Synchrotron and neutron techniques in biological crystallography

Synchrotron radiation (SR) techniques are continuously pushing the frontiers of wavelength range usage, smaller crystal sample size, larger protein molecular weight and complexity, as well as better diffraction resolution. The new research specialism of probing functional states directly in crystals, via time-resolved Laue and freeze trapping structural studies, has been developed, with a range of examples, based on research stretching over some 20 years. Overall, SR X-ray biological crystallography is complemented by neutron protein crystallographic studies aimed at cases where much more complete hydrogen details are needed involving synergistic developments between SR and neutron Laue methods. A big new potential exists in harnessing genome databases for targeting of new proteins for structural study. Structural examples in this tutorial review illustrate new chemistry learnt from biological macromolecules.

Unravelling the structural chemistry of the colouration mechanism in lobster shell

Biochemistry, biological crystallography, spectroscopy, solution X-ray scattering and microscopy have been applied to study the molecular basis of the colouration in lobster shell. This article presents a review of progress concentrating on recent results but set in the context of more than 50 years of work. The blue colouration of the carapace of the lobster Homarus gammarus is provided by a multimolecular carotenoprotein, alpha-crustacyanin. The complex is a 16-mer of five different subunits each binding the carotenoid, astaxanthin (AXT). A breakthrough in the structural studies came from the determination of the structure of beta-crustacyanin (protein subunits A1 with A3 with two shared bound astaxanthins). This was solved by molecular replacement using apocrustacyanin A1 as the search motif. A molecular movie has now been calculated by linear interpolation based on these two 'end-point' protein structures, i.e. apocrustacyanin A1 and A1 associated with the two astaxanthins in beta-crustacyanin, and is presented with this paper. This movie highlights the structural changes forced upon the carotenoid on complexation. In contrast, the protein-binding site remains relatively unchanged in the binding region, but there is a large conformational change occurring in a more remote surface-loop region. It is suggested here that this loop could be important in complexation of AXT and contributes to the spectral properties. Also presented here is the first observation of single-crystal diffraction of the full 'alpha-crustacyanin' complex comprising 16 protein subunits and 16 bound AXT molecules (i.e eight beta-crustacyanins) at 5 A resolution. Optimization of crystallization conditions is still necessary as these patterns show multiple crystallite character, however, 10 A resolution single-crystal diffraction has now been achieved. Provision of the new SRS MPW 10 and SRS MPW 14 beamline robotic systems will greatly assist in the surveying of the many alpha-crustacyanin crystallization trials that are being made. New solution X-ray scattering (SXS) measurements of beta- and alpha-crustacyanin are also presented. The beta-crustacyanin SXS data serve to show how the holo complex fits the SXS curve, whereas the apocrustacyanin A1 homodimer from the crystal data naturally does not. Reconstructions of alpha-crustacyanin were accomplished from its scattering-profile shape. The most plausible ultrastructure, based on a fourfold symmetry constraint, was found to be a stool with four legs. The latter is compared with published electron micrographs. A detailed crystal structure of alpha-crustacyanin is now sought in order to relate the full 150 nm bathochromic shift of AXT to that complete molecular structure, compared with the 100 nm achieved by the beta-crustacyanin protein dimer alone. Rare lobster colourations have been brought to attention as a result of this work and are discussed in an appendix.

Apocrustacyanin C(1) crystals grown in space and on earth using vapour-diffusion geometry: protein structure refinements and electron-density map comparisons

Models of apocrustacyanin C(1) were refined against X-ray data recorded on Bending Magnet 14 at the ESRF to resolutions of 1.85 and 2 A from a space-grown and an earth-grown crystal, respectively, both using vapour-diffusion crystal-growth geometry. The space crystals were grown in the APCF on the NASA Space Shuttle. The microgravity crystal growth showed a cyclic nature attributed to Marangoni convection, thus reducing the benefits of the microgravity environment, as reported previously [Chayen et al. (1996), Q. Rev. Biophys. 29, 227-278]. A subsequent mosaicity evaluation, also reported previously, showed only a partial improvement in the space-grown crystals over the earth-grown crystals [Snell et al. (1997), Acta Cryst. D53, 231-239], contrary to the case for lysozyme crystals grown in space with liquid-liquid diffusion, i.e. without any major motion during growth [Snell et al. (1995), Acta Cryst. D52, 1099-1102]. In this paper, apocrustacyanin C(1) electron-density maps from the two refined models are now compared. It is concluded that the electron-density maps of the protein and the bound waters are found to be better overall for the structures of apocrustacyanin C(1) studied from the space-grown crystal compared with those from the earth-grown crystal, even though both crystals were grown using vapour-diffusion crystal-growth geometry. The improved residues are on the surface of the protein, with two involved in or nearby crystal lattice-forming interactions, thus linking an improved crystal-growth mechanism to the molecular level. The structural comparison procedures developed should themselves be valuable for evaluating crystal-growth procedures in the future.

Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase

The enzyme hydroxymethylbilane synthase (HMBS, EC 4.3.1.8), 313 amino acid residues and MW 34 kDa, also known as porphobilinogen deaminase (PBGD), catalyses the stepwise polymerization of four molecules of porphobilinogen (PBG) to the linear tetrapyrrole 1-hydroxymethylbilane. Several crystallographic structures of HMBS have been previously determined, most recently including by time-resolved Laue protein crystallography of the Lys59Gln mutant form with reaction initiation undertaken by use of a flow cell carrying the substrate PBG. In this paper we review these structures and add new molecular graphics representations and analyses. Moreover we present a new structure refined at 1.66 A resolution using diffraction data recorded at cryo-temperature (100 K) in an attempt at trapping the polypeptide loop (residues 47 to 58) in the vicinity of the enzyme active site, missing in all previous structure determinations. This loop still has not appeared in the electron density maps, in spite of the advantage of cryo-temperature, but nevertheless the 1.66 A cryo-structure extends the ensemble of known HMBS structures. The cryomodel of protein, cofactor and 320 bound water molecules has been refined to a final R-factor and R-free of 0.198 and 0.247 respectively; the PDB deposition codes, coordinates and structure factors are 1GTK and R1GTKSF respectively. Finally a protein comparison study is presented of the Mycobacterium tuberculosis (MTb) HMBS, with the E. coli HMBS. This has been done as preparation for future structural studies on the MTb HMBS from this important disease bearing organism. The overall amino acid sequence identity is 41%. Most interestingly there is a two-residue reduction in length of the loop referred to above (Asp 50 and Gly 58 being missing in the MTb form). This gives the hope that this loop will be less flexible and thus might become visible to crystallographic analysis.

The properties of (2Fo - Fc) and (Fo - Fc) electron-density maps at medium-to-high resolutions

This paper reports on the efficacy of (F(o) - F(c)) versus (2F(o) - F(c)) electron-density maps at 3.2 A resolution. Firstly, a study is reported of a simple truncation at 2.3 and 3.2 A of the 1.6 A resolution crystal structure of concanavalin A at room temperature [Emmerich et al. (1994), Acta Cryst. D50, 749-756] with 149 known bound water molecules. Secondly, the concanavalin A 1.6 A resolution model was re-refined but with the data truncated to 3.2 A. In a similar evaluation, these procedures were repeated for the apocrustacyanin A1 cryotemperature 1.4 A resolution model [Cianci et al. (2001), Acta Cryst. D57, 1219-1229]. Maps at 1.4, 2.3 and 3.2 A resolutions were first generated and the structure was then re-refined at 3.2 A and additionally at 2.3 A resolution. The results on concanavalin A show that the number of bound water molecules that are resolved decreases by two thirds from 1.6 to 3.2 A, but that key structural waters, for example at the transition metal and the calcium ion, are still resolved in the (F(o) - F(c)) map but not in the (2F(o) - F(c)) map. For apocrustacyanin A1, the results with these two difference maps were less clear-cut. Two key structural bound waters (w93 and w105) were selected that had been previously identified in beta-crustacyanin [Cianci et al. (2002), Proc. Natl Acad. Sci. USA, 99, 9795-9800] in protein-carotenoid interactions. The behaviour of w93 is similar to that of concanavalin A key waters, but that of w105 is not. These behaviours were therefore explored in finer resolution increments, namely 2.9, 2.7 and 2.5 A. Finally, further tests on "real" data sets for peanut lectin and concanavalin A at medium resolution confirm these map properties, namely that an (F(o) - F(c)) difference electron-density map is more effective than a (2F(o) - F(c)) map in showing bound water structure at lower resolutions ( approximately 3.2 A). This result is important since a growing number of protein crystal structure studies are concerned with multi-macromolecular complexes and are at such resolutions. Details of the bound solvent can still be revealed at 3.2 A via the (F(o) - F(c)) map calculation. The physical basis of the limitation of the (2F(o) - F(c)) map presumably lies in the series-termination error effect on such a map involving the first negative ripple from the protein atom to which a bound water oxygen is hydrogen bonded, sufficiently cancelling its peak. In addition, re-refinements at 3.2 A show distances that can agree with known values but B values that do not agree with known values.

Microgravity protein crystallization: are we reaping the full benefit of outer space?

Protein crystallography, which has a growing role in the human genome project, is one of the most powerful techniques in modern biology. However, it can only be applied providing suitable crystals can be obtained. The ability to produce suitable crystals is currently the major bottleneck to structure determination. Microgravity, which is used as a tool for improving crystal growth, is a high-profile enterprise, especially with the upcoming prospects for utilizing the International Space Station, yet the issue of crystallization in microgravity is an extremely controversial one. In spite of numerous experiments conducted in microgravity during 16 years, the reported success rate, measured in terms of various improvements witnessed in the perfection of protein crystals, has been a mere 20%. In this paper we present experimental evidence, supporting previous fluid physics calculations to show that in many cases the potential benefits of the microgravity environment have not been fully exploited. These findings offer an explanation for the low rate of success and open up the possibility for enhancing the efficiency of experimentation in microgravity. Furthermore, these findings extend into a number of other disciplines involving fluid physics.

