Selected Spin Labels and Labelling Methods

Since the development of the SDSL technique the methanethiosulfonate spin label (MTSSL, 5) is the most frequently used label in literature, especially in EPR distance measurements.

protein backbone

Scheme 3: Left: The MTSSL 5 can be attached to the protein of interest via a disulfide formation (linked side chain known as R1, 6). Right: Rotating single bonds which increase the conformational space for the spin density. Reprinted with permission from [21]. Copyright 2009 by Springer Science.

MTSSL reacts selectively with thiol groups and therefore, it can be easily attached to cysteine residues in proteins via disulfide formation (6, disulfide-linked side-chain commonly known as R1).^[5] Due to the small size and the flexible linker between the pyrroline-oxyl moiety and the protein backbone, the influence on the native fold of proteins is minimal. However, this flexibility allows rotational dynamics which opens a large conformational space and leads to a ’blurring’ of the spin density (Scheme 3, right).

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The internal dynamics and rotamers have been intensively studied and rotamer libraries have been developed for -helices and -sheets, which allow plausible distance prediction.^[22,23] Yet, e.g. in 2013, MATALON et al. published a PELDOR study on a labelled WALP23 peptide in a lipid environment that illustrates the limitations of 6.^[24] The distance distributions were broadened and did not match the calculated distribution due to the variety of possible rotamers of the label, which are furthermore influenced by the lipid environment.^[24]

In order to decrease the internal motion, MTSSL analogues have been created (Figure 3).

Figure 3: Derivatives of MTSSL. The motion of the label is restricted through substitution on the pyrroline-oxyl moiety (7) or by two-point binding (8).

It was demonstrated that the motion of the label can be restricted either by substitution, like in the case of the 4-pyridyl substituted label 7 (R1p)^[25], or by two-point binding strategies which effectively reduce the conformational freedom like in the case of label 8 (RX)^[26]. The latter was successfully applied in a membrane protein study and delivered narrow distances.^[27] However, its usage is obviously limited, since it requires two suitable proximal binding sides for each label.

The methanethiosulfonate linkage (9) is most commonly used owing to its straightforward handling but over the years different linker and labelling methods were developed. These allow orthogonal labelling strategies. Also, the aspects of increased rigidity with minimal impact on the protein’s structure and the use in cells were addressed. Several linkers are illustrated in Figure 4.

7 Figure 4: Selected structures of common nitroxide linkers. Top: 9 and 10 linkers react with thiol groups. Centre: Linkers address serine (11), tyrosine (12) and arginine (13).

Bottom: 14 and 15 linkers which give the opportunity for click reactions to introduce the spin label.

Besides the MTSSL also maleimide linked nitroxides (10) address cysteine residues within a peptide and due to the different coupling chemistry, it can be used under mild reducing conditions.^[28] However, side reactions have to be considered, like hydrolysis to the maleamic acid which in turn may react with other maleimides.^[29] Besides cysteine also amino acids like serine (11)^[30], tyrosine (12)^[31] and arginine (13)^[32] can be specifically addressed, which enables orthogonal linker chemistry.

Furthermore, KÁLAI et al. showed that nitroxide modified azides (14) and alkynes (15) can be linked to biomolecules via Cu(I) catalysed ‘click-chemistry’ and thus showed that site-selective labelling is also possible by forming triazoles.^[33] Another linking strategy exploits the specific binding to polyhistidine motifs (known as His6-tags), which are often attached to the N- or C-terminus to enable the purification of recombinant proteins. One example is the label 2,2,5,5-tetramethylpyrrolidine-1-oxyl (PROXYL) tris-nitrilotriacetic acid (P-trisNTA, 16).

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Figure 5: Structure of the P-trisNTA label (16). The label binds to a His6-tag.

It was shown by BALDAUCH et al. in 2013 that this label binds successfully to an His6 -tagged MalE in cell lysate.^[34] This may open up a new route towards the use of spin labels in living cells.

Nitroxide labels can also be introduced by unnatural amino acids via endogenous expression of specifically coded DNA.^[35] This in vivo method enables the selective labelling of cysteine rich proteins. It is possible to introduce amino acids which already bear a paramagnetic centre like 17^[36] as well as amino acids which can be modified after the insertion like the popular p-acetylphenylalanine (modified to 18, K1)^[37] or p-azidophenylalanine (modified to 19, T1)^[38,39].

Figure 6: The unnatural amino acids are introduced into the peptide via endogenous expression. In the cases of 18 and 19 the nitroxide label is attached after the expression.

The motif 19 was successfully incorporated into T4-lysozym via a copper-free click

9 cycloaddition.^[38] However, these labels contain flexible linkers and the post-modification method usually requires harsh labelling conditions.^[37]

Finally, non-native amino acids can also be introduced in peptide sequences during solid-phase peptide synthesis (SPPS). This has the advantage that no connection to a flexible linker is needed which then allows the investigation of peptide backbone conformations. So far, the most frequently used nitroxide peptide building block in this field is 2,2,6,6-tetramethyl-N-oxyl-4-amino-4-carboxylic acid (TOAC, 20)^[40] (Figure 7).

Figure 7: Structures of TOAC, -TOAC and POAC which are used as peptide building blocks in SPPS. The motion of the TOAC is restricted due to the cyclic property of the label. Reprinted with permission from [21]. Copyright 2009 by Springer Science.

TOAC belongs to the family of C,-disubstituted glycines and due to the cyclic structure, its flexibility is effectively restricted (the cyclic ring has one degree of freedom (Figure 7)). It has been applied in several studies to deliver details about dynamics^[41,42], backbone conformation^[40,41,43] and orientation^[44] of peptides. Yet, its restricted conformational space can disrupt the functional structures of peptides.^[40,45] Other labels derived from this cyclic nitroxide are -TOAC (21)^[46] and 3-amino-1-oxyl-2,2,5,5-tetramethyl pyrrolidine-4-carboxylic acid (POAC, 22)^[47].

To circumvent the impact of the restricted backbone conformation, STOLLER et al.

developed the non-natural amino acid 4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazine-1-yl)-L-phenylglycine (TOPP, Figure 8, 23).^[48]

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Figure 8: Structure of the TOPP label. The label has two rotatable single bonds on the same axis as the nitroxide radical.

The label is designed based on the amino acid phenylglycine (Phg). As hinted in Figure 8 the C‒C bond and the nitroxyl group are aligned on the same axis, since the piperazine-2,6-dione moiety is nearly planar, which was confirmed by density functional theory (DFT) calculations.^[48] A first study on a double TOPP-labelled alanine-rich peptide showed that the TOPP label 23 does not influence the secondary structure formation in solution and delivers a narrow distance distribution that confirms the calculated distance from the computationally modelled peptide (Figure 9).^[48]

Figure 9: Left: The computationally modelled alanine-rich peptide labelled with two TOPPs. The inter-spin vector was calculated as 2.7 nm. Right: The distance distribution measured by PELDOR. The predominantly measured distance was 2.8 nm. Reprinted with permission from [48]. Copyright 2011 by Wiley-VCH.

In order to utilise its rigidity, the label was also employed in an orientation-selective PELDOR study performed by TKACH and co-workers.^[49] The experimental data suggests that the label has a certain rotational freedom around the two single bonds, since a fit

11 to a libration of ±20° around the two bonds was required.^[49] Note that through one-axis librational averaging this did not alter the position of the nitroxide moiety in space, thus this has no impact on the distance and the width of distribution. Hence, the TOPP is a promising candidate for further applications in the field of structural investigations of e.g. transmembrane peptides and it is a suitable spin label motif that allows a variety of modifications to further enhance its abilities.

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