research papers
A first low-resolution difference Fourier map of phosphorus in a membrane protein from near-edge anomalous diffraction
aESRF, F-38043 Grenoble, France, bEMBL, F-38043 Grenoble, France, cMax-Planck-Institut für Biophysik, D-60438 Frankfurt, Germany, dInstitut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF, F-38027 Grenoble, France, eUniversity of Aarhus, Department of Molecular Biology, DK-8000 Aarhus, Denmark, and fGKSS Forschungszentrum, D-21494 Geesthacht, Germany
*Correspondence e-mail: heinrich.stuhrmann@orange.fr
Crystal diffraction of three membrane proteins (cytochrome bc1 complex, sarcoplasmic reticulum Ca2+ ATPase, ADP-ATP carrier) and of one nucleoprotein complex (leucyl synthetase bound to tRNAleu, leuRS:tRNAleu) was tested at wavelengths near the X-ray K-absorption edge of phosphorus using a new set-up for soft X-ray diffraction at the beamline ID01 of the ESRF. The best result was obtained from crystals of Ca2+ ATPase [adenosin-5′-(β,γ-methylene) triphosphate complex] which diffracted out to 7 Å resolution. Data were recorded at a wavelength at which the real factor of phosphorus reaches the extreme value of −20 electron units. The positions of the four triphosphates of the monoclinic of the ATPase have been obtained from a difference Fourier synthesis based on a limited set of anomalous diffraction data.
Keywords: anomalous dispersion; phosphorus; membrane proteins; nucleoproteins.
1. Introduction
Phosphorus is a regular constituent of a number of biomolecules found in living matter. It is relatively abundant in DNA and RNA and to a smaller extent in et al., 1995; Biou et al., 2005). All of them attempt to use the relatively strong of the of phosphorus(V), which amounts to a change of both the real and the imaginary factors, f ′ and if ′′, by almost 20 electron units near the X-ray K-absorption edge at a wavelength λk = 5.761 Å corresponding to a photon energy of Ek = 2152 eV (Biou et al., 2005).
and in some proteins. Its ubiquitous presence would make it an ideal native label for the study of the interaction of the main components of living cells. So far, there have been very few attempts in macromolecular structure research in this direction (StuhrmannInteresting as this is, the use of soft X-rays in diffraction experiments means coping with a reduced
of this radiation in almost any kind of matter. The of 5.76 Å photons in water is 20 µm, and it is 2 cm in air. These numbers impose new rules, which are rather different from those of conventional techniques of protein crystallography. The optimal set for soft X-ay diffraction is not yet at hand, but this paper will present a technical progress which has been achieved recently at the European Synchrotron Radiation Facility (ESRF).Various types of protein crystals were tested: rod-like crystals of leuRS:tRNAleu complex, thin flat crystals of ADP-ATP carrier (Pebay-Peyroula et al., 2003) and sarcoplasmic reticulum Ca2+ ATPase (SERCA) (Sorensen et al., 2004) and the more compact crystals of the cytochrome bc1 complex (Lange et al., 2001). The choice of the samples reflects the potential of the of phosphorus for the study of the interaction of proteins with RNA and of membrane proteins with lipids.
2. Experimental
The technical design of the presently used set-up for soft X-ray diffraction has been described by Biou et al. (2005). Its realisation by a joint effort of the Institut de Biologie Structurale (IBS), the European Molecular Biology Laboratory (EMBL) and the ESRF is shown in Fig. 1.
The main part of the set-up is a cylindrical box covered by two-thirds of its jacket by a flexible image plate sensitive to (soft) X-rays. Hence, the intensity diffracted by the sample in the centre of the cylinder can be detected within the angular range −150° to +100° along the azimuth and from −52° to +66° in the orthogonal direction. With 5.76 Å X-ray photons, a wavelength close to the K-absorption edge of phosphorus, the largest accessible scattering angle of 150° allows for a structural resolution of 3 Å. This is one of the technical challenges in soft X-ray diffraction; another arises from the absorption of soft X-rays already mentioned above. Ideally, the beam path between the source of soft X-rays down to the detector should be completely evacuated. In practice, windows will be necessary at some places to maintain a protective atmosphere for the sample, particularly for very sensitive samples like protein crystals. Although various solutions have been suggested (Stuhrmann et al., 1995; Djinović et al., 2005; Biou et al., 2005), the choice of a helium atmosphere appears to be convenient for two reasons: (i) helium is transparent at X-ray wavelengths below 10 Å, and (ii) cold helium gas is a good coolant of the sample. This led to the set-up shown in Fig. 1.