The molecular basis of the coloration mechanism in lobster shell: beta-crustacyanin at 3.2-A resolution

The binding of the carotenoid astaxanthin (AXT) in the protein multimacromolecular complex crustacyanin (CR) is responsible for the blue coloration of lobster shell. The structural basis of the bathochromic shift mechanism has long been elusive. A change in color occurs from the orange red of the unbound dilute AXT (lambda(max) 472 nm in hexane), the well-known color of cooked lobster, to slate blue in the protein-bound live lobster state (lambda(max) 632 nm in CR). Intriguingly, extracted CR becomes red on dehydration and on rehydration goes back to blue. Recently, the innovative use of softer x-rays and xenon derivatization yielded the three-dimensional structure of the A(1) apoprotein subunit of CR, confirming it as a member of the lipocalin superfamily. That work provided the molecular replacement search model for a crystal form of the beta-CR holo complex, that is an A(1) with A(3) subunit assembly including two bound AXT molecules. We have thereby determined the structure of the A(3) molecule de novo. Lobster has clearly evolved an intricate structural mechanism for the coloration of its shell using AXT and a bathochromic shift. Blue/purple AXT proteins are ubiquitous among invertebrate marine animals, particularly the Crustacea. The three-dimensional structure of beta-CR has identified the protein contacts and structural alterations needed for the AXT color regulation mechanism.

Spoilt for choice: protein target selection in a time of plenty

Experiences in the application of Boolean logic to the clusters of orthologous groups of proteins (COGs) database for target selection in the Mycobacterium tuberculosis genome are described.

New opportunities in biological and chemical crystallography

Banerjee [Proc. R. Soc. (1933), 141, 188-193] offered a new way of approaching the crystallographic phase problem which not only broke new ground beyond the 'trial and error' structure solution method of that time but also heralded the extremely powerful direct methods of crystallography of the modern era from the 1970s onwards in chemical crystallography. Some 200000 crystal structures are known today. More complex crystal structures such as proteins required new experimental and theoretical methods to solve the phase problem. These are still evolving, and new methods and results involving synchrotron radiation at softer X-ray wavelengths (2 A) are reported. In addition, an overview is given of the new opportunities that are possible for biological and chemical crystallography, especially via harnessing synchrotron radiation and neutron beams.

The combination of molecular dynamics with crystallography for elucidating protein-ligand interactions: a case study involving peanut lectin complexes with T-antigen and lactose

Peanut lectin binds T-antigen [Galbeta(1-3)GalNAc] with an order of magnitude higher affinity than it binds the disaccharide lactose. The crystal structures of the two complexes indicate that the higher affinity for T-antigen is generated by two water bridges involving the acetamido group. Fresh calorimetric measurements on the two complexes have been carried out in the temperature range 280-313 K. Four sets of nanosecond molecular-dynamics (MD) simulations, two at 293 K and the other two at 313 K, were performed on each of the two complexes. At each temperature, two somewhat different protocols were used to hydrate the complex in the two runs. Two MD runs under slightly different conditions for each complex served to assess the reliability of the approach for exploring protein-ligand interactions. Enthalpies based on static calculations and on MD simulations favour complexation involving T-antigen. The simulations also brought to light ensembles of direct and water-mediated protein-sugar interactions in both the cases. These ensembles provide a qualitative explanation for the temperature dependence of the thermodynamic parameters of peanut lectin-T-antigen interaction and for the results of one of the two mutational studies on the lectin. They also support the earlier conclusion that the increased affinity of peanut lectin for T-antigen compared with that for lactose is primarily caused by additional water bridges involving the acetamido group. The calculations provide a rationale for the observed sugar-binding affinity of one of the two available mutants. Detailed examination of the calculations point to the need for exercising caution in interpreting results of MD simulations: while long simulations are not possible owing to computational reasons, it is desirable to carry out several short simulations with somewhat different initial conditions.

