- Research article
- Open Access
Search for allosteric disulfide bonds in NMR structures
BMC Structural Biologyvolume 7, Article number: 49 (2007)
Allosteric disulfide bonds regulate protein function when they break and/or form. They typically have a -RHStaple configuration, which is defined by the sign of the five chi angles that make up the disulfide bond.
All disulfides in NMR and X-ray protein structures as well as in refined structure datasets were compared and contrasted for configuration and strain energy.
The mean dihedral strain energy of 55,005 NMR structure disulfides was twice that of 42,690 X-ray structure disulfides. Moreover, the energies of all twenty types of disulfide bond was higher in NMR structures than X-ray structures, where there was an exponential decrease in the mean strain energy as the incidence of the disulfide type increased. Evaluation of protein structures for which there are X-ray and NMR models shows that the same disulfide bond can exist in different configurations in different models. A disulfide bond configuration that is rare in X-ray structures is the -LHStaple. In NMR structures, this disulfide is characterised by a particularly high potential energy and very short α-carbon distance. The HIV envelope glycoprotein gp120, for example, is regulated by thiol/disulfide exchange and contains allosteric -RHStaple bonds that can exist in the -LHStaple configuration. It is an open question which form of the disulfide is the functional configuration.
It appears that introduction of disulfide bonds into proteins is an important mechanism by which they have evolved and are evolving [1–3]. A recent analysis of the trend in amino gain and loss in protein evolution showed that Cys have accrued in all 15 taxa studied . In fact, Cys was the most frequently acquired amino acid in 8 of the 15 taxa. Considering that disulfide bonds will only form between optimally placed Cys in the tertiary structure, it follows that these bonds are a relatively recent addition to proteins.
Most protein disulfide bonds are motifs that stabilise the tertiary and quaternary protein structure. These bonds are also thought to assist protein folding by decreasing the entropy of the unfolded form . A minor population of disulfide bonds serve a functional role. There are two types of functional disulfides; the catalytic and allosteric bonds.
The catalytic bonds are typically at the active sites of enzymes that mediate thiol/disulfide exchange in other proteins. These enzymes are the oxidoreductases [5, 6]. The allosteric bonds, in contrast, control the function of the protein in which they reside by mediating a change when they break and/or form [7, 8]. The type of change depends on the protein. It may be conformational as described for the HIV receptor, CD4 [9, 10], or the resulting unpaired thiols of the cleaved allosteric bond may act as sites of alkylation by thiol modifiers as described for the blood clotting initiator, tissue factor [11, 12]. The actions of the two functional disulfides are linked in that the redox state of the known allosteric disulfides are controlled by catalytic disulfides [9, 12, 13]. In an attempt to identify a common structural motif for allosteric disulfides the geometry and strain of 6,874 unique disulfide bonds in X-ray structures was recently examined .
A disulfide bond is made up of six atoms linking the two α-carbon atoms of the cysteine residues; Cα-Cβ-Sγ-Sγ'-Cβ'-Cα'. These six atoms define five chi angles, which are the rotation about the bonds linking the atoms. Each chi angle can be either positive or negative, which equates to 20 possible disulfide bond configurations. The three basic types of disulfide are the spirals, hooks or staples and depending on the sign of the χ3 angle they are either right- or left-handed . We expanded these standard definitions to reflect the sign of the χ1 and χ1' torsional angles . For instance, a disulfide is a minus right handed spiral (-RHSpiral) if the χ1 χ2 χ3 χ2' and χ1' angles are -, +, +, + and -, respectively. The disulfides are treated as symmetrical. For example, a disulfide is a +/-RHSpiral if the χ1, χ2, χ3, χ2', χ1' angles are +, +, +, +, - or -, +, +, +, +.
The spirals are the main structural disulfides. With one or two exceptions all the catalytic disulfides are +/-RHHooks, while the known allosteric disulfides are -RHStaples . The allosteric bonds are also defined by closely-spaced α-carbon atoms of the two cysteine residues. The -RHStaple bonds have a mean α-carbon atom distance of 4.3 Å, compared to a mean of 5.6 Å for all disulfides . This is because of their position in protein structures. These bonds often link adjacent strands in the same β-sheet secondary structure [7, 15]. The strands are usually so close in the β-sheet that they need to pucker to accommodate the disulfide bond .
