Solvent Content Of Crystals Research Articles

A general method for directly phasing diffraction data from high-solvent-content protein crystals.

A procedure is described for direct phase determination in protein crystallography, applicable to crystals with high solvent content. The procedure requires only the diffraction data and an estimate of the solvent content as input. Direct phase determination is treated as a constraint satisfaction problem, in which an image is sought that is consistent with both the diffraction data and generic constraints on the density distribution in the crystal. The problem is solved using an iterative projection algorithm, the Difference Map algorithm, which has good global convergence properties, and can locate the correct solution without any initial phase information. Computational efficiency is improved by breaking the problem down into two stages; initial approximation of the molecular envelope at low resolution, followed by subsequent phase determination using all of the data. The molecular envelope is continually updated during the phase determination step. At both stages, the algorithm is initiated with many different and random phase sets, which are evolved subject to the constraints. A clustering procedure is used to identify consistent results across multiple runs, which are then averaged to generate consensus envelopes or phase sets. The emergence of highly consistent phase sets is diagnostic of success. The effectiveness of the procedure is demonstrated by application to 42 known structures of solvent fraction 0.60-0.85. The procedure works robustly at intermediate resolutions (1.9-3.5 Å) but is strongly dependent on crystal solvent content, only working routinely with solvent fractions greater than 0.70.

Transmission electron microscopy for the evaluation and optimization of crystal growth.

The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that the presence of well ordered lattices with higher order Bragg spots, revealed by Fourier analysis of TEM images, is a good predictor of diffraction-quality crystals. Moreover, the use of TEM allowed (i) comparison of lattice quality among crystals from different conditions in crystallization screens; (ii) the detection of crystal pathologies that could contribute to poor X-ray diffraction, including crystal lattice defects, anisotropic diffraction and crystal contamination by heavy protein aggregates and nanocrystal nuclei; (iii) the qualitative estimation of crystal solvent content to explore the effect of lattice dehydration on diffraction and (iv) the selection of high-quality crystal fragments for microseeding experiments to generate reproducibly larger sized crystals. Applications to X-ray free-electron laser (XFEL) and micro-electron diffraction (microED) experiments are also discussed.

Synthesis, structure and electronic configuration of [Rh6Te8(PPh3)6]·4C6H6

Abstract [Rh6Te8(PPh3)6]·4C6H6, the first compound with a molecular Chevrel-type [Rh6Te8] cluster core has been synthesized and structurally characterized. By means of quantum chemical calculation, the close relationship of its electronic configuration to that of the lighter homologue has been demonstrated. The different crystal solvent content prevents an isostructural crystallization.

A survey of global radiation damage to 15 different protein crystal types at room temperature: a new decay model.

The radiation damage rates to crystals of 15 model macromolecular structures were studied using an automated radiation sensitivity characterization procedure. The diffracted intensity variation with dose is described by a two-parameter model. This model includes a strong resolution-independent decay specific to room-temperature measurements along with a linear increase in overall Debye-Waller factors. An equivalent representation of sensitivity via a single parameter, normalized half-dose, is introduced. This parameter varies by an order of magnitude between the different structures studied. The data show a correlation of crystal radiation sensitivity with crystal solvent content but no dose-rate dependency was detected in the range 0.05-300 kGy s(-1). The results of the crystal characterization are suitable for either optimal planning of room-temperature data collection or in situ crystallization plate screening experiments.