Structure of lobster apocrustacyanin A1 using softer X-rays

The molecular basis of the camouflage colouration of marine crustacea is often provided by carotenoproteins. The blue colour of the lobster carapace, for example, is intricately associated with a multimacromolecular 16-mer complex of protein subunits each with a bound astaxanthin molecule. The protein subunits of crustacyanin fall into two distinct subfamilies, CRTC and CRTA. Here, the crystal structure solution of the A(1) protein of the CRTC subfamily is reported. The problematic nature of the structure solution of the CRTC proteins (both C(1) and A(1)) warranted consideration and the development of new approaches. Three putative disulfides per protein subunit were likely to exist based on molecular-homology modelling against known lipocalin protein structures. With two such subunits per crystallographic asymmetric unit, this direct approach was still difficult as it involved detecting a weak signal from these sulfurs and suggested the use of softer X-rays, combined with high data multiplicity, as reported previously [Chayen et al. (2000), Acta Cryst. D56, 1064-1066]. This paper now describes the structure solution of CRTC in the form of the A(1) dimer based on use of softer X-rays (2 A wavelength). The structure solution involved a xenon derivative with an optimized xenon L(I) edge f" signal and a native data set. The hand of the xenon SIROAS phases was determined by using the sulfur anomalous signal from a high-multiplicity native data set also recorded at 2 A wavelength. For refinement, a high-resolution data set was measured at short wavelength. All four data sets were collected at 100 K. The refined structure to 1.4 A resolution based on 60 276 reflections has an R factor of 17.7% and an R(free) of 22.9% (3137 reflections). The structure is that of a typical lipocalin, being closely related to insecticyanin, to bilin-binding protein and to retinol-binding protein. This A(1) monomer or dimer can now be used as a search motif in the structural studies of the oligomeric forms alpha- and beta-crustacyanins, which contain bound astaxanthin molecules.

Neutron Laue diffraction experiments on a large unit cell: concanavalin A complexed with methyl-α-D-glucopyranoside

A neutron Laue diffraction experiment on a complex of concanavalin A with methyl-α-D-glucopyranoside extensively soaked in D2O (space groupI213,a= 167.8 Å), which resulted in 3.5 Å diffraction data, is described. In a programme of structural studies of crystalline saccharide complexes of concanavalin A, the unit cell of the cubicI213 complex of concanavalin A with methyl-α-D-glucopyranoside is one of the largest. With its cell edge of 167.8 Å and its asymmetric unit of molecular weight 50 kDa, it represents a challenge for current neutron diffraction technology. The size of the crystal used in this experiment, although large (4 × 3 × 2 mm), was not the largest ever produced for this complex. The degree of spatial overlapping observed in the Laue experiment, however, suggests that use of larger crystals would be a disadvantage. On the basis of these observations, several technical improvements for macromolecular neutron crystallography are suggested.

The 1.2 A resolution structure of the Con A-dimannose complex

The complex between concanavalin A (Con A) and alpha1-2 mannobiose (mannose alpha1-2 mannose) has been refined to 1.2 A resolution. This is the highest resolution structure reported for any sugar-lectin complex. As the native structure of Con A to 0.94 A resolution is already in the database, this gives us a unique opportunity to examine sugar-protein binding at high resolution. These data have allowed us to model a number of hydrogen atoms involved in the binding of the sugar to Con A, using the difference density map to place the hydrogen atoms. This map reveals the presence of the protonated form of Asp208 involved in binding. Asp208 is not protonated in the 0.94 A native structure. Our results clearly show that this residue is protonated and hydrogen bonds to the sugar. The structure accounts for the higher affinity of the alpha1-2 linked sugar when compared to other disaccharides. This structure identifies different interactions to those predicted by previous modelling studies. We believe that the additional data presented here will enable significant improvements to be made to the sugar-protein modelling algorithms.

Integration of macromolecular diffraction data using radial basis function networks

This paper presents a novel approach for intensity calculation of X-ray diffraction spots based on a two-stage radial basis function (RBF) network. The first stage uses pre-determined reference profiles from a database as basis functions in order to locate the diffraction spots and identify any overlapping regions. The second-stage RBF network employs narrow basis functions capable of local modifications of the reference profiles leading to a more accurate observed diffraction spot approximation and therefore accurate determination of spot positions and integrated intensities.

Apocrustacyanin A1 from the lobster carotenoprotein alpha-crustacyanin: crystallization and initial X-ray analysis involving softer X-rays

The A1 subunit of the carotenoprotein alpha-crustacyanin, isolated from lobster carapace, has been crystallized using the vapour-diffusion method. The crystals, grown in solutions of ammonium sulfate containing methylpentanediol (MPD), diffracted to 2. 0 A. The crystals are stable to radiation. The space group of the crystals is P2(1)2(1)2(1). The unit-cell parameters are a = 41.9, b = 80.7, c = 110.8 A. 'Standard structure determination' has been unsuccessful within this crustacyanin family. Instead, an approach based on the S atoms is being undertaken involving softer X-rays at the SRS, Daresbury.

Synchrotron X-ray reciprocal-space mapping, topography and diffraction resolution studies of macromolecular crystal quality

A comprehensive study of microgravity and ground-grown chicken egg-white lysozyme crystals is presented using synchrotron X-ray reciprocal-space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed reduced intrinsic mosaicities on average, but no differences in terms of strain over their ground-grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the ground-control case only a small volume of the crystal contributed to the intensity at the diffraction peak. The techniques prove to be highly complementary, with the reciprocal-space mapping providing a quantitative measure of the crystal mosaicity and strain (or variation in lattice spacing) and the topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out at the synchrotron.

