Protecting role of cosolvents in protein denaturation by SDS: a structural study
© Michaux et al; licensee BioMed Central Ltd. 2008
Received: 17 March 2008
Accepted: 03 June 2008
Published: 03 June 2008
Recently, we reported a unique approach to preserve the activity of some proteins in the presence of the denaturing agent, Sodium Dodecyl Sulfate (SDS). This was made possible by addition of the amphipathic solvent 2,4-Methyl-2-PentaneDiol (MPD), used as protecting but also as refolding agent for these proteins. Although the persistence of the protein activity in the SDS/MPD mixture was clearly established, preservation of their structure was only speculative until now.
In this paper, a detailed X-ray study addresses the pending question. Crystals of hen egg-white lysozyme were grown for the first time in the presence of MPD and denaturing concentrations of SDS. Depending on crystallization conditions, tetragonal crystals in complex with either SDS or MPD were collected. The conformation of both structures was very similar to the native lysozyme and the obtained complexes of SDS-lysozyme and MPD-lysozyme give some insights in the interplay of protein-SDS and protein-MPD interactions.
This study clearly established the preservation of the enzyme structure in a SDS/MPD mixture. It is hypothesized that high concentrations of MPD would change the properties of SDS and lower or avoid interactions between the denaturant and the protein. These structural data therefore support the hypothesis that MPD avoids disruption of the enzyme structure by SDS and can protect proteins from SDS denaturation.
Sodium dodecyl sulfate (SDS) is a highly effective and widely used protein denaturant [1, 2]. Our previous work has shown that amphipathic solvents, like 2-methyl-2,4-pentanediol (MPD), a commonly used precipitant for crystallization studies , can protect proteins from SDS denaturation, and in several cases can drive the transition from the SDS-denatured state to a functional folded state . This protecting effect of MPD is observed with a wide range of proteins including membrane proteins and soluble enzymes, and is not applicable if proteins are denatured in guanidine or urea, two other denaturant agents. In the case of hen egg-white lysozyme, SDS concentrations above 1.0 mM abolished the activity of the enzyme in the absence of MPD. However, in 2 M MPD, the activity was preserved in the presence of SDS. In addition, when the enzyme was first denatured with SDS for 24 hours prior to adding MPD, full enzymatic activity was recovered in 2 M MPD following a further 24 hour incubation period. Although the persistence of the enzyme activity in the SDS/MPD mixture was clearly established, preservation of its structure was only speculative until now.
In the present contribution, a detailed X-ray study addresses the pending question. Crystals of hen egg-white lysozyme could be grown for the first time in a SDS/MPD medium, providing support that adding MPD to proteins can avoid SDS denaturation. The obtained complexes of SDS-lysozyme and MPD-lysozyme give some insights in the interplay of protein-SDS and protein-MPD interactions. A previous report described the structure of cross-linked lysozyme crystals soaked in SDS solutions . In the latter, unlike both structures described in this paper, SDS was found at three different locations inside the protein inducing a major structural deformation in the interior of lysozyme.
Results and discussion
Statistics of data collection and structure refinement
Expected MPD concentration in the drop after equilibration
close to 0 M
Expected SDS concentration in the protein droplet
Unit-cell parameters (Ǻ)
a = b = 77.59, c = 37.57
a = b = 77.90, c = 37.53
Maximum resolution (Ǻ)
R merge (%)
R (%) a
R free (%) a
RMSD bond lengths (Ǻ)
RMSD angle distances (Ǻ) RMSD bond angles (°)
Average B value (Ǻ 2 )
Most favored, additional, generously allowed (%)
No. of MPD molecules
No. of SDS molecules
No. of Na ion
No. of Cl ion
No. of water molecules
The presence of high concentration of MPD can therefore avoid disruption of the structure of the enzyme by SDS. Indeed, as shown by Yonath , SDS, by binding deeply into the hydrophobic core of the protein, induces separation of the two wings of lysozyme. In addition, the form I crystal, where few MPD is expected to remain in the drop, shows that MPD was able to induce irreversibly the correct folding of lysozyme in the presence of a denaturing concentration of SDS (2 mM).
