Ma, D., Tillman, T.S., Tang, P., Meirovitch, E., Eckenhoff, R., Carninie, A., Xu, Y. (2008) NMR studies of a channel
protein without membranes: Structure and dynamics of water-solubilized KcsA. Proc. Natl. Acad. Sci. USA
105:16537–16542.
Magnani, F., Serrano-Vega, M.J., Shibata, Y., Abdul-Hussein, S., Lebon, G., Miller-Gallacher, J., Singhal, A.,
Strege, A., Thomas, J.A., Tate, C.G. (2016) A mutagenesis and screening strategy to generate optimally
thermostabilized membrane proteins for structural studies. Nat. Protoc. 11:1554–1571.
Magnani, F., Shibata, Y., Serrano-Vega, M.J., Tate, C.G. (2008) Co-evolving stability and conformational homogeneity
of the human adenosine A 2A receptor. Proc. Natl. Acad. Sci. USA 105:10744–10749.
Marrink, S.J., Mark, A.E. (2002) Molecular dynamics simulations of mixed micelles modeling human bile. Biochemistry
41:5375–4382.
Marrink, S.J., Tieleman, D.P., Mark, A.E. (2000) Molecular dynamics simulation of the kinetics of spontaneous micelle
formation. J. Phys. Chem. B 104:12165–12173.
Matar-Merheb, R., Rhimi, M., Leydier, A., Huché, F., Galián, C., Desuzinges-Mandon, E., Ficheux, D., Flot, D.,
Aghajari, H., Kahn, R., Di Pietro, A., Jault, J.-M., Coleman, A.W., Falson, P. (2011) Structuring detergents for
extracting and stabilizing functional membrane proteins. PLoS One 6:e18036.
Miller, J.L., Tate, C.G. (2011) Engineering an ultra-thermostable β 1 -adrenoceptor. J. Mol. Biol. 413:628–638.
Miyagishi, S., Okada, K., Asakawa, T. (2001) Salt effect on critical micelle concentrations of nonionic surfactants,
N-acyl-N-methylglucamides (MEGA-n). J. Colloid Interface Sci. 238:91–95.
Molina-Bolívar, J.A., Hierrezuelo, J.M., Carnero Ruiz, C. (2013) Energetics of clouding and size effects in non-ionic
surfactant mixtures: The influence of alkyl chain length and NaCl addition. J. Chem. Thermodynamics 57:59–66.
Neugebauer, J.M. (1988) A Guide to the Properties and Uses of Detergents in Biology and Biochemistry. Calbiochem
Co., La Jolla, 64 p.
Neugebauer, J.M. (1990) Detergents: An overview. Meth. Enzymol. 182:239–253.
Norimatsu, Y., Hasegawa, K., Shimizu, N., Toyoshima, C. (2017) Protein-phospholipid interplay revealed with crystals
of a calcium pump. Nature 545:193–198.
Orwick-Rydmark, M., Arnold, T., Linke, D. (2016) The use of detergents to purify membrane proteins. Curr. Protoc.
Protein Sci. 84:4.8.1–4.8.34.
Ostermeier, C., Harrenga, A., Ermler, U., Michel, H. (1997) Structure at 2.7 Å resolution of the Paracoccus denitrificans
two-subunit cytochrome c oxidase complexed with an antibody Fv fragment. Proc. Natl. Acad. Sci. USA
94:10547–10553.
Otzen, D.E. (2015) Proteins in a brave new surfactant world. Curr. Opin. Colloid Interface Sci. 20:161–169.
Pagliano, C., Barera, S., Chimirri, F., Saracco, G., Barber, J. (2012) Comparison of the α and β isomeric forms of the
detergent n-dodecyl-D-maltoside for solubilizing photosynthetic complexes from pea thylakoid membranes. Biochim.
Biophys. Acta 1817:1506–1515.
Palczewski, K., Kumasaka, T., Hori, T., Behnke, C.A., Motoshima, H., Fox, B.A., Le Trong, I., Teller, D.C., Okada, T.,
Stenkamp, R.E., Yamamoto, M., Miyano, M. (2000) Crystal structure of rhodopsin: a G protein-coupled receptor.
Science 289:739–745.
Patargias, G., Bond, P.J., Deol, S.S., Sansom, M.S.P. (2005) Molecular dynamics simulations of GlpF in a micelle vs. in a
bilayer: Conformational dynamics of a membrane protein as a function of environment. J. Phys. Chem. B
109:575–582.