While most protein structures have been solved by X-ray crystallography, a growing number of NMR structures are becoming available. There are also some proteins whose structure has been determined by both methods. A recent analysis of 78 protein structures determined by both X-ray and NMR methods showed that 18 of the 78 structures are significantly different, while the other 60 structures are very similar . The large scale differences likely reflect crystal versus solution structures.
The primary limitation in determining protein structure by NMR is the size of the protein. The size limitation for complete atomic-resolution structure determination by NMR is currently ~30 kDa, though backbone assignments and general folds have been described for proteins up to 100 kDa. X-ray crystallography does not suffer from the size restrictions of NMR, with protein size having no direct bearing on the solvability of the protein or protein complex. This is at least partly why most protein structures have been determined by X-ray rather than NMR. The limitation of X-ray crystallography is its static nature. This means that only a single structure can be determined and any protein movement during data collection results in decreased resolution. Indeed, in many structures there are segments of the protein that are so disordered they are not contained in the structure. With the advent of time-resolved crystallography some dynamic data can be obtained. However, each individual snapshot is still limited by the requirement of an unmoving structure.
In this study, we compare and contrast the disulfide configurations and energies of all NMR and X-ray protein structures. Analysis of the points of contrast between the datasets have led to the identification of a new potential allosteric disulfide defined by the -LHStaple configuration.
Results and discussion
As of June 20, 2006, there were 37,141 structure files available in the protein databank. Of these, 31,611 were determined by X-ray crystallography, 5,476 were determined by NMR and 54 were determined by cryo-electron microscopy or powder diffraction. There was a mean of 15 structural models in each NMR file deposited, resulting in 84,584 total NMR structural models. There were 97,741 disulfides in all files, as determined by the presence of an SSBOND line in the PDB file. Of these disulfides, 42,690 were found in X-ray structures, 55,005 in the separate NMR structures, and 46 were from structures determined by the other methods.
There is a mean of 1.4 disulfide bonds listed per X-ray structure file in the PDB. This is higher than the mean of 0.6 disulfide bonds per NMR structure and 0.9 disulfide bonds per structure determined by other methods. The prototypical structural disulfide configuration, the -LHSpiral , accounts for nearly 30% of all disulfides in X-ray structures (Table 1) and 20% of the disulfides in NMR structures (Table 2).
The five chi angles of the disulfide bond was used to estimate the potential energy of each bond, or dihedral strain energy [8, 17, 18]. This energy measurement is approximate but has been shown to be a useful measure of disulfide strain [19–22]. A striking feature is the disparity in dihedral strain energy between NMR and X-ray disulfides. The mean dihedral strain energy of all NMR disulfides (26.5 kJ.mol-1, Table 2) is twice that of X-ray disulfides (13.1 kJ.mol-1, Table 1). The ordering of the mean strain energies between the different dihedral configurations, though, is nearly the same between NMR and X-ray structures. This supports the validity of the analysis and highlights the difference in tolerance for highly strained disulfides in NMR versus X-ray structures. This is demonstrated graphically in Fig. 1A, where the dihedral strain energies of disulfides in NMR structures have a much broader distribution across the energy range. In NMR structures there is only a modest linear decrease in the mean strain energy as a function of the incidence of each disulfide configuration. In X-ray structures, however, there is an exponential decrease in the mean strain energy as the incidence of the configuration increases (Fig. 1B). The overall spread of values is similar, however, with the strain energies ranging from 2.1 to 79.1 kJ.mol-1 in NMR structures and from 2.1 to 75.6 kJ.mol-1 in X-ray structures.
There are several possible explanations for the higher average strain energy of disulfide bonds in NMR-determined structures. One possibility is a higher degree of error in defining disulfide bond structures in NMR compared to X-ray structures. To test this notion, the disulfide bonds in a dataset of uniformly refined NMR structures [23, 24] was analysed.