Interaction of SDS or MPD with lysozyme
The S configuration of both MPD molecules is quite clear by lowering the contour level to around 0.6 but at this stage, it is impossible to deduce that S-MPD is more stabilizing than the R one.
A comparison of the above structure with the one of lysozyme crystallized in the presence of MPD, without SDS, (PDB code 1DPW, 1.64 Ǻ)  yields RMSD of 0.14 Ǻ for the superposition of Cα atoms. The location of the second MPD molecule in the present study matches the one previously described, except the configuration which is switched. The water molecule between MPD and Arg114 is also conserved. Moreover, two chloride ions were identified in the same binding site as in the 1DPW structure. Additionally, a sodium ion was observed ligated to the main chain carbonyl oxygen's of residues Ser60, Cys64, Arg73, Oγ of Ser72 side chain, and two water molecules. This sodium ion binding site was present in the enzyme in the presence of low concentration of DMSO and guanidinium chloride .
This study, where crystals of lysozyme were grown for the first time in the presence of the amphipathic solvent MPD and denaturing concentrations of SDS, clearly established the preservation of the enzyme structure in a SDS/MPD mixture. It is hypothesized that high concentrations of MPD, changing the properties of SDS, would lower (condition I) or avoid (condition II) interactions between SDS and the protein. Indeed, in the form II crystal, even though it contains higher SDS concentration, but also higher MPD concentration, than in the form I, no SDS molecule was observed. This assumption is in agreement with the size-exclusion chromatography study described earlier , demonstrating that the protein no longer interacts strongly with SDS in a MPD buffer system. These structural data therefore support the hypothesis that MPD can protect proteins from SDS denaturation.
In addition, it is worth noting that this contribution shows one of the very few structures of proteins, in its native form, co-crystallized with SDS.
Lyophilized hen egg-white lysozyme, obtained from Sigma, was solubilized in 4 mM SDS, 50 mM Tris pH8, 150 mM NaCl and 2 M MPD (racemic form) (around 10 mg/ml protein). Crystals were grown at room temperature by the hanging drop vapor diffusion method using two different conditions. First 4 μl of the protein solution was mixed with 4 μl of a MPD-free reservoir solution containing 100 mM sodium acetate buffer pH 4.6 and 2 M sodium formate (condition I), and equilibrated with 1 mL of reservoir solution. In the second condition, the reservoir solution consists of 50 mM Tris pH8, 70% (~4.6 M) MPD (racemic form) and 6 mM SDS (condition II).
Data collection, processing and refinement
Crystals harvested directly from mother liquor were flash-frozen in a 100 K nitrogen stream with no added cryoprotectant. Diffraction data of the form I crystals were collected using a Bruker MICROSTAR generator with a Bruker Proteum X8 CCD X-ray detector. The crystal-to-detector distance was 60 mm; 180 images (0.5° as oscillation range/image) with a 120 sec exposure time per image were collected; SAINT-Plus/Proteum was used to process the data.
For the form II crystals, a Gemini Ultra R system (4-circle kappa platform, Ultra Enhanced Cu Source, Ruby CCD detector) was used. The crystal-to-detector distance was 50 mm; 180 images with a 90 sec exposure time per image were collected; CrysAlis CCD and CrysAlis RED were used to process the data.
A molecular replacement solution was found using Phaser  with the molecular model of the native lysozyme (PDB entry 1Z55). Refinement was performed either with the Shelxl97 (Form II)  or Refmac5 (Form I) program . Electron density maps were inspected with the graphic program Xtalview (Form II)  or Coot (Form I) , and the quality of the model was analyzed with the program Procheck . The atomic coordinates and structure factors have been deposited in the Protein Data Bank (3B6L and 3B72).