Substrate and Metal Ion Promiscuity in Mannosylglycerate Synthase

The enzymatic transfer of the sugar mannose from activated sugar donors is central to the synthesis of a wide range of biologically significant polysaccharides and glycoconjugates. In addition to their importance in cellular biology, mannosyltransferases also provide model systems with which to study catalytic mechanisms of glycosyl transfer. Mannosylglycerate synthase (MGS) catalyzes the synthesis of α-mannosyl-D-glycerate using GDP-mannose as the preferred donor species, a reaction that occurs with a net retention of anomeric configuration. Past work has shown that the Rhodothermus marinus MGS, classified as a GT78 glycosyltransferase, displays a GT-A fold and performs catalysis in a metal ion-dependent manner. MGS shows very unusual metal ion dependences with Mg(2+) and Ca(2+) and, to a lesser extent, Mn(2+), Ni(2+), and Co(2+), thus facilitating catalysis. Here, we probe these dependences through kinetic and calorimetric analyses of wild-type and site-directed variants of the enzyme. Mutation of residues that interact with the guanine base of GDP are correlated with a higher k(cat) value, whereas substitution of His-217, a key component of the metal coordination site, results in a change in metal specificity to Mn(2+). Structural analyses of MGS complexes not only provide insight into metal coordination but also how lactate can function as an alternative acceptor to glycerate. These studies highlight the role of flexible loops in the active center and the subsequent coordination of the divalent metal ion as key factors in MGS catalysis and metal ion dependence. Furthermore, Tyr-220, located on a flexible loop whose conformation is likely influenced by metal binding, also plays a critical role in substrate binding.

Crystallization and preliminary crystallographic analysis of the complex of the second and third regulatory subunits of human Pol δ

Human DNA polymerase delta (Pol delta) consists of four subunits: p125, p50, p66 and p12. A heterodimer containing a His-tagged p50 subunit (p50) and a p50-interacting domain of the p66 subunit (p66(N)) was crystallized. The crystal was in the form of a prism with a rhombic cross-section and belonged to space group P2(1). The crystal had unit-cell parameters a = 95.13, b = 248.54, c = 103.46 A, beta = 106.94 degrees and diffracted to a resolution of 3 A. Four molecules of p50-p66(N) in an asymmetric unit corresponded to a crystal solvent content of 72.2%.

Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals.

Estimating the number of molecules in the crystallographic asymmetric unit is one of the first steps in a macromolecular structure determination. Based on a survey of 15641 crystallographic Protein Data Bank (PDB) entries the distribution of V(M), the crystal volume per unit of protein molecular weight, known as Matthews coefficient, has been reanalyzed. The range of values and frequencies has changed in the 30 years since Matthews first analysis of protein crystal solvent content. In the statistical analysis, complexes of proteins and nucleic acids have been treated as a separate group. In addition, the V(M) distribution for nucleic acid crystals has been examined for the first time. Observing that resolution is a significant discriminator of V(M), an improved estimator for the probabilities of the number of molecules in the crystallographic asymmetric unit has been implemented, using resolution as additional information.

Heat transfer from protein crystals: implications for flash-cooling and X-ray beam heating.

Three problems involving heat transfer from a protein crystal to a cooling agent are analyzed: flash-cooling in a cold nitrogen- or helium-gas stream, plunge-cooling into liquid nitrogen, propane or ethane and crystal heating in a cold gas stream owing to X-ray absorption. Heat transfer occurs by conduction inside the crystal and by convection from the crystal's outer surface to the cooling fluid. For flash-cooling in cold gas streams, heat transfer is limited by the rate of external convection; internal temperature gradients and crystal strains during cooling are very small. Helium gas provides only a threefold improvement in cooling rates relative to nitrogen because its much larger thermal conductivity is offset by its larger kinematic viscosity. Characteristic cooling times vary with crystal size L as L(3/2) and theoretical estimates of these times are consistent with experiments. Plunge-cooling into liquid cryogens, which can give much smaller convective thermal resistances provided that surface boiling is eliminated, can increase cooling rates by more than an order of magnitude. However, the internal conduction resistance is no longer negligible, producing much larger internal temperature gradients and strains that may damage larger crystals. Based on this analysis, factors affecting the success of flash-cooling experiments can be ordered from most to least important as follows: (1) crystal solvent content and solvent composition, (2) crystal size and shape, (3) amount of residual liquid around the crystal, (4) cooling method (liquid plunge versus gas stream), (5) choice of gas/liquid and (6) relative speed between cooling fluid and crystal. Crystal heating by X-ray absorption on present high-flux beamlines should be small. For a fixed flux and illuminated area, heating can be reduced by using crystals with areas normal to the beam that are much larger than the beam area.

Structural studies of the Hrp secretion system: expression, purification, crystallization and preliminary X-ray analysis of the C-terminal domain of the HrcQB protein from Pseudomonas syringae pv. phaseolicola.