In most cases, helium gas cooled to 100 K by a Oxford Cryogenic System 700 is used. A major improvement with respect to the previous version (Biou et al., 2005) is the double window filled with warm helium which prevents the formation of frost on the outer surface of the window. The cold helium gas leaving the central cylinder is warmed up and pumped into the double window from where it is recovered. The cryogenic system for soft X-ray diffraction has been developed by EMBL.
In the absence of a sample, 40% of the 5.76 Å photons arriving at the front end of the set-up shown in Fig. 1 will reach the image plate. The absorbing elements are 25 µm beryllium, 300 mm helium and 12 µm Mylar foil of the double window.
Other items of the set-up are needed for the alignment of the crystal in the X-ray beam. The special φ-axis with its long rod is one of the contributions of the ESRF to this project. The crystal is observed by a telescope in two ways, simultaneously: (i) directly and (ii) by its shadow in the soft X-ray beam on a fluorescent screen a few millimetres behind the sample. Another camera is used to align the nozzle of the helium transfer line; this explains one of the two holes in the aluminium plate (Fig. 1).
Moreover, the increase of the X-ray synchrotron radiation intensity at wavelengths near the K-edge of phosphorus by a factor of 10 owing to the replacement of the wiggler by a new undulator at beamline ID01 of the ESRF has been highly beneficial both to the quality of the X-ray diffraction data and to the proper functioning of a part of the optical system.
The diffracted intensity was recorded using a cylindrically bent image plate. The readout time of one picture is 10 min. With a measuring time of another 10 min, the turnaround time comes close to half an hour. The long feedback time is the only weak point of a set-up with an otherwise excellent performance.
3. Crystal diffraction at wavelengths near the K-absorption edge of phosphorus
The protein crystals used for diffraction experiments at wavelengths near the K-edge of phosphorus are listed in Table 1. The crystals were rotated by 5° in 10 min for one picture recorded by the bent image plate. All of them diffract soft X-rays. The limit of structural resolution varies strongly with the crystal used (Table 2). As the experiment was meant to test a larger number of protein crystals, data were recorded at one wavelength only for a given crystal (Table 2).
|
|
Best results were obtained from one of the SERCA crystals which showed well resolved peaks of the diffracted intensity up to 7 Å resolution at the initial scan of 5° (Fig. 3). The resolution limit varies with the orientation of the crystal; it changes to 12 Å in adjacent scan intervals and to 20 Å in more remote scan intervals. The initial scan interval was revisited twice. The diffracted intensity had decreased to half of the original value after two hours. Finally the crystal was moved to a different orientation.
The crystals of the cytochrome bc1 complex diffract to a slightly lower resolution of about 10 Å.1 Numerous weak diffraction peaks were observed, but mostly as streaks, between 20 Å and 10 Å resolution (Fig. 4). The indices [hkl] are inserted for the stronger reflections only. The crystal of the LeuRS:tRNAleu complex diffracted to 20 Å resolution (Fig. 5).
4. Difference Fourier maps of phosphorus
The spatial phosphorus density distribution ρP(x,y,z) in a of a crystal can be obtained to a good approximation from the diffracted intensity measured at two wavelengths, e.g. at λ1 and λ2 (Fig. 2), near the K-absorption edge of phosphorus,
where Fh,k,l is the square root of the intensity Ih,k,l. The phases αh,k,l can be those of the known protein structure or derived by heavy-atom derivatives.
As mentioned in the previous section, diffraction data of the crystals cited in Table 2 were collected at one wavelength, λ1 or λ2, only (Fig. 2). Moreover, the data sets are far from being complete: around 30% at 20 Å resolution (Table 3) and even less at still higher resolution. These two facts together with the accuracy of the measured intensities of diffraction set serious limits to a difference Fourier synthesis.
In a first step, one needs to show to what extent a given set of diffracted intensities Ih,k,l measured at a wavelength near the K-absorption edge agrees with the corresponding intensities calculated from the known structure. Second, one has to make sure that the agreement at the wavelength actually used is better than that obtained at other wavelengths close to the absorption edge.