Of the 100 validated structures, 25 contain one or more disulfide bonds (PDB IDs 1b2t, 1bbn, 1bf0, 1bf9, 1bgk, 1ce3, 1chl, 1cw5, 1cw6, 1df6, 1du9, 1e5b, 1e5c, 1e8p, 1e8q, 1efe, 1eig, 1eih, 1eot, 1eph, 1epj, 1eww, 1fgp, 1fo7 and 1fwo). There is a total of 60 disulfides in the 25 summary structures and 713 total disulfides in all individual models. As for the total NMR structures dataset (Table 2), the -LHSpiral is the most common disulfide in these refined structures, representing 15 of the 60 disulfides in the summary structures and 185 of the 713 disulfides in all individual models. Notably, the mean dihedral strain energy of the -LHSpiral disulfides in the refined structures (n = 713; 21.3 kJ.mol-1; 95% CI, 19.8–22.9 kJ.mol-1) is almost the same as it is for all NMR structures (n = 11137, 19.2 kJ.mol-1; 95% CI, 19.0–19.5 kJ.mol-1, Table 2). This strain energy is roughly twice that found for -LHSpiral disulfides in X-ray structures (n = 12684, 10.5 kJ.mol-1; 95% CI, 10.4–10.6 kJ.mol-1, Table 1) . Thus, while it is likely that there are errors in the modelling of both NMR and X-ray structures, particularly for disulfides with high strain, the significant differences noted in average strain energies of disulfides in NMR versus X-ray structures most probably indicate preference for lower energy disulfides in crystallized proteins.
The lower tolerance for disulfide strain energy in X-ray structures is also apparent when comparing the data for all X-ray structures in Table 1 with the data we reported earlier for a set of unique X-ray disulfides  and the disulfides of a culled set of X-ray structures described by Guoli Wang and Roland Dunbrack, Jr.  (Table 3, Fig. 1C). The Wang and Dunbrack structures represent non-redundant sequences across all PDB files and were selected based on the highest resolution structure available and then the best R-values. The overall trend in relative strain energies of the different configurations and their incidence is the same for the non-culled and culled datasets. This finding indicates that the analysis of the non-culled dataset has not been unduly biased by those proteins for which there are numerous X-ray structures, such as serine proteinases like trypsin.
Direct comparison of disulfide bond characteristics in NMR and X-ray structures can be made for proteins whose structures have been determined by both methods. The disulfide bond configurations in 10 proteins that have very similar X-ray and NMR structures (MaxSub ≥ 0.77) has been determined (Table 4). The differences in the X-ray versus NMR models of the proteins is comparable to the differences between various X-ray or various NMR structures of a given protein . It is apparent that a given disulfide can exist in different configurations in NMR models. Most often, the configuration found in the X-ray structure is also found in one or more of the NMR models. For example, the Cys26–Cys84 disulfide in ribonuclease A is a -LHSpiral in the X-ray structure and in 16 of the 32 NMR models. In the other 16 models it is a -RHHook (13) or -RHSpiral (3). There are some notable exceptions however. The Cys11–Cys27 disulfide in tendamistat is a -/+RHHook in the X-ray structure and a +/-LHStaple in all 9 NMR models. Also, the Cys25–Cys80 disulfide in β2-microglobulin is a -LHStaple in the X-ray structure but a -LHSpiral (10), -RHSpiral (7) or -RHHook (3) in the 20 NMR models. These findings indicate that structures of some disulfides are particularly malleable.
There are 10 disulfides in this dataset of comparable structures where the X-ray configuration is also the predominant NMR configuration. Notably, nine of the ten dihedral strain energies for the matching disulfide configurations are significantly higher in NMR structures (Table 4). This finding supports the notion that the propensity for a protein to crystallize relates, at least in part, to the amount of strain in its disulfide bonds.
The mean distance between the α-carbon atoms of the disulfide bond is the same in NMR and X-ray structures, at 5.6 Å (Tables 1 and 2). The -RHStaple configuration is the standout for α-carbon distance, with mean distances of 4.5 Å and 4.2 Å in NMR and X-ray structures, respectively (Fig. 2). As discussed previously [8, 15], this is because -RHStaples are often found linking adjacent strands in the same antiparallel β-sheet. The -RHStaple configuration is favoured by allosteric disulfides . The finding that -RHStaples have the same features in NMR and X-ray structures further supports this motif as a hallmark of allosteric bonds. The catalytic disulfides in X-ray structures are nearly always +/-RHHooks . They are also predominantly +/-RHHooks in NMR structures of oxidoreductases (data not shown), but can exist in subsets of the RHHook configuration. The catalytic disulfide in one NMR structure of thioredoxin (PDB ID 1xoa), for example, is a -RHHook in 15 of the 20 models and a +/-RHHook in the other 5 (Table 4).