Direct determination of the positions of the deuterium atoms of the bound water in -concanavalin A by neutron Laue crystallography

The correct positions of the deuterium (D) atoms of many of the bound waters in the protein concanavalin A are revealed by neutron Laue diffraction. The approach includes cases where these water D atoms show enough mobility to render them invisible even to ultra-high resolution synchrotron-radiation X-ray crystallography. The positions of the bound water H atoms calculated on the basis of chemical and energetic considerations are often incorrect. The D-atom positions for the water molecules in the Mn-, Ca- and sugar-binding sites of concanavalin A are described in detail.

LSCALE– the new normalization, scaling and absorption correction program in the DaresburyLauesoftware suite

A new program in the DaresburyLauesoftware suite has been developed for the scaling and normalization of Laue intensity data, to yield fully corrected structure amplitudes. Previously available routines have been improved, and additional options for refinement, control and statistical diagnostic output provided. A new feature, namely a wavelength- and position-dependent absorption correction that models a two-dimensional surface derived from the Laue data alone, is discussed in detail; it is tested on simulated and real data, and the improvement in data quality is demonstrated. The wavelength normalization function is now able, when sufficiently redundant experimental data are available, to model fine details such as the features arising from the modification of the incident intensity spectrum by a platinum mirror in the beamline optics. A full data set for tetragonal lysozyme is processed with the new program, and extensive statistical output is given.

Bound-solvent structures for microgravity-, ground control-, gel- and microbatch-grown hen egg-white lysozyme crystals at 1.8 A resolution

A number of methods can be used to improve the stability of the protein crystal-growth environment, including growth in microgravity without an air-liquid phase boundary, growth in gels and growth under oil ('microbatch'). In this study, X-ray data has been collected from and structures refined for crystals of hen egg-white lysozyme (HEWL) grown using four different methods, liquid-liquid dialysis on Earth and in microgravity using the European Space Agency's (ESA) Advanced Protein Crystallization Facility (APCF) on board the NASA Space Shuttle Life and Microgravity Spacelab (LMS) mission (STS-78), crystallization in agarose gel using a tube liquid-gel diffusion method and crystallization in microbatch under oil. A comparison of the overall quality of the X-ray data, the protein structures and especially the bound-water structures has been carried out at 1.8 A. The lysozyme protein structures corresponding to these four different crystallization methods remain similar. A small improvement in the bound-solvent structure is seen in lysozyme crystals grown in microgravity by liquid-liquid dialysis, which has a more stable fluid physics state in microgravity, and is consistent with a better formed protein crystal in microgravity.

Determination of the structure of seleno-methionine-labelled hydroxymethylbilane synthase in its active form by multi-wavelength anomalous dispersion

The enzyme hydroxymethylbilane synthase (HMBS, E.C. 4.3.1.8) catalyzes the conversion of porphobilinogen into hydroxymethylbilane, a key intermediate for the biosynthesis of heme, chlorophylls, vitamin B12 and related macrocycles. The enzyme is found in all organisms, except viruses. The crystal structure of the selenomethionine-labelled enzyme ([SeMet]HMBS) from Escherichia coli has been solved by the multi-wavelength anomalous dispersion (MAD) experimental method using the Daresbury SRS station 9.5. In addition, [SeMet]HMBS has been studied by MAD at the Grenoble ESRF MAD beamline BM14 (BL19) and this work is described especially with respect to the use of the ESRF CCD detector. The structure at ambient temperature has been refined, the R factor being 16.8% at 2. 4 A resolution. The dipyrromethane cofactor of the enzyme is preserved in its reduced form in the crystal and its geometrical shape is in full agreement with the crystal structures of authentic dipyrromethanes. Proximal to the reactive C atom of the reduced cofactor, spherical density is seen consistent with there being a water molecule ideally placed to take part in the final step of the enzyme reaction cycle. Intriguingly, the loop with residues 47-58 is not ordered in the structure of this form of the enzyme, which carries no substrate. Direct experimental study of the active enzyme is now feasible using time-resolved Laue diffraction and freeze-trapping, building on the structural work described here as the foundation.

Purification, crystallization and initial X-ray analysis of the C1 subunit of the astaxanthin protein, V600, of the chondrophore Velella velella

The subunit C1 of the carotenoid-binding protein, V600, of the chondrophore Velella velella has been purified and crystallized. The crystals, which were grown by the vapour-diffusion method from ammonium sulfate as the major precipitant, diffract beyond 3 A and show little radiation damage over long periods (greater than 100 h) on a Cu Kalpha rotating-anode X-ray source. The space group of the crystals is P212121 with cell dimensions a = 42.0, b = 80.9, c = 110. 6 A.