If this is the case, the Fh,k,l(λ) difference in (1) may be completed. A set of diffracted intensities obtained at short wavelengths could be a useful reference, particularly for the measurements at λ = λ1, where f ′ is strongly negative (Fig. 2). Fh,k,l(λ2) then would be replaced by Fh,k,l (off resonance). This approach would be less useful for the measurements at λ = λ2 where the contribution of to the diffracted intensity is relatively small. This is one reason why the missing set of Fh,k,l(λ) in (1) will be calculated from the model throughout. The other reason is that the large difference f ′(λ2) − f ′(λ1) = 20 electron units at practically no change of absorption owing to f ′′ provides optimal conditions for the evaluation of the phosphorus density map from a difference Fourier synthesis. As the change in wavelength on passing from λ1 to λ2 is very small, the trajectory of the beam through the crystal will be the same. In the absence of a systematic error which might have come from a change in absorption or a change of the beam trajectory across the crystal, the accuracy of the intensity difference depends on the statistical error of the intensity measurements at λ1 and λ2 only.
Before entering into a more detailed discussion of the data, parts of which are shown in Figs. 3, 4 and 5, a summary of their statistical accuracy and of the expected intensity of anomalous diffraction within the structural resolution limit of 20 Å is presented in Table 3. Rather accurate data were obtained from SERCA crystals. Their completeness of 0.37 is slightly better than that of the data obtained from the other crystals. The triphosphates of AMPPCP are expected to give rise to a relatively strong anomalous diffraction.
The diffraction peaks from the cytochrome bc1 complex are more numerous than with SERCA, but they are weaker. Although the ratio between the number of phosphorus atoms per protein mass is similar for SERCA and the cytochrome bc1 complex, the expected intensity owing to of the phosphates of lipid molecules associated with the latter is considerably lower in the resolution range under discussion.
The leuRS:tRNAleu complex gives rise to a very strong contribution of
The analysis is likely to be limited mainly by the low completeness of the data.4.1. SERCA
One of the members of the family of the ATP driven cation pumps is the sarcoplasmic reticulum calcium pump from skeletal muscle (SERCA). It is a monomeric membrane protein, responsible for transporting calcium ions across biological membranes up to the limiting electrochemical gradient from the cytoplasm into sarcoplasmic reticulum (Moller et al., 1996). The binding of AMPPCP to the Ca2+ATPase in some sense simulates the binding of ATP (Sorensen et al., 2004).
The quality of the soft X-ray diffraction patterns collected from SERCA crystals changes both with time and the orientation of the crystal with respect to the X-ray beam. Starting from the crystal orientation giving rise to the image shown in Fig. 3, the number of reflections is roughly halved in the neighbouring scan intervals, and only 10% of the reflections, mainly at low resolution, are observed in the scan intervals after next. These measurements have been repeated with the same crystal. The diffracted intensity shown in Fig. 3 decreases to half of the initial value in about two hours.
The strong variation in the quality of the diffraction pattern with the crystal orientation is somehow linked to the size and shape of the crystal and to the loop on which it is mounted. Both are more or less opaque at wavelengths near the K-absorption edge of phosphorus. The crystals had typical dimensions of 200 × 200 × 50 µm and rhomboid shape (Fig. 6).
The large surface of the crystal covered a major part of the loop (insert of Fig. 6). On direct incidence, 92% of the 5.76 Å photons would be absorbed by 50 µm of the protein crystal. It might well be that a larger fraction of the diffracted intensity comes from the thinner edge regions of the protein crystal.
The peak intensities obtained from the experiment were corrected for the Lorentz kinematical factor and for the polarization factor (Kahn et al., 1982). A further improvement of the fit was obtained by assuming an angle-dependent probability (W) of the emission of the diffracted intensity, described by
where r is the distance from the centre of the diffraction pattern and ψ is the azimuth angle in the detector plane. The coefficients a and Cl,n of the expansion as a series of Legendre polynomials, Pl, are determined by a least-squares method, where
is minimized.
W, shown in Fig. 7, takes into account various factors influencing the emission of the diffracted intensity, e.g. the shape of the crystal, its non-uniform opacity, radiation damage of the crystal surface which may be non-uniform, the shadow cast by the loop, and last but not least the resolution limit of the crystal.
The value of R is quite sensitive to the of phosphorus (Fig. 2). Its variation with the wavelength is similar to the dispersion of f ′. R is lowest at λ = λ1, i.e. at the wavelength which has been used for the diffraction experiment for this crystal. Fh,k,l(λ1) is now obtained as the square root of Ih,k,l(λ1). Fh,k,l(λ2) calculated from the model substitutes for the missing experimental data Ih,k,l(λ2).
