteins. Proc Natl Acad Sci U S A
106:1760–1765. https://doi.org/10.1073/
pnas.0813167106
38. Shirai A, Matsuyama A, Yashiroda Y,
Hashimoto A, Kawamura Y, Arai R,
Komatsu Y, Horinouchi S, Yoshida M (2008)
Global analysis of gel mobility of proteins and
its use in target identification. J Biol Chem
283:10745–10752.
https://doi.org/10.
1074/jbc.M709211200
39. Duhoo Y, Girault V, Turchetto J, Ramond L,
Durbesson F, Fourquet P, Nomine ´ Y,
Cardoso V, Sequeira AF, Bra ´s JLA, Fontes
CMGA, Trave ´ G, Wolff N, Vincentelli R
(2019) High-throughput production of a new
library of human single and tandem PDZ
domains allows quantitative PDZ-peptide
interaction
screening
through
highthroughput holdup assay. Methods Mol Biol
2025:439–476.
https://doi.org/10.1007/
978-1-4939-9624-7_21
40. Ivarsson Y, Wawrzyniak AM, Kashyap R,
Polanowska J, Betzi S, Lembo F,
Vermeiren E, Chiheb D, Lenfant N,
Morelli X, Borg J-P, Reboul J, Zimmermann
P (2013) Prevalence, specificity and determinants of lipid-interacting PDZ domains from
an in-cell screen and in vitro binding experiments. PLoS One 8:e54581. https://doi.org/
10.1371/journal.pone.0054581
41. Wawrzyniak AM, Kashyap R, Zimmermann P
(2013) Phosphoinositides and PDZ domain
scaffolds. Adv Exp Med Biol 991:41–57.
https://doi.org/10.1007/978-94-007-63319_4
42. Layne E (1957) Spectrophotometric and turbidimetric methods for measuring proteins.
Methods Enzymol 3:447–454
43. Lees JG, Miles AJ, Wien F, Wallace BA (2006)
A reference database for circular dichroism
spectroscopy covering fold and secondary
structure
space.
Bioinformatics
22:1955–1962. https://doi.org/10.1093/bio
informatics/btl327
44. Page R, Peti W, Wilson IA, Stevens RC,
Wu ¨thrich K (2005) NMR screening and crystal
quality of bacterially expressed prokaryotic and
PDZ Sample Quality Assessment
123