Pebay-Peyroula, E., Garavito, R.M., Rosenbusch, J.P., Zulauf, M., Timmins, P. (1995) Detergent structure in tetragonal
crystals of OmpF porin. Structure 3:1051–1059.
Penel, S., Pebay-Peyroula, E., Rosenbusch, J., Rummel, G., Schirmer, T., Timmins, P.A. (1998) Detergent binding in
trigonal crystals of OmpF porin from Escherichia coli. Biochimie 80:543–551.
Pérez-Victoria, I., Pérez-Victoria, F.J., Roldán-Vargas, S., García-Hernández, R., Carvalho, L., Castanys, S., Gamarro,
F., Morales, J.C., Pérez-Victoria, J.M. (2011) Non-reducing trisaccharide fatty acid monoesters: novel detergents in
membrane biochemistry. Biochim. Biophys. Acta 1808:717–726.
Perlmutter, J.D., Popot, J.-L., Sachs, J.N. (2014) Molecular dynamics simulations of a membrane protein/amphipol
complex. J. Membr. Biol. 247:883–895.
Perozo, E., Cortes, D.M., Cuello, L.G. (1998) Three-dimensional architecture and gating mechanism of a K
+ channel
studied by EPR spectroscopy. Nat. Struct. Biol. 5:459–469.
Pierre, Y., Breyton, C., Kramer, D., Popot, J.-L. (1995) Purification and characterization of the cytochrome b 6 f complex
from Chlamydomonas reinhardtii. J. Biol. Chem. 270:29342–29349.
Poget, S.F., Girvin, M.E. (2007) Solution NMR of membrane proteins in bilayer mimics: small is beautiful, but
sometimes bigger is better. Biochim. Biophys. Acta 1768:3098–3106.
Pomroy, N.C., Deber, C.M. (1998) Solubilization of hydrophobic peptides by reversible cysteine PEGylation. Biochem.
Biophys. Res. Commun. 245:618–621.
Popot, J.-L. (2010) Amphipols, nanodiscs, and fluorinated surfactants: Three non-conventional approaches to studying
membrane proteins in aqueous solutions. Annu. Rev. Biochem. 79:737–775.
92
2 Extracting Membrane Proteins from Their Native Environment
protein without membranes: Structure and dynamics of water-solubilized KcsA. Proc. Natl. Acad. Sci. USA
105:16537–16542.
Magnani, F., Serrano-Vega, M.J., Shibata, Y., Abdul-Hussein, S., Lebon, G., Miller-Gallacher, J., Singhal, A.,
Strege, A., Thomas, J.A., Tate, C.G. (2016) A mutagenesis and screening strategy to generate optimally
thermostabilized membrane proteins for structural studies. Nat. Protoc. 11:1554–1571.
Magnani, F., Shibata, Y., Serrano-Vega, M.J., Tate, C.G. (2008) Co-evolving stability and conformational homogeneity
of the human adenosine A 2A receptor. Proc. Natl. Acad. Sci. USA 105:10744–10749.
Marrink, S.J., Mark, A.E. (2002) Molecular dynamics simulations of mixed micelles modeling human bile. Biochemistry
41:5375–4382.
Marrink, S.J., Tieleman, D.P., Mark, A.E. (2000) Molecular dynamics simulation of the kinetics of spontaneous micelle
formation. J. Phys. Chem. B 104:12165–12173.
Matar-Merheb, R., Rhimi, M., Leydier, A., Huché, F., Galián, C., Desuzinges-Mandon, E., Ficheux, D., Flot, D.,
Aghajari, H., Kahn, R., Di Pietro, A., Jault, J.-M., Coleman, A.W., Falson, P. (2011) Structuring detergents for
extracting and stabilizing functional membrane proteins. PLoS One 6:e18036.
Miller, J.L., Tate, C.G. (2011) Engineering an ultra-thermostable β 1 -adrenoceptor. J. Mol. Biol. 413:628–638.
Miyagishi, S., Okada, K., Asakawa, T. (2001) Salt effect on critical micelle concentrations of nonionic surfactants,
N-acyl-N-methylglucamides (MEGA-n). J. Colloid Interface Sci. 238:91–95.
Molina-Bolívar, J.A., Hierrezuelo, J.M., Carnero Ruiz, C. (2013) Energetics of clouding and size effects in non-ionic
surfactant mixtures: The influence of alkyl chain length and NaCl addition. J. Chem. Thermodynamics 57:59–66.