CCD video observation of microgravity crystallization of lysozyme and correlation with accelerometer data

Lysozyme has been crystallized using the ESA Advanced Protein Crystallization Facility onboard the NASA Space Shuttle Orbiter during the IML-2 mission. CCD video monitoring was used to follow the crystallization process and evaluate the growth rate. During the mission some tetragonal crystals were observed moving over distances of up to 200 micrometers. This was correlated with microgravity disturbances caused by firings of vernier jets on the Orbiter. Growth-rate measurement of a stationary crystal (which had nucleated on the growth reactor wall) showed spurts and lulls correlated with an onboard activity: astronaut exercise. The stepped growth rates may be responsible for the residual mosaic block structure seen in crystal mosaicity and topography measurements.

Partial Improvement of Crystal Quality for Microgravity-Grown Apocrustacyanin C1

The protein apocrustacyanin C(1) has been crystallized by vapour diffusion in both microgravity (the NASA space shuttle USML-2 mission) and on the ground. Rocking width measurements were made on the crystals at the ESRF Swiss-Norwegian beamline using a high-resolution psi-circle diffractometer from the University of Karlsruhe. Crystal perfection was then evaluated, from comparison of the reflection rocking curves from a total of five crystals (three grown in microgravity and two earth controls), and by plotting mosaicity versus reflection signal/noise. Comparison was then made with previous measurements of almost 'perfect' lysozyme crystals grown aboard IML-2 and Spacehab-I and reported by Snell et al. [Snell, Weisgerber, Helliwell, Weckert, Hölzer & Schroer (1995). Acta Cryst. D51, 1099-1102]. Overall, the best diffraction-quality apocrustacyanin C(1) crystal was microgravity grown, but one earth-grown crystal was as good as one of the other microgravity-grown crystals. The remaining two crystals (one from microgravity and one from earth) were poorer than the other three and of fairly equal quality. Crystal movement during growth in microgravity, resulting from the use of vapour-diffusion geometry, may be the cause of not realising the 'theoretical' limit of perfect protein crystal quality.

Partial improvement of crystal quality for microgravity-grown apocrustacyanin C1

The protein apocrustacyanin C1 has been crystallized by vapour diffusion in both microgravity (the NASA space shuttle USML-2 mission) and on the ground. Rocking width measurements were made on the crystals at the ESRF Swiss-Norwegian beamline using a high-resolution psi-circle diffractometer from the University of Karlsruhe. Crystal perfection was then evaluated, from comparison of the reflection rocking curves from a total of five crystals (three grown in microgravity and two earth controls), and by plotting mosaicity versus reflection signal/noise. Comparison was then made with previous measurements of almost 'perfect' lysozyme crystals grown aboard IML-2 and Spacehab-1 and reported by Snell et al. [Snell, Weisgerber, Helliwell, Weckert, Holzer & Schroer (1995). Acta Cryst. D51, 1099-1102]. Overall, the best diffraction-quality apocrustacyanin C1 crystal was microgravity grown, but one earth-grown crystal was as good as one of the other microgravity-grown crystals. The remaining two crystals (one from microgravity and one from earth) were poorer than the other three and of fairly equal quality. Crystal movement during growth in microgravity, resulting from the use of vapour-diffusion geometry, may be the cause of not realising the 'theoretical' limit of perfect protein crystal quality.

Trends and challenges in experimental macromolecular crystallography

Macromolecular X-ray crystallography underpins the vigorous field of structural molecular biology having yielded many protein, nucleic acid and virus structures in fine detail. The understanding of the recognition by these macromolecules, as receptors, of their cognate ligands involves the detailed study of the structural chemistry of their molecular interactions. Also these structural details underpin the rational design of novel inhibitors in modern drug discovery in the pharmaceutical industry. Moreover, from such structures the functional details can be inferred, such as the biological chemistry of enzyme reactivity. There is then a vast number and range of types of biological macromolecules that potentially could be studied. The completion of the protein primary sequencing of the yeast genome, and the human genome sequencing project comprising some 105proteins that is underway, raises expectations for equivalent three dimensional structural databases.

Lysozyme Crystal Growth Kinetics Monitored Using a Mach–Zehnder Interferometer

A Mach-Zehnder interferometer has been developed for the monitoring of the kinetics of the diffusion process in protein crystal growth. This device can be used in conjunction with the ESA Advanced Protein Crystallization Facility (APCF), which allows experiments under microgravity conditions (e.g. on board the NASA Space Shuttle). Experimental trials on the ground have been carried out with the interferometer using the engineering model of the APCF and a protein dialysis reactor. Chicken egg-white lysozyme crystal growth, as a test, has thereby been monitored directly. The changes of concentration in the solution over time have been determined via the refractive index measurements made and subsequently correlated with visual monitoring of crystal growth in a repeat experiment.