While the average features of most configurations are generally comparable between NMR and X-ray structures, the features of the -LHStaple bond are very different between the two. Overall, the -LHStaples in NMR structures have a mean strain energy of 36.1 kJ.mol-1 (n = 1805; 95% CI, 35.4–36.7 kJ.mol-1) and a mean Cα-Cα' distance of 4.88 Å (95% CI, 4.84–4.93 Å). This is compared to a mean strain energy of 14.9 kJ.mol-1 (n = 599; 95% CI, 13.8–16.0 kJ.mol-1) and a mean Cα-Cα' distance of 5.80 Å (95% CI, 5.70–5.89 Å) for this configuration in X-ray structures. From visual inspection of all the -LHStaples (Fig. 3), it is apparent that the majority of these bonds in NMR structures have a high strain energy (~50 kJ.mol-1) and short α-carbon distance (~4 Å) (Fig. 3A). In contrast, most of these bonds in X-ray structures have a low strain energy (~10 kJ.mol-1) and long α-carbon distance (~6.5 Å)  (Fig. 3B).
Due to the high strain energies of these short -LHStaples, it is understandable that they would be rare in X-ray structures due to the generally low tolerance for high energy bonds. In NMR and X-ray structures that contain -RHStaple disulfides, it is apparent that these bonds can often exist in the -LHStaple configuration and vice versa. Moreover, the disulfides that can exist in both -RHStaple and -LHStaple configurations almost invariably have high strain energy and a short α-carbon separation in both the right-handed and left-handed configurations (data not shown). These findings suggest that the -LHStaple should be considered a potential allosteric bond. Indeed, it remains in question if it is the -RHStaple or the strained -LHStaple that is the functional form of allosteric disulfide bonds. Two proteins in which this switching occurs, fibronectin and HIV gp120, will be discussed in more detail.
Fibronectin is a major component of extracellular matrices where it influences a variety of cellular functions by binding to surface integrin receptors . Following secretion from cells it assembles into a fibrillar network that once formed is resistant to all denaturants except reducing agents . The mechanism of fibril formation is not well understood but it may involve domain swapping [28, 29]. The five N-terminal type 1 repeats of fibronectin are essential for fibril formation . Type 1 domains are ~40 residues in length and contain two disulfide bonds in a 1–3, 2–4 pattern. The 1–3 disulfide in each domain can exist in hook or spiral configurations, while the 2–4 disulfide is always a -RHStaple or -LHStaple with a very short α-carbon distance of ≤ 4 Å (Table 5). Given the apparent necessity for a -RHStaple or -LHStaple in the 2–4 disulfides, we suggest that these are allosteric disulfides that might regulate fibril formation. The fact that the -LHStaple configuration of these bonds uniformly have a higher DSE and shorter α-carbon separation than the -RHStaple configuration can be interpreted to suggest either that there is some uniform defect in the modelling of this configuration or that the -LHStaple is the functional configuration.
The HIV envelope glycoprotein consists of the surface glycoprotein gp120 bound non-covalently to transmembrane gp41 that is anchored in the viral membrane . The two proteins dissociate when gp120 binds to CD4 and a chemokine receptor. This allows the gp41 fusion peptide to be inserted into the target membrane, which drives the membrane merger . Cleavage of two of the nine disulfide bonds in gp120 appears to be important in this process [32, 33]. It has been proposed that cleavage of the gp120 bonds facilitate unmasking of the gp41 fusion peptide and its insertion into the target cell membrane [32, 33]. Seven of the nine disulfide bonds are present in the eight core structures of gp120 in the protein databank, and five of these bonds can exist in either -RHStaple or -LHStaple configurations in the different structures (Table 6). Considering that the V3 domain binds chemokine receptor and that cleavage of gp120 disulfides ablates this interaction , the Cys296–Cys331 bond that tethers the ends of V3 is most likely one of the two disulfides cleaved in gp120. There is currently no experimental data to suggest what other disulfide is cleaved. Our analysis leads us to propose that the Cys385–Cys418 disulfide is the other bond cleaved.
