Hannah S.
Leese‡
a,
Lata
Govada‡
b,
Emmanuel
Saridakis
c,
Sahir
Khurshid
b,
Robert
Menzel§
a,
Takuya
Morishita
ad,
Adam J.
Clancy
a,
Edward. R.
White
a,
Naomi E.
Chayen
*b and
Milo S. P.
Shaffer
*a
aDepartment of Chemistry, Imperial College London, London SW7 2AZ, UK. E-mail: m.shaffer@imperial.ac.uk
bComputational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK. E-mail: n.chayen@imperial.ac.uk
cLaboratory of Structural and Supramolecular Chemistry, Institute of Nanoscience and Nanotechnology, National Centre for Scientific Research ‘Demokritos’, Athens, Greece
dToyota Central R&D Labs., Inc., Nagakute, Aichi 480-1192, Japan
First published on 29th January 2016
A range of carbon nanomaterials, with varying dimensionality, were dispersed by a non-damaging and versatile chemical reduction route, and subsequently grafted by reaction with methoxy polyethylene glycol (mPEG) monobromides. The use of carbon nanomaterials with different geometries provides both a systematic comparison of surface modification chemistry and the opportunity to study factors affecting specific applications. Multi-walled carbon nanotubes, single-walled carbon nanotubes, graphite nanoplatelets, exfoliated few layer graphite and carbon black were functionalized with mPEG-Br, yielding grafting ratios relative to the nanocarbon framework between ca. 7 and 135 wt%; the products were characterised by Raman spectroscopy, TGA-MS, and electron microscopy. The functionalized materials were tested as nucleants by subjecting them to rigorous protein crystallization studies. Sparsely functionalized flat sheet geometries proved exceptionally effective at inducing crystallization of six proteins. This new class of nucleant, based on PEG grafted graphene-related materials, can be widely applied to promote the growth of 3D crystals suitable for X-ray crystallography. The association of the protein ferritin with functionalized exfoliated few layer graphite was directly visualized by transmission electron microscopy, illustrating the formation of ordered clusters of protein molecules critical to successful nucleation.
The availability of three dimensional protein crystals is a fundamental bottleneck limiting structure determination of target proteins relevant to future drug design. Well-designed nucleants (protein crystal nucleation-inducing substrates) aid the crystallization of new target proteins and potentially provide a deeper understanding of different protein crystallization mechanisms.31,32 It may not be the case that one nucleant fits all, but the versatility of carbon nanomaterial chemistry provides an exciting platform to crystallize a variety of proteins. Two previous works have considered using carbon nanomaterials as additives or nucleants for three dimensional protein crystallization: one used gelatine-coated CNT buckypapers33 and the other colloidal graphenes;34 however, there has not been a controlled and systematic study which correlates CNM chemistry and geometry with nucleation. TEM imaging studies have observed protein adsorption, ordering and/or 2D crystallization on unfunctionalized MWNTs35,36 but have not grown 3D crystals for X-ray crystallography. General nucleation studies, which have provided theoretical models for heterogeneous nucleation mechanisms, conclude that geometry and pore size are two important driving forces.32,37,38 A broad pore size distribution is favourable for nucleating different proteins, due to significant variations in protein size and their critical nuclei. Theoretical models have shown that pores may confine and stabilise protein molecules and in-turn encourage crystalline nuclei to form and grow.34,37 Functionalized CNMs are, therefore, interesting substrates for protein nucleation due to their high accessible surface areas and ability to form networks, heterogeneous in both topography and chemistry, providing a broad distribution of ‘pockets’ in which proteins may accumulate. Chemical modification enhances compatibility and solubility with (usually aqueous) protein conditions. Although this study focuses on one family of chemical functionality (polyethylene glycol), it is possible to graft a variety of functionalities, providing a versatile methodology to adjust geometry and chemistry for crystallizing proteins.