MAD Phasing Strategies Explored with a Brominated Oligonucleotide Crystal at 1.65A Resolution

The crystal structure of a brominated oligonucleotide d(CGCG(Br)CG), chemical formula C(114)N(48)O(68)P(10)Br(2), has been analysed by multiwavelength anomalous dispersion (MAD) methods. The oligonucleotide crystallizes in space group P2(1)2(1)2(1) with a = 17.97, b = 30.98, c = 44.85 A, alpha = beta = gamma 90 degrees . Data to a resolution of 1.65 A were collected at four wavelengths about the K-absorption edge of the bromine atom (lambda(1) = 0.9323 A, a reference wavelength at the long-wavelength side of the edge; lambda(2) = 0.9192 A, at the absorption-edge inflection point; lambda(3) = 0.9185 A, at the ;white line' absorption maximum; lambda(4) = 0.8983 A, a reference wavelength at the short-wavelength side) using synchrotron radiation at Station PX9.5, SRS, Daresbury. Multiwavelength data could be collected on a single-crystal as the sample was radiation stable. Anomalous and dispersive Patterson maps were readily interpretable to give the bromine anomalous scatterer positions. Phase calculations to 1.65 A, resolution, using all four wavelengths, gave a figure of merit of 0.825 for 2454 reflections. The electron-density map was readily interpretable showing excellent connectivity for the sugar/phosphate backbone and each base was easily characterized. The two nucleotide strands paired up as expected in an antiparallel Watson-Crick-type manner. The structure was refined to 1.65 A using all the data (R-factor = 17.0% based on 3151 reflections, with a data-to-parameter ratio of 2.6). In addition to the four-wavelength analysis, a variety of other phasing strategies, and the associated quality of the resulting electron-density maps, were compared. These included use of either of the reference wavelength data sets in the two possible three-wavelength phasing combinations to assess their relative effectiveness. Moreover, the time dependence upon measuring the Bijvoet differences and its effect upon phasing was also investigated. Finally, the use of only two wavelengths, including Friedel pairs, is demonstrated (the theoretical minimum case); this is of particular interest when considering overall beam time needs and is clearly a feasible experimental strategy, as shown here.

Structure solution of a cubic crystal of concanavalin A complexed with methyl α-D-glucopyranoside

The solution of the cubic crystal form (a = 167.8 A) of concanavalin A complexed with the monosaccharide methyl alpha-D-glucopyranoside is described. The space group has been determined as I2(1)3 rather than I23. The use of cadmium to replace cobalt at the transition metal-ion binding site and to replace calcium at its binding site proved to be crucial to the successful solution of the crystal structure. The relatively small isomorphous signals of 21 e(-) for the replacement of cobalt and 28 e(-) for the replacement of calcium, yielded interpretable difference Patterson maps. The electron-density map calculated in space group I2(1)3 at 5.4 A resolution, based on phases derived from single- and double-substituted cadmium differences, revealed a classical concanavalin A tetramer of 222 point symmetry, as seen in all the known crystal structures of concanavalin A. Rigid-body refinement at 3.6 A using the refined coordinates of saccharide-free concanavalin A converged to an R factor of 27.4%. A molecular-replacement analysis, consistent with this crystal structure, and initial experiences in the incorrect space group I23 are described as these also prove to be instructive.

Self-association of a DNA loop creates a quadruplex: crystal structure of d(GCATGCT) at 1.8 A resolution

BACKGROUND

The flexibility of DNA enables it to adopt three interconvertible types of duplex termed the A-, B- and Z-forms. It can also produce hairpin loops, triplex structures and guanine-rich quadruplex structures. Conformational flexibility assists in the tight packaging of DNA, for example in chromosomes. This is important given the large quantity of genetic information that must be packaged efficiently. Moreover, the ability of DNA to specifically self-associate or interact with complementary sequences is fundamental to many biological processes. Structural studies provide information about DNA conformation and DNA-DNA interactions and suggest features that might be relevant to how the molecule performs its biological role.

RESULTS

We have characterized the structure of a synthetic heptanucleotide that folds into a novel loop structure. The loop is stabilized by association with a cation, by intra-strand hydrogen bonds between guanine and cytosine that are distinct from the normal Watson-Crick hydrogen bonds, and by van der Waals interactions. Two loops associate through the formation of four G.C pairs that exhibit pronounced base-stacking interactions. The formation of a symmetric A.A base pair further stabilizes loop dimerization. Stacking of the A.A pair on a symmetry-related A.A pairing assists the formation of a four-stranded assembly. A T.T pairing is also observed between symmetry-related loops.

CONCLUSIONS

This analysis provides a rare example of an experimentally determined non-duplex DNA structure. It provides conformational detail relevant to the tight packaging or folding of a DNA strand and illustrates how a cation might modulate phosphate-phosphate repulsion in a tightly packed structure. The observation of base quartets involving G.C base pairs suggests a further structure to be considered in DNA-DNA interactions. The structure also provides detailed geometries for A.A and T.T base pairs.