Neugebauer, J.M. (1988) A Guide to the Properties and Uses of Detergents in Biology and Biochemistry. Calbiochem
Co., La Jolla, 64 p.
Neugebauer, J.M. (1990) Detergents: An overview. Meth. Enzymol. 182:239–253.
Norimatsu, Y., Hasegawa, K., Shimizu, N., Toyoshima, C. (2017) Protein-phospholipid interplay revealed with crystals
of a calcium pump. Nature 545:193–198.
Orwick-Rydmark, M., Arnold, T., Linke, D. (2016) The use of detergents to purify membrane proteins. Curr. Protoc.
Protein Sci. 84:4.8.1–4.8.34.
Ostermeier, C., Harrenga, A., Ermler, U., Michel, H. (1997) Structure at 2.7 Å resolution of the Paracoccus denitrificans
two-subunit cytochrome c oxidase complexed with an antibody Fv fragment. Proc. Natl. Acad. Sci. USA
94:10547–10553.
Otzen, D.E. (2015) Proteins in a brave new surfactant world. Curr. Opin. Colloid Interface Sci. 20:161–169.
Pagliano, C., Barera, S., Chimirri, F., Saracco, G., Barber, J. (2012) Comparison of the α and β isomeric forms of the
detergent n-dodecyl-D-maltoside for solubilizing photosynthetic complexes from pea thylakoid membranes. Biochim.
Biophys. Acta 1817:1506–1515.
Palczewski, K., Kumasaka, T., Hori, T., Behnke, C.A., Motoshima, H., Fox, B.A., Le Trong, I., Teller, D.C., Okada, T.,
Stenkamp, R.E., Yamamoto, M., Miyano, M. (2000) Crystal structure of rhodopsin: a G protein-coupled receptor.
Science 289:739–745.
Patargias, G., Bond, P.J., Deol, S.S., Sansom, M.S.P. (2005) Molecular dynamics simulations of GlpF in a micelle vs. in a
bilayer: Conformational dynamics of a membrane protein as a function of environment. J. Phys. Chem. B
109:575–582.
Pebay-Peyroula, E., Garavito, R.M., Rosenbusch, J.P., Zulauf, M., Timmins, P. (1995) Detergent structure in tetragonal
crystals of OmpF porin. Structure 3:1051–1059.
Penel, S., Pebay-Peyroula, E., Rosenbusch, J., Rummel, G., Schirmer, T., Timmins, P.A. (1998) Detergent binding in
trigonal crystals of OmpF porin from Escherichia coli. Biochimie 80:543–551.
Pérez-Victoria, I., Pérez-Victoria, F.J., Roldán-Vargas, S., García-Hernández, R., Carvalho, L., Castanys, S., Gamarro,
F., Morales, J.C., Pérez-Victoria, J.M. (2011) Non-reducing trisaccharide fatty acid monoesters: novel detergents in
membrane biochemistry. Biochim. Biophys. Acta 1808:717–726.
Perlmutter, J.D., Popot, J.-L., Sachs, J.N. (2014) Molecular dynamics simulations of a membrane protein/amphipol
complex. J. Membr. Biol. 247:883–895.
Perozo, E., Cortes, D.M., Cuello, L.G. (1998) Three-dimensional architecture and gating mechanism of a K
+ channel
studied by EPR spectroscopy. Nat. Struct. Biol. 5:459–469.
Pierre, Y., Breyton, C., Kramer, D., Popot, J.-L. (1995) Purification and characterization of the cytochrome b 6 f complex
from Chlamydomonas reinhardtii. J. Biol. Chem. 270:29342–29349.
Poget, S.F., Girvin, M.E. (2007) Solution NMR of membrane proteins in bilayer mimics: small is beautiful, but
sometimes bigger is better. Biochim. Biophys. Acta 1768:3098–3106.
Pomroy, N.C., Deber, C.M. (1998) Solubilization of hydrophobic peptides by reversible cysteine PEGylation. Biochem.
Biophys. Res. Commun. 245:618–621.
Popot, J.-L. (2010) Amphipols, nanodiscs, and fluorinated surfactants: Three non-conventional approaches to studying
membrane proteins in aqueous solutions. Annu. Rev. Biochem. 79:737–775.
92
2 Extracting Membrane Proteins from Their Native Environment