The aim is to design nucleants which encourage protein nucleation deep into metastable supersaturated solutions (promoting single crystal growth) and at low protein concentrations. This study uses reduction chemistry to graft methoxy poly(ethylene glycol) (mPEG) on an array of carbon nanomaterials. mPEG was selected following preliminary trials and its particular effectiveness in grafted form is intriguing since free PEGs are already used in many protein crystallization conditions. PEG-modified CNMs, especially CNTs, are also of interest for biological applications, such as drug delivery39,40 and biosensing,41,42 but have generally been prepared via either non-covalent methods43 or coupling to acid-oxidized materials.44,45 This study provides an exploration of reductive chemistry to graft mPEGs to a variety of CNMs, specifically including multi-walled carbon nanotubes (MWNTs), single-walled carbon nanotubes (SWNTs), exfoliated few layer graphite (FLG), graphite nanoplatelets (GNPs) and carbon black (CB), providing a panel of materials to assess systematically the effect of geometry on both reductive functionalization and protein crystallization. These materials provide a full range of dimensionality FLG (2D), SWNT (1D, high curvature), MWNT (1D, low curvature), and CB (0D), with broadly similar chemistry.
Thermogravimetric analysis (TGA) under nitrogen (Fig. 1) indicates successful grafting of mPEG and was used to determine the polymer grafting ratio (wt% of grafted organics relative to initial carbon framework, Table 1) from the mass loss attributable to the decomposition of grafted mPEG (see Fig. S1a†). The functionalized MWNT, SWNT and GNP samples all display one significant weight loss between 450–550 °C; control experiments, examining samples treated equivalently using unreactive poly(ethylene glycol) dimethyl ether, showed no significant mass loss after washing, and were used as a baseline for calculating grafting ratio. Mass spectrometry showed that the mass loss in grafted samples correlates with units observed in PEG decomposition, including the monomer (m/z = 44 –C2H2O+), methyl (m/z = 15 –CH3+) and methoxy groups (m/z = 31 –OCH3+), although for the MWNTs, the weakest m/z = 15 feature was not observed due to the low grafting ratio. The peak degradation temperature was significantly higher (ca. 70 °C) for the grafted materials than the pure mPEG 5 kDa-Br reference (ESI Fig. S1b† for TGA-MS of pure mPEG control), for which the decomposition was completed by 450 °C; such shifts are often attributed to covalent grafting,56 or at least an intimate interaction at the interface. Similar grafted PEG decomposition features were observed for both FLG and carbon black samples; however, additional features also appeared. For FLG-mPEG, there is a clear initial step at 220–250 °C, attributed to a combination of residual polymer and THF trapped within graphene layers, as confirmed by TGA-MS data (Fig. S2†). In this case, the control sample, (Fig. 1b) shows a similar first step but a very much reduced second step; the grafting ratio was therefore calculated from the relative increase in the second step (450–600 °C). The weight loss temperature for FLG-mPEG was slightly higher than for the other nanocarbons, most likely due to the constraint of the grafted polymer trapped between layers. In the carbon black sample, there is a broader decomposition feature with an early onset around 250 °C (in this case, TGA-MS shows no significant residual solvent). Although the control sample shows no physisorption of the unreactive polymer, the relatively large and broad weight loss in CB-mPEG may include some physisorbed polymer trapped by the grafted polymer chains. High structure carbon black has a large number of primary nanoparticles fused within each aggregate (TEM in Fig. 1e), generating a highly convoluted internal pore volume.
Fig. 1 TGA-MS characterization of washed samples and controls (addition of unreactive poly(ethylene glycol) dimethyl ether), Raman mapping histograms (counts of region with given D/G) and TEM images of mPEG grafted (a) MWNTs, (b) SWNTs, (c) FLG (including before and after heating control in TGA), (d) GNPs and (e) carbon black. m/z = 15 –CH3+, m/z = 44 –CH2CH2O+ and m/z = 31 –OCH3+ are fragments of mPEG (see TGA-MS of pure mPEG and Raman spectra in ESI†). |
Nucleant material | r CNM (nm) | Grafting ratio (wt% of PEG) | Grafted stoichiometry (C:PEG) | Dispersibility (μg ml−1) | Dry surface areab (m2 g−1) | Surface concentration of grafted PEG (μmol m−2) | PEG separation, D (nm) |