The Cys126–Cys196 bond is found in the -RHStaple configuration in seven of the eight structures and has strain energies ranging from 20 to 40 kJ.mol-1 (Table 5). However, the distance between α-carbons for this bond is longer than for the other -RHStaples in this protein. The Cys218–Cys247 is also found in the -RHStaple configuration in the solved structures and the α-carbon separation is less than 4 Å. The strain energies for this bond are modest, though, ranging from 12 to 20 kJ.mol-1. By comparison, the Cys385–Cys418 bond is found as a -RHStaple in two of the reported structures and as a -LHStaple in one structure. In the remaining structures, it is found as a -LHHook. The strain energies are around 30 kJ.mol-1, however, with the -LHStaple configuration having a strain of 43 kJ.mol-1. Additionally, the α-carbon separation is short, ranging from 3.7 to 3.9 Å in all of the structures. While the predominant configuration of this bond, -LHHook, has not been associated with allosteric disulfides, the high strain of this bond disposes it to cleavage. Although, given the preference for lower energy bond configurations in X-ray structures, it is possible that the predominance of the -LHHook configuration in this structure is a biproduct of crystal packing. We suggest that it is the -LHStaple configuration of this bond that is most susceptible to cleavage and is the second disulfide cleaved during viral entry. The Cys385–Cys418 bond is in the same β-barrel as the Cys296–Cys331 disulfide. It is plausible that accessibility of one of these bonds to the reductant leads to the accessibility of the other bond as well. The cleavage of two strained, cross-strand disulfides in one structural motif should allow for a large conformational change in the domain.
Comparison of the same disulfide bonds in very similar X-ray and NMR structures indicates that the bonds often exist in different configurations in different NMR models and usually with a higher potential energy than found in X-ray structures. One bond configuration that is scarce in X-ray structures is the -LHStaple. In NMR structures, this disulfide is characterised by a particularly high potential energy and very short α-carbon distance. Moreover, allosteric -RHStaple disulfides often exist in the -LHStaple configuration in different NMR models. The rarity of -LHStaple disulfides in X-ray structures is consistent with the finding that disulfides in crystallized proteins generally have lower strain energy than those found in solution structures. We suggest that the -LHStaple is an allosteric configuration.
All structures released in the protein databank  as of June 20, 2006 were analyzed. Disulfide bonds in structures were determined by the presence of an SSBOND line in the PDB file. NMR structures were analyzed once, using the first model listed as the representative structure. The files were then separated into each individual model and analyzed.
Determination of the dihedral strain energy (DSE) was performed as described previously . Briefly, the DSE of each disulfide was predicted from the magnitude of the five χ angles that define the disulfide using the empirical formula [17, 18]:DSE (kJ.mol-1) = 8.37(1+cos3χ1) + 8.37(1+cos3χ1') + 4.18(1+cos3χ2) + 4.18(1+cos3χ2') + 14.64(1+cos2χ3) + 2.51(1+cos3χ3)
χ1 is the dihedral angle about the Cα-Cβ bond, χ2 about the Cβ-Sγ bond, χ3 about the Sγ-Sγ' bond, χ2' about the Sγ'-Cβ' bond and χ1' about the Cβ'-Cα' bond. This relationship has been shown experimentally to reflect the amount of strain in a disulfide bond [19–22].
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RCSB protein data bank[http://www.rcsb.org]
DeLano WL: The PyMOL Molecular Graphics System. San Carlos, CA, USA , DeLano Scientific; 2002.
We thank Lorraine Ho for assistance with the data mining. This study was supported by grants from the Australian Research Council, the National Health and Medical Research Council of Australia, the Cancer Council NSW and an infrastructure grant from the NSW Health Department.
Both authors made substantive contributions to conception and design of the study, and analysis and interpretation of data.