CM is grateful to FNRS for financial support. This work was funded in part by a CIHR grand to GGP.
- Gimel JC, Brown W: A light-scattering investigation of the sodium dodecyl sulfate-lysozyme system. J Chem Phys 1996, 104: 8112–8117. 10.1063/1.471496View Article
- Otzen DE: Protein unfolding in detergents: effect of micelle structure, ionic strength, pH, and temperature. Biophys J 2002, 83: 2219–2230.View Article
- Anand K, Pal D, Hilgenfeld R: An overview on 2-methyl-2,4-pentanediol in crystallization and in crystals of biological macromolecules. Acta Cryst D 2002, 58: 1722–1728. 10.1107/S0907444902014610View Article
- Michaux C, Pomroy N, Privé GG: Refolding SDS-denatured proteins by the addition of amphipathic cosolvents. J Mol Biol 2008, 375: 1477–1488. 10.1016/j.jmb.2007.11.026View Article
- Yonath A, Podjarny A, Honig B, Sielecki A, Traub W: Crystallographic studies of protein denaturation and renaturation. 2. Sodium dodecyl sulfate induced structural changes in triclinic lysozyme. Biochemistry 1977, 16: 1418–1424. 10.1021/bi00626a028View Article
- Weiss MS, Palm GJ, Hilgenfeld R: Crystallization, structure solution and refinement of hen egg-white lysozyme at pH 8.0 in the presence of MPD. Acta Cryst D 2000, 56: 952–958. 10.1107/S0907444900006685View Article
- Deshpande A, Nimsadkar S, Mande SC: Effect of alcohols on protein hydration: crystallographic analysis of hen egg-white lysozyme in the presence of alcohols. Acta Cryst D 2005, 61: 1005–1008. 10.1107/S0907444905009364View Article
- Mande SC, Sobhia ME: Structural characterization of protein-denaturant interactions: crystal structures of hen egg-white lysozyme in complex with DMSO and guanidinium chloride. Protein Eng 2000, 13: 133–141. 10.1093/protein/13.2.133View Article
- Pike AC, Acharya KR: A structural basis for the interaction of urea with lysozyme. Protein Sci 1994, 3: 706–710.View Article
- Salem M, Mauguen Y, Prangé T: On the edge of the denaturation process: application of X-ray diffraction to barnase and lysozyme cross-linked crystals with denaturants in molar concentrations. Biochim Biophys Acta 2006, 1764: 903–912.View Article
- Storoni LC, McCoy AJ, Read RJ: Likelihood-enhanced fast rotation functions. Acta Cryst D 2004, 60: 432–438. 10.1107/S0907444903028956View Article
- Sheldrick GM, Schneider TR: SHELXL: High-resolution refinement. In Methods in Enzymol. Volume 277. Elsevier, San Diego, CA, Etats-Unis; 1997:319–343. Sheldrick GM: SHELXS97 and SHELXL97. Université de Göttingen, Allemagne 1997
- Murshudov GN, Vagin AA, Dodson EJ: Refinement of Macromolecular Structures by the Maximum-Likelihood Method. Acta Cryst 1997, D53: 240–255.
- McRee DE: XtalView/Xfit – A Versatile Program for Manipulating Atomic Coordinates and Electron Density. J Struct Biol 1999, 125: 156–165. 10.1006/jsbi.1999.4094View Article
- Emsley P, Cowtan K: Coot: model-building tools for molecular graphics. Acta Cryst 2004, D60: 2126–2132.
- Laskowski RA, MacArthur MW, Moss DS, Thornton JM: PROCHECK: a program to check the stereochemical quality of protein structures. J App Cryst 1993, 26: 283–291. 10.1107/S0021889892009944View Article
- DeLano WL: The PyMOL Molecular Graphics System.DeLano Scientific, San Carlos, CA, USA; 2002. [http://www.pymol.org]
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.