---|---|---|---|---|---|---|---|
a Average CNM primary radius/local radius of curvature. b Specific surface area measured by BET. c Small value due to restacking sheets on drying. d Estimated using surface area of GNP to approximate a realistic surface area in solution. | |||||||
MWNT-mPEG | 5.0 ± 1.2 | 6.8 ± 1.5 | 6094 | 68 ± 5 | 180 | 0.076 | 5.3 |
SWNT-mPEG | 0.8 ± 0.4 | 12.6 ± 1.1 | 3303 | 51 ± 5 | 670 | 0.038 | 7.5 |
FLG-mPEG | n/a | 10.6 ± 3.2 | 3924 | 35 ± 5 | 10c | 0.031d | 8.2 |
GNP-mPEG | n/a | 11.0 ± 2.2 | 3792 | 200 ± 5 | 680 | 0.032 | 8.1 |
CB-mPEG | 6.5 ± 1.1 | 135.3 ± 6.1 | 308 | 100 ± 5 | 220 | 1.230 | 1.3 |
Polymer grafting ratio (wt%) can be converted into an estimate of the number of structural nanoparticle carbons per mPEG chain (C:PEG ratio, ‘grafted stoichiometry’, Table 1). MWNT-mPEG has the lowest grafting ratio and therefore highest grafted stoichiometry compared to other nanocarbons, in part, as it has the lowest specific surface area of the materials studied (∼180 m2 g−1); conversely, SWNT-mPEG has a higher proportion of grafted polymer than MWNTs most likely due to the larger accessible surface area of SWNTs (670 m2 g−1). GNPs have a slightly higher specific surface area and exhibit a similar degree of functionalization when compared to SWNTs, whereas CB has a similar specific surface area to functionalized MWNTs but shows a much higher apparent degree of functionalization. The surface concentration of grafted polymer was estimated by relating PEG concentration to CNM specific surface area (Table 1). Generally, the materials have a similar density of functionalization on their exposed surfaces, except for CB-mPEG, which is significantly greater, due either to its convoluted geometry or higher defect density.
Although the details are complex, Raman spectroscopy is widely used to provide a semi-quantitative indication of crystallinity and subsequent degree of functionalization by comparing the relative intensity (D/G) of the defect band (D-band) at ∼1350 cm−1 and the graphite band (G-band) at ∼1580 cm−1. Raman mapping provides a reliable means to assess the degree of functionalization, using the D/G ratio,57,58 including in heterogeneous materials, since it is possible to analyze thousands of independent spectra to obtain an overall statistical change before and after grafting. The Raman data generally confirms the covalent functionalization of the carbon nanomaterials through an increase in D/G ratio (Fig. 1a–e) which is known to correlate with disruption of the conjugated framework.59,60 For CB, the D/G ratio is either unchanged or slightly decreased on functionalization, as expected for extremely defective graphitic materials,57,61 for which the sensitivity is lost or even inverted.62 The much lower perfection for CB compared to the MWNTs is indicated by much broader and weaker Raman peaks (average Raman spectra in ESI Fig. S3†). On the other hand, average Raman spectra of FLG-mPEG generally showed a broad, shifted 2D band, with a shape consistent with the formation of functionalized bi/tri-layer graphene.63,64 In addition, single point Raman spectra of graphene layers were detected (Fig. S3†), containing a symmetrical Lorentzian 2D band of high intensity and relatively narrow band width (FWHM 55 cm−1); functionalized FLG layers were also observed by AFM with average flake size 1–3 μm and 1–5 nm height (see ESI, Fig. S4†). TEM observations (Fig. 1a–e) highlight the variation in geometry of the different grafted materials, and the different modes of agglomeration in the dried forms, as discussed in more detail below.
The dispersibility of each (functionalized) nanocarbon was measured by UV-Vis absorbance after sonicating in water for 10–15 minutes and centrifugation at 1000–5000g (see Fig. S5† for an example of FLG-mPEG in water). All materials showed improved dispersibility post-functionalization (Table 1), as expected with grafted mPEG chains. In some cases, particularly the as-received GNPs, the solubility in water was already significant (value 200 μg ml−1 with initial loading 1 mg ml−1), most likely due to oxidation during the commercial exfoliation process. Despite the mPEG functionalization, which improves water compatibility, the relatively low grafting ratio and amphiphilic character of the products lead to slow sedimentation over a period of 24–72 h at a rate of ∼6.5 μg ml−1 per day, (∼6% per day) as monitored by UV-Vis.