Time differences between friedel reflections: accuracy of crystal setting and requirements on beam stability

In synchrotron radiation data collections where the wavelength is carefully set to optimize f''-derived crystallography intensity differences (Friedel pairs), careful alignment of the crystal is useful to minimize the time differences of stimulation of the reflections in the pairs. This paper quantifies these time differences as a function of crystal misorientation, with typical parameters, using the angular velocity of the crystal. Likewise, the time spent in the diffraction condition is also calculated via the angular reflecting range for a common synchrotron beam geometry. These times offer the user direct insight into the time-dependent aspects of the diffraction measurements. This therefore allows the optimum conditions to be set up so as to extract as accurate anomalous differences as possible in the context of synchrotron radiation beam stability and lifetime.

Image-plate synchrotron laue data collection and subsequent structural analysis of a small test crystal of a nickel-containing aluminophosphate

Image plates have advantages over photographic films, which include wider dynamic range, higher detector quantum efficiency, reduced exposure time and large size. In this study, an on-line image-plate system has been used to record crystallographic data from a small crystal. In particular, synchrotron Laue data were recorded with lambda(min) = 0.455, lambda(max) = 1.180 A, in 20 images 10 degrees apart and with an exposure time of 0.3 s each from a crystal (0.02 x 0.05 x 0.25 mm) of a nickel-containing aluminophosphate, NiAPO. The Laue data were analyzed with the Daresbury Laue software, including the application of an absorption correction. The structure was solved by a combination of the Patterson method and successive difference Fourier calculations using SHELXS86 and SHELXL93; the final R value for 1934 unique reflections (all data) and 310 parameters was 7.90%. The structure agrees with that determined by monochromatic diffractometry using the same crystal and reported by Helliwell, Gallois, Kariuki, Kaucic & Helliwell [Acta Cryst. (1993), B49, 420-428] with an r.m.s. deviation of 0.03 A. Hence, this study shows the image-plate device to be very effective for synchrotron data collection and subsequent structure analysis from small crystals, i.e. 0.02 x 0.05 x 0.25 mm, in chemical crystallography as well as providing further confirmation of the practicability of Laue data in structure solution and refinement.

High-resolution structures of single-metal-substituted concanavalin A: the Co,Ca-protein at 1.6 Å and the Ni,Ca-protein at 2.0 Å

The molecular structures of cobalt- and nickel-substituted concanavalin A have been refined at 1.6 and 2.0 A resolution, respectively. Both metal derivatives crystallize in space group I222 with approximate cell dimensions a = 89, b = 87 and c = 63 A and one monomer in the asymmetric unit. The final R factor for Co-substituted concanavalin A is 17.8% for 29 211 reflections with F > 1.0sigma(F) between 8.0 and 1.6 A. For Ni-substituted concanavalin A the final R factor is 15.9% for 16 128 reflections with F > 1.0sigma(F) between 8.0 and 2.0 A resolution. Both structures contain a transition-metal binding site and a calcium-binding site but, unlike Cd-substituted concanavalin A, do not have a third metal-binding site. The Co-substituted concanavalin A structure diffracts to the highest resolution of any concanavalin A structure reported to date. A comparison of the structures of Ni-, Co-, Cd-substituted and native concanavalin A gives an indication of coordinate errors, which is a useful baseline for comparisons with saccharide complexes of concanavalin A described in other work. We also give a detailed account of multiple conformations which were found for five side-chain residues.

Distal pocket polarity in ligand binding to myoglobin: deoxy and carbonmonoxy forms of a threonine68(E11) mutant investigated by X-ray crystallography and infrared spectroscopy

The crystal structures of the deoxy and carbonmonoxy forms of a distal pocket myoglobin mutant in which valine68(E11) is replaced by threonine have been solved to 2.1- and 2.2-A resolution, respectively. This substitution has been shown previously to cause large decreases in the rate of oxygen binding and to lower the equilibrium association constants for O2 and CO. The synchrotron Laue method was used for the rapid acquisition of X-ray diffraction data to overcome problems caused by the very rapid rate of autooxidation of the mutant protein. The refined deoxy structure shows that the noncoordinated water molecule in the distal pocket is in a position to form strong hydrogen bonds with both the N epsilon-H of the distal histidine64 and O gamma of threonine68 with no other unexpected alterations in the protein structure. In the carbonmonoxy form, the bound ligand is well-defined and inclined away from the two hydrogen-bonding groups, refining to a position in which the Fe-C-O angle is 162 degrees. This value is very close to that previously observed in recombinant wild-type and position-64 (E7) mutants of sperm whale myoglobin (160-170 degrees). The similarity of the CO conformations contrasts with the 150-fold range in equilibrium binding constants (KCO) among the distal pocket myoglobin mutants and indicates that CO affinities cannot be predicted from the coordination geometry of the bound ligand. Furthermore, a comparison of the infrared stretching frequencies of CO in wild-type, valine64 and threonine68 single mutant, and valine64-threonine68 double mutant pig carbonmonoxymyoglobins shows a lack of correlation between KCO and vCO. These effects can be understood in terms of the stability of noncovalently bound water in deoxymyoglobin and electrostatic interactions between bound ligands and the distal pocket residues.