At 20 Å resolution, all the phosphorus atoms of a triphosphate contribute jointly to the anomalous diffraction with a weight which is comparable with that of a heavy atom. A difference Fourier synthesis starting from Fh,k,l(λ1) and Fh,k,l(λ2) at 20 Å resolution calculated from the known structure (Sorensen et al., 2004) shows the sites of the triphosphates of the SERCA–AMPPCP complex as intense spots (Fig. 8).
The result of the difference Fourier synthesis starting from a mixture of experimental and calculated Fh,k,l is shown in Fig. 9. The phosphorus density map clearly shows the sites of the phosphorus atoms of AMPPCP as large intense spots, that are elongated mainly due to the low completeness of the data.
4.2. Cytochrome bc1 complex
Tightly bound bc1 complex, an integral membrane protein of the respiratory chain (Lange et al., 2001). There are two phosphatidylethanolamines (PEs), one phosphatidylcholin (PC), one phosphatidylinositol (PI), and one cardiolipin (CL) bound to the cytochrome bc1 complex. A difference Fourier synthesis starting from Fh,k,l(λ1) and Fh,k,l(λ2) at 20 Å resolution calculated from the known structure reveals the sites of the phosphorus atoms. The two phosphorus atoms of cardiolipin at 7 Å distance give rise to a single spot (CL in Fig. 10) in the phosphorus density map. The projection of the map along the b-axis is shown in Fig. 10. This result is expected from a complete set of data measured at two wavelengths λ1 and λ2 near the K-absorption edge of phosphorus.
are essential for the activity of the cytochromeThe diffraction experiment was carried out at the wavelength λ2 (Fig. 2). The difference Fourier synthesis starts from a mixture of experimental Fh,k,l(λ2) and Fh,k,l(λ1) calculated from the model. The statistical accuracy of the experimental data, their completeness and the expected intensity of anomalous diffraction at 20 Å resolution are all lower than in the preceding case of SERCA (Table 3). Hence, the variation of R (not shown here) with the wavelength is much less pronounced than with SERCA (Fig. 2): R(λ2) − R(λ1) = −0.015. The positions of only three of the six phosphorus atoms appear to be reasonably well resolved along the a-axis and hardly at all along the c-axis (Fig. 11).
4.3. LeuRS:tRNAleu complex
The leucyl-tRNA synthetase is an enzyme that catalyzes the esterification of leucine to its cognate tRNAleu. The intermediate LeuRS:tRNAleu complex is an example of a nucleic acid protein interaction. As such it is rich in phosphorus. The expected intensity of anomalous diffraction at 20 Å resolution is large (Table 3). The phosphorus density map from a difference Fourier synthesis using Fh,k,l(λ1) and Fh,k,l(λ2) from the known as determined by one of us (TC) is shown in Fig. 12. This result would have been obtained from a complete set of data measured at two wavelengths λ1 and λ2 near the K-absorption edge of phosphorus (Fig. 2).
The diffraction experiments were carried out at the wavelength λ1. The change in the diffracted intensity owing to the dispersion of phosphorus is much more important than the statistical error. The spatial distribution of the phosphorus atoms of obtained by the difference Fourier synthesis using the experimental data is best resolved in the projection onto the ab plane (Fig. 13). It agrees fairly well with the corresponding difference Fourier synthesis at 20 Å resolution starting from the known structure of the leuRS:tRNAleu complex shown in Fig. 12.
5. Outlook
From the results shown in Figs. 9, 11 and 13, it appears that there is plenty of room for further improvement of the measurement of anomalous diffraction from protein crystals near the K-absorption edge of phosphorus. The gain in structural information from a phosphorus density map as obtained from a difference Fourier synthesis using complete data sets taken at λ1 and λ2 would be considerable, even at a structural resolution of 20 Å, as shown in Figs. 8, 10 and 12. The head groups of interacting with membrane proteins or taking part in lipid bilayer arrangements in type 1 membrane protein crystals (Deisenhofer & Michel, 1989) could then be localized providing for a deeper understanding of protein–membrane interactions. Furthermore, the contours of bound to proteins could be visualized. Needless to say that close arrangements of phosphorus atoms as they occur in cardiolipin or in triphosphates are most easily detected.
Another lesson to be learned from our experiment is that the quality of the diffraction pattern may vary strongly with the orientation of the crystal with respect to the X-ray beam. A more detailed study of this behaviour might help to optimize the conditions of soft X-ray diffraction.
There is also a loss of the intensity diffracted by a protein crystal after prolonged irradiation with soft X-rays. At a temperature of 100 K, the intensity decreases to half of the initial value within two hours. Earlier experiments at a wavelength near the MV edge of uranium (λMV = 3.5 Å) showed that there was hardly any degradation of a lysozyme crystal within a period of 12 h at a temperature of 40 K maintained by cold helium gas (Chesne, 2002). Whether this is a general property of soft X-ray diffraction at lower temperatures needs to be shown.