Two liquid nucleants, FLG-mPEG and GNP-mPEG induced crystallization of thaumatin, lysozyme and trypsin at lower protein concentrations, within 48 h, compared to either no crystals or appearance only after 72 h with other nucleants (as summarized in Table 2). In comparison, all control drops (no nucleant present) were clear at these conditions. Trypsin (which is more difficult to crystallize at lower protein concentrations than lysozyme and thaumatin) did not crystallize in droplets containing functionalized MWNT, SWNT or CB nucleants. Crystallization trials with the raw carbon nanomaterials were also conducted and did not yield good crystallization results. As-received MWNTs and SWNTs crystallized lysozyme, whereas graphite crystallized thaumatin. However, the proteins only crystallized at higher protein and crystallization condition concentrations when compared to the functionalized materials. The proteins did not crystallize with as-received CB and GNP. To ensure reproducibility, FLG-mPEG and GNP-mPEG were synthesized independently five times (see Fig. S6†) and each time the product successfully and consistently crystallized proteins. In addition, the crystallization experiments were conducted over several weeks and repeated several times. In order to also test whether the amount of mPEG grafted surface was more significant than geometry, another crystallization trial was conducted, for which the PEGylated nucleant loading was adjusted to maintain a constant concentration of grafted PEG; FLG-mPEG continued to be the most effective nucleant (Fig. 2, additional crystal images are provided in Fig. S7†). In summary, compared to alternatives with similar surface chemistry, grafting density, and surface area, the flat graphene-related geometries, FLG-mPEG and GNP-mPEG, proved to be the most effective as protein nucleants.
Nucleant | Crystal appearance time | ||
---|---|---|---|
Lysozyme | Thaumatin | Trypsin | |
MWNT-mPEG | x | x | x |
SWNT-mPEG | 72 h | 72 h | x |
GNP-mPEG | 48 h | 48 h | 48 h |
FLG-mPEG | 48 h | 48 h | 48 h |
CB-mPEG | x | x | x |
Fig. 2 Polarized optical microscopy of 30 mg ml−1 trypsin drops: (a and c) containing mPEG functionalized nanocarbons: FLG, SWNTs, MWNTs, GNPs and CB (b) the circled single crystal formed within 24 h is surrounded by the FLG-mPEG flakes (d) highlights the clear control after 72 h at this protein concentration and crystallization condition. The smaller, black features are agglomerates of functionalized CNMs. Other examples of protein crystals are available in Fig. S7.† |
To investigate the potency of the flat graphene-related nucleants further, three more proteins: hemoglobin, catalase and RoAb13 were tested (full conditions in Table S2†). Hemoglobin and RoAb13 produced single crystals with FLG-mPEG. Interestingly, catalase only crystallized with FLG-mPEG, and no other nucleants tested in this study including GNP-mPEG. In the case of catalase, to the authors' knowledge, FLG-mPEG is the only nucleant to date that has induced crystal formation at metastable conditions. Most proteins, such as thaumatin, lysozyme and trypsin form crystals from solution whilst catalase first forms a precipitate from which crystals are grown. The success of FLG-mPEG with catalase as well as with the other proteins indicates that this material may have the potential to become a more universal nucleant for protein crystallization.
The study has specifically shown that PEGylated CNMs can act as effective nucleants for three dimensional protein crystals, when compared to both as-received CNMs and mPEG homopolymer, as well as other commercial nucleants; however the 2D-platelet systems, FLG and GNP functionalized with mPEG, were most successful, consistently producing single crystals for a range of proteins (both models and targets). These types of crystals are suitable for structural determination by X-ray diffraction. TEM investigations of ferritin on FLG-mPEG strongly indicate that the proteins nucleate from both stacked/folded edges and in domains on the basal plane surface; the combination of a large flat surface area, with heterogeneous surface chemistry and topography seems to be especially effective. Direct visualization of the early stages of protein nucleation on these electron transparent nucleants offers exciting opportunities for further fundamental studies. Surface functionalization not only enables the nucleation but stabilises CNM dispersions in water. Compared with existing protein nucleation methods such as seeding, the ability to readily disperse and dispense the nucleants in liquid phase, in order to reproducibly crystallize proteins at low concentrations, is very attractive. It is particularly useful for target protein trials as usually only a very small amount of purified protein is available. In principle, the density and size of the grafted domains may be used to adjust nucleant behaviour, especially as polymer radius of gyration appears to be a key factor in controlling grafting density. The CNM chemistry developed over the past decade, now offers many opportunities for the development of new materials for use in future protein crystallization studies, where more hydrophobic or specific interactions are critical, for example, with membrane proteins, which are notoriously difficult to crystallize.
Footnotes |
† Electronic supplementary information (ESI) available: Experimental details, characterization and example calculations. See DOI: 10.1039/c5sc03595c |
‡ Contributed equally. |
§ School of Chemistry, University of Leeds, LS2 9JT, UK. |
This journal is © The Royal Society of Chemistry 2016 |