Abstract
Size exclusion chromatography coupled online to a Tetra Detector Array in combination with analytical ultracentrifugation (or with quasi-elastic light scattering) is a useful methodology to characterize hydrodynamic properties of macromolecules, including intrinsically disordered proteins. The time-averaged apparent hydration and the shape factor of proteins can be estimated from the measured parameters (molecular mass, intrinsic viscosity, hydrodynamic radius) by these techniques. Here we describe in detail this methodology and its application to characterize hydrodynamic and conformational changes in proteins.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Abbreviations
- M :
-
Molecular mass, g/mol
- T :
-
Absolute temperature, K
- C :
-
Protein concentration, mol/L (M)
- \( {\hbox{d}}n/{\hbox{d}}c \) :
-
Refractive index increment, mL/g
- \( {\hbox{d}}A/{\hbox{d}}c \) :
-
Absorbance increment, L/g cm
- \( \left[ \eta \right] \) :
-
Intrinsic viscosity, mL/g
- \( \nu \) :
-
Hydrodynamic shape function, viscosity increment, Simha–Saito shape factor, unitless
- \( \delta \) :
-
Time-averaged apparent hydration, \( {{\hbox{g}}_{{{{\rm{H}}_{{2}}}{\rm{O}}}}}/{\hbox{g}}_{\rm{protein}} \)
- \( {{f} \left/ {{{f_0}}} \right.} \) :
-
Translational frictional ratio of the protein, including shape and hydration parameters
- \( f \) :
-
Frictional coefficient of the protein, g/s
- \( {f_0} \) :
-
Frictional coefficient of an anhydrous sphere of the mass of the protein, g/s
- R H :
-
Hydrodynamic radius of the protein, cm
- R 0 :
-
Radius of an anhydrous sphere of the mass of the protein, cm
- V H :
-
Hydrodynamic volume calculated from the R H, cm3
- D t :
-
Translational diffusion coefficient, cm2/s
- s :
-
Sedimentation coefficient obtained at the temperature of the experiment, Svedberg, 10−13s
- \( \eta \) :
-
Viscosity of the solvent, Poise: g/cm s
- \( \rho \) :
-
Density of the solvent, g/mL
- k B :
-
Boltzmann’s constant, erg/K (K B: 1.38065 × 10−16 erg/K, with erg: g cm2/s2 = 10−7 J 1.38065 × 10−23 J/K)
- N A :
-
Avogadro’s number, molecules/mol
- \( \bar{\nu } \) :
-
Partial specific volume, mL/g
- \( a/b \) :
-
Axial ratio of ellipsoid
- RALS :
-
Right Angle Light-Scattering
- LALS :
-
Low Angle Light-Scattering
- IP :
-
Internal Pressure
- DP :
-
Differential Pressure
- UV :
-
Ultraviolet absorption
- RI:
-
Refractive Index
References
Chenal A, Guijarro JI, Raynal B, Delepierre M, Ladant D (2009) RTX calcium binding motifs are intrinsically disordered in the absence of calcium: implication for protein secretion. J Biol Chem 284:1781–1789
Sotomayor Perez AC, Karst JC, Davi M, Guijarro JI, Ladant D, Chenal A (2010) Characterization of the regions involved in the calcium-induced folding of the intrinsically disordered RTX motifs from the bordetella pertussis adenylate cyclase toxin. J Mol Biol 397:534–549
Sotomayor-Pérez AC, Ladant D, Chenal A (2011) Calcium-induced folding of intrinsically disordered repeat-in-toxin (RTX) motifs via changes of protein charges and oligomerization states. J Biol Chem 286:16997–17004.
Chenal A, Vendrely C, Vitrac H, Karst JC, Gonneaud A, Blanchet CE, Pichard S, Garcia E, Salin B, Catty P, Gillet D, Hussy N, Marquette C, Almunia C, Forge V (2011) Amyloid fibrils formed by the programmed cell death regulator Bcl-xL. J Mol Biol 415:584–599.
Chenal A, Vendrely C, Vitrac H, Karst JC, Gonneaud A, Blanchet CE, Pichard S, Garcia E, Salin B, Catty P, Gilltet D, Hussy N, Marquette C, Almunia C, Gorge V (2011) Amyloid fibrils formed by the programmed cell death regulator Bcl-xL. J Mol Biol 415:584–599
Bourdeau RW, Malito E, Chenal A, Bishop BL, Musch MW, Villereal ML, Chang EB, Mosser EM, Rest RF, Tang WJ (2009) Cellular functions and X-ray structure of anthrolysin O, a cholesterol-dependent cytolysin secreted by Bacillus anthracis. J Biol Chem 284:14645–14656
Simha R (1940) The influence of Brownian movement on the viscosity of solutions. J Phys Chem 44:25–34
Harding SE (1997) The intrinsic viscosity of biological macromolecules. Progress in measurement, interpretation and application to structure in dilute solution. Prog Biophys Mol Biol 68:207–262
Harding SE, Colfen H (1995) Inversion formulae for ellipsoid of revolution macromolecular shape functions. Anal Biochem 228:131–142
Harding SE, Horton JC, Colfen H (1997) The ELLIPS suite of macromolecular conformation algorithms. Eur Biophys J 25:347–359
Perrin F (1936) Mouvement brownien d’un ellipsoïde (II). Rotation libre et dépolarisation des fluorescences. Translation et diffusion de molécules ellipsoïdales. J Phys Rad 7:1–11
Squire PG, Himmel ME (1979) Hydrodynamics and protein hydration. Arch Biochem Biophys 196:165–177
Chenal A, Karst JC, Perez AC, Wozniak AK, Baron B, England P, Ladant D (2010) Calcium-induced folding and stabilization of the intrinsically disordered RTX domain of the CyaA toxin. Biophys J 99:3744–3753
Acknowledgements
This work was supported by the Institut Pasteur (Grant PTR374), the Centre National de la Recherche Scientifique (CNRS UMR 3528), and the Agence Nationale de la Recherche, programme Jeunes Chercheurs (ANR, grant ANR-09-JCJC-0012).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media New York
About this protocol
Cite this protocol
Karst, J.C., Sotomayor-Pérez, A.C., Ladant, D., Chenal, A. (2012). Estimation of Intrinsically Disordered Protein Shape and Time-Averaged Apparent Hydration in Native Conditions by a Combination of Hydrodynamic Methods. In: Uversky, V., Dunker, A. (eds) Intrinsically Disordered Protein Analysis. Methods in Molecular Biology, vol 896. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-3704-8_10
Download citation
DOI: https://doi.org/10.1007/978-1-4614-3704-8_10
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4614-3703-1
Online ISBN: 978-1-4614-3704-8
eBook Packages: Springer Protocols