As protein crystals may suffer from radiation damage, it is important to measure the intensity of diffraction at two wavelengths at the e.g. at λ1 and λ2 mentioned above) almost simultaneously. Using an image plate as a detector, this can be achieved by recording the intensity diffracted by the crystal at λ1 and λ2 on one image where the corresponding two sets of diffraction peaks have been separated by a small shift of the plate (Chesne, 2002).
(Image plates are very convenient detectors for soft X-ray diffraction. Being flexible, they can cover a large solid angle of X-ray diffraction as shown in Fig. 1. Data taking could be a lot faster with an on-line readout system for flexible image plates. The better solution appears to be a new type of detector, a semiconductor pixel array, PILATUS, which has been developed at the Paul Scherrer Institut (PSI), Villigen. It combines a large solid angle, fast readout and a sensitivity for soft X-rays at 2.1 keV which can be high (Bitter et al., 2006).
Footnotes
‡Present address: Institute of Membrane and Systems Biology, University of Leeds, Leeds LS2 9JT, UK.
1One of the crystals with a maximum size of almost 1 mm diffracted in the backwards direction. Several peaks were observed at 3.3 Å resolution, with a spacing which is not incompatible with that of the unit-cell dimensions of the cytochrome bc1 complex.
Acknowledgements
The soft X-ray diffraction experiments reported in this paper are a part of the project MX518, to which beam time at ID01 of the ESRF had been allocated. Important contributions to the project came from the Institut de Biologie Structurale Jean-Pierre Ebel (IBS), the European Molecular Biology Laboratory (EMBL) and the European Synchrotron radiation Facility (ESRF). The support by Otto Dideberg (IBS) and Stephen Cusack (EMBL) is gratefully acknowledged.
References
Biou, V., Bösecke, P., Bois, J.-M., Brandolin, G., Kahn, R., Mas, C., Nauton, L., Nury, H., Pebay-Peyroula, E., Vicat, J. & Stuhrmann, H. (2005). J. Synchrotron Rad. 12, 402–409. Web of Science CrossRef CAS IUCr Journals Google Scholar
Bitter, M. L., Broennimann, Ch., Eickenberry, E. F., Hill, K. W., Ince-Cushman, A., Lee, S. G., Rice, J. E. & Scott, S. (2006). IEEE Nucl. Sci. Symp. Conf. Record, R06-37, pp. 3721–3723. CrossRef Google Scholar
Chesne, M. L. (2002). Thesis. Université Joseph Fourier, Grenoble, France. Google Scholar
Deisenhofer, J. & Michel, H. (1989). EMBO J. 8, 2149–2170. CAS PubMed Web of Science Google Scholar
Djinović Carugo, K., Helliwell, J. R., Stuhrmann, H. & Weiss, M. S. (2005). J. Synchrotron Rad. 12, 410–419. Web of Science CrossRef IUCr Journals Google Scholar
Kahn, R., Fourme, R., Gadet, A., Janin, J., Dumas, C. & André, D. (1982). J. Appl. Cryst. 15, 330–337. CrossRef CAS Web of Science IUCr Journals Google Scholar
Lange, C., Nett, J. H., Trumpower, B. L. & Hunte, C. (2001). EMBO J. 20, 6591–6600. Web of Science CrossRef PubMed CAS Google Scholar
Moller, J. V., Juul, B. & le Maire, M. (1996). Biochim. Biophys. Acta, 1286, 1–51. PubMed Web of Science Google Scholar
Pebay-Peyroula, E., Dahout-Gonzales, C., Kahn, R., Trézéguet, V., Lauqin, G. J.-M. & Brandolin, G. (2003). Nature (London), 426, 39–44. Web of Science CrossRef PubMed CAS Google Scholar
Sorensen, T. L., Moller, J. V. & Nissen, P. (2004). Science, 304, 1672–1675. Web of Science CrossRef PubMed CAS Google Scholar
Stuhrmann, S., Hütsch, M., Trame, C., Thomas, J. & Stuhrmann, H. B. (1995). J. Synchrotron Rad. 2, 83–86. CrossRef CAS Web of Science IUCr Journals Google Scholar
© International Union of Crystallography. Prior permission is not required to reproduce short quotations, tables and figures from this article, provided the original authors and source are cited. For more information, click here.