The C-terminal domain of the HrcQ(B) protein from the Hrp secretion system of the plant pathogenic bacterium Pseudomonas syringae pv. phaseolicola has been crystallized from MPD using the hanging-drop vapour-diffusion method. The crystals belong to space group P2(1), with unit-cell parameters a = 51.6, b = 27.3, c = 97.2 A and beta = 99.8 degrees. A complete native data set extending to 3.0 A resolution was collected from a single cryoprotected crystal. The crystal solvent content and calculation of self-rotation functions showing non-crystallographic twofold symmetry axes are consistent with the presence of an oligomeric assembly in the asymmetric unit.

Structural studies of streptococcus agalactiae hyaluronate lyase.

The bacteria Streptococcus agalactiae, part of normal human flora, produce an enzyme, hyaluronate lyase, which appears to contribute to the invasive capacity of this pathogen by degrading hyaluronan and chondroitin sulfates of the extracellular matrix of host tissues. The native enzyme, the product of the hylB(3502) allele, has a molecular mass of 111 kDa but undergoes an autocatalytic conversion to a smaller enzymatically active 92 kDa form. To initiate the determination of the catalytic mechanism of action of these enzymes, the 111 and 92 kDa enzymes were crystallized by a vapor-diffusion method using polyethylene glycol monomethyl ether 5000 and potassium thiocyanate as precipitating agents. The 111 kDa enzyme crystals are of poor quality and diffract X-rays to a very low resolution. However, the crystals of the truncated 92 kDa enzyme diffract X-rays to 2.1 A resolution. The crystal symmetry is C222(1) and the unit-cell parameters are a = 51.69, b = 157.03, c = 239.20 A (alpha = beta = gamma = 90 degrees ). The V(m) of 2.64 A(3) Da(-1) is consistent with the presence of one molecule of hyaluronate lyase in the asymmetric unit and a crystal solvent content of 53%. An isomorphous ethylmercuricthiosalicylic acid heavy-atom derivative diffraction data set has been obtained in order to solve the structure.

Structural Studies of a Crystalline Insulin Analog Complex with Protamine by Atomic Force Microscopy

Crystallographic studies of insulin–protamine complexes, such as neutral protamine Hagedorn (NPH) insulin, have been hampered by high crystal solvent content, small crystal dimensions, and extensive disorder in the protamine molecules. We report herein in situ tapping mode atomic force microscopy (TMAFM) studies of crystalline neutral protamine Lys B28Pro B29 (NPL), a complex of Lys B28Pro B29 insulin, in which the C-terminal prolyl and lysyl residues of human insulin are inverted, and protamine that is used as an intermediate time-action therapy for treating insulin-dependent diabetes. Tapping mode AFM performed at 6°C on bipyramidally tipped tetragonal rod-shaped NPL crystals revealed large micron-sized islands separated by 44-Å tall steps. Lattice images obtained by in situ TMAFM phase and height imaging on these islands were consistent with the arrangement of individual insulin–protamine complexes on the P4 12 12 (110) crystal plane of NPH, based on a low-resolution x-ray diffraction structure of NPH, arguing that the NPH and NPL insulins are isostructural. Superposition of the height and phase images indicated that tip-sample adhesion was larger in the interstices between NPL complexes in the (110) crystal plane than over the individual complexes. These results demonstrate the utility of low-temperature TMAFM height and phase imaging for the structural characterization of biomolecular complexes.

The Mannose-specific Bulb Lectin from Galanthus nivalis(Snowdrop) Binds Mono- and Dimannosides at Distinct Sites. Structure Analysis of Refined Complexes at 2.3 Å and 3.0 Å Resolution

Galanthus nivalisagglutinin (GNA, a 50 kDa tetramer) is a mannose-specific lectin of the Amaryllidaceae family of bulb lectins. Crystal structures of GNA complexed with methyl-α- D-mannose (MeMan) and mannose-α1,3- D- mannose-α-OMe (MeMan-2) have been determined and analyzed in terms of internal structural symmetry and saccharide binding. The final model of the 2.29 Å orthorhombic Δmethyl-α-Man complex refined with an R-factor of 0.167 (all data) includes 12 bound sugar ligands and 327 water molecules. The four independent subunits (A, B, C and D) of the 222 tetramer and the three four-stranded β-sheets (I,II and III) that constitute each subunit compare closely (r.m.sΔ=<1.0 Å). The 12 bound methyl-α- Man molecules refined with B-factors <22 Å 2and occupancies in the range of 0.5 to 1.0. The highest occupied site is located in β-sheet I (site 1), where interactions from the dimer-related subunit contribute to complex stabilization. These subunit pairs (A-D and B-C) associate tightly with a buried surface area of 1738 Å 2and 33 interchain hydrogen bonds resulting from C-terminal strand exchange. In comparison, the A-B and C-D subunit pairs have narrow interfaces (476 Å 2) and no direct H-bond contacts. The 3.0 Å structure of the cubic Man-α1,3-Man-OMe complex, determined by molecular replacement and refined with X-PLOR using NCS constraints and density modification methods, is less well ordered due to a high crystal solvent content (68%). Complexed disaccharide is responsible for the most crucial lattice contacts, which involve only one of the two independent subunits (A). The second subunit (C) shows a high degree of flexibility ( B av=41.7 Å 2). The complete disaccharide molecule is visible in both subunits at site 3, which is the only extended site. The ligand is oriented with its reducing end positioned in the specificity pocket. The non-reducing mannose is in contact through hydrogen bonding with a charged subsite (D37-K38) on the 2-fold-related subunit (A-B or C-D interfaces). Bound Man-α1,3-MeMan is also well defined in site 2 of subunit A, as a result of favorable lattice contacts, while only the mannose residue bound in the specificity pocket is visible at site 2 of subunit C and site 1 of both subunits. Together these results suggest that strong binding correlates with the presence of subsidiary contacts coming either from a dimer-related subunit or from lattice interactions. Site 1 is most specific for terminal non-reducing or reducing mannose, while site 3 is extended and complementary to α-1,3 linked mannose oligosaccharides.

Nitrogen inversion in 9- O-Demethylhomolycorine

(+)-9- O-Demethylhomolycorine, which has been isolated from Galanthus elwesii, belongs to Amaryllidaceae alkaloids. From five different subfractions five different crystalline samples were observed, all their spectra are superimposible with each other. Two of them, 1b and 1c, differ in the configuration at the N-atom. The other samples differ by changing solvent content in crystals.

Preliminary Analysis of Crystals of 4-Oxalocrotonate Tautomerase, an Enzyme Composed of Unusually Small Monomers

Crystals of 4-oxalocrotonate tautomerase have been obtained by the vapor-diffusion method using polyethylene glycol as precipitant. The crystals belong to the orthorhombic space group P 2 12 12 1, with unit cell parameters a = 118·1, b = 95·6, c = 97·4, α = β = γ = 90° and diffract well to at least 2·7 Å resolution. There are approximately ten 6811 dalton subunits of the enzyme per asymmetric unit, giving a crystal solvent content of 70%.

The growth and characterization of crystals of human immunodeficiency virus (HIV) reverse transcriptase

Extensive studies on the crystallization of HIV-1 reverse transcriptase (RT) have yielded several crystal forms, two of which show diffraction to minimum Bragg spacings of 6 Å or better. Type 1 crystals belong to the space group P2 12 12 1 with unit cell dimensions a = 147 A ̊ , b = 190 A ̊ and c = 182 A ̊ . Crystal density measurement indicate a very high crystal solvent content of 77% consistent with the presence of two RT heterodimers (66k/51k) per crystallographic asymmetric unit. These crystals are suitable for a low resolution determination of the apoenzyme structure. The second well ordered crystal form (space group P4 222 with unit cell dimensions a = b = 120 A ̊ , c = 320 A ̊ ) results from the co-crystallization of RT heterodimer and a double-stranded DNA oligonucleotide. Crystal density measurements again yield a relatively high value for the solvent content (7%; one RT heterodimer per crystallographic asymmetric unit) and elemental analysis indicates that one DNA oligonucleotide is associated with each RT heterodimer. This is consistent with each heterodimer possessing a single, competent, active site.