Discriminating between homodimeric and monomeric proteins in the crystalline state

Scores calculated from intermolecular contacts of proteins in the crystalline state are used to differentiate monomeric and homodimeric proteins, by classification into two categories separated by a cut-off score value. The generalized classification error is estimated by using bootstrap re-sampling on a nonredundant set of 172 water-soluble proteins whose prevalent quaternary state in solution is known to be either monomeric or homodimeric. A statistical potential, based on atom-pair frequencies across interfaces observed with homodimers, is found to yield an error rate of 12.5%. This indicates a small but significant improvement over the measure of solvent accessible surface area buried in the contact interface, which achieves an error rate of 15.4%. A further modification of the latter parameter relating the two most extensive contacts of the crystal results in an even lower error rate of 11.1%.     

Spectroscopic investigations of Panulirus interruptus hemocyanin in the crystalline state

Single-crystal ultraviolet spectroscopy, X-ray absorption spectroscopy and EPR measurements have been used to examine the oxidation and oxygenation state of the dinuclear copper site of several types of hemocyanin crystals. The crystals contain Panulirus interruptus hemocyanin which forms hexameric molecules with a molecular mass of approximately 470 kDa. Three types of crystals have been investigated. Type-I monoclinic crystals, which have been used for the X-ray structure determination, contain virtually only deoxyhemocyanin. Type-II monoclinic crystals, which are less well ordered than the type-I crystals, contain a mixture of deoxy, oxy and met forms. Older crystals contain relatively more methemocyanin. A third, hexagonal, crystal form is also partially oxygenated, and, like the type-II monoclinic form, subject to gradual conversion to methemocyanin.     

Inference of macromolecular assemblies from crystalline state

We discuss basic physical-chemical principles underlying the formation of stable macromolecular complexes, which in many cases are likely to be the biological units performing a certain physiological function. We also consider available theoretical approaches to the calculation of macromolecular affinity and entropy of complexation. The latter is shown to play an important role and make a major effect on complex size and symmetry. We develop a new method, based on chemical thermodynamics, for automatic detection of macromolecular assemblies in the Protein Data Bank (PDB) entries that are the results of X-ray diffraction experiments. As found, biological units may be recovered at 80-90% success rate, which makes X-ray crystallography an important source of experimental data on macromolecular complexes and protein-protein interactions. The method is implemented as a public WWW service.     

Three-dimensional structure of d(GGGATCCC) in the crystalline state.

The structure of the self-complementary octamer d(GGGATCCC) has been analysed by single crystal X-ray diffraction methods at a nominal resolution of 2.5 A. With acceptable stereochemistry of the model the crystallographic R factor was 16.6% after restrained least-squares refinement. In the crystal, d(GGGATCCC) forms an A-DNA double helix with slightly varying conformation of the two strands. The average displacement of the base pairs from the helix axis is unusually large and is accompanied by pronounced sliding of the base pairs along their long axes at all dinucleotide steps except for the central AT. With 12 base pairs per complete turn the helix is considerably underwound. As observed with most oligodeoxyribonucleotides analysed by X-ray crystallography so far, the octamer displays reduced base pair tilt, increased rise per base pair and a more open major groove compared with canonical A-DNA. We propose that, based on these parameters, three A-helical sub-families may be defined; d(GGGATCCC) then is a representative of the class with intermediate tilt, rise, and major groove width.     

Phosphate ion inactivation of rabbit skeletal muscle aldolase in the crystalline state

Catalytically active crystals of rabbit skeletal muscle aldolase are inactivated by phosphate ion and D-glyceraldehyde-3-phosphate. Four moles of phosphate are incorporated per mole of tetrameric enzyme. The inactivation rates are first order in time and demonstrate saturation behaviour. Competition inactivation experiments are consistent with the two substrates competing for the same site on the enzyme. Protection is afforded by substrates binding to the active site on the enzyme. No phosphate inactivation is observed in solution under identical experimental conditions and D-glyceraldehyde-3-phosphate inactivation in solution is unaffected by phosphate ion concentrations. Inactivation by phosphate is apparently due to an unique enzyme conformation stabilized upon protein crystallization.     

Dynamics of phosphatidylcholine-cholesterol mixed model membranes in the liquid crystalline state.

The effects of cholesterol on the dynamics of cholestane spin probe (CSL) in various phosphatidylcholine-cholesterol mixed model membranes are examined. The lateral diffusion, D of CSL in DMPC/POPC/cholesterol ternary mixtures, is measured utilizing an improved dynamic imaging electron spin resonance method. It shows a factor of two decrease at 10 mol % and 25 degrees C, whereas it shows only a 40% decrease at 50 mol % and 50 degrees C. A comparison with results in POPC/cholesterol mixtures, which show a stronger effect of cholesterol on D, indicates that acyl chain unsaturation leads to stronger self association of cholesterol in PC model membranes. An S2CSL dependence of the activation energy for D, has been confirmed for the DMPC/POPC/cholesterol mixtures. Here SCSL is the order parameter for CSL. A similar correlation of R perpendicular, the perpendicular component of the rotational diffusion coefficient, with SCSL, which is true for all three mixtures (DMPC/cholesterol, POPC/cholesterol, and DMPC/POPC/cholesterol) we have studied, is also found. These are associated with the effects of enhanced local ordering on the free volume needed for translation and reorientation. Such correlations of dynamic properties D and R perpendicular with the thermodynamic quantity S, as well as the consistent interpretations of the effect of acyl chain unsaturation on the dynamics in terms of the activity coefficients, strongly emphasize the interrelation between the dynamic structure and the thermodynamics of the PC/cholesterol mixtures.     

Aqueous trifluorethanol solutions simulate the environment of DNA in the crystalline state.

We took 28 fragments of DNA whose crystal structures were known and used CD spectroscopy to search for conditions stabilising the crystal structures in solution. All 28 fragments switched into their crystal structures in 60-80% aqueous trifluorethanol (TFE) to indicate that the crystals affected the conformation of DNA like the concentrated TFE. The fragments crystallising in the B-form also underwent cooperative TFE-induced changes that took place within the wide family of B-form structures, suggesting that the aqueous and crystal B-forms differed as well. Spermine and magnesium or calcium cations, which were contained in the crystallisation buffers, promoted or suppressed the TFE-induced changes of several fragments to indicate that the crystallisation agents can decide which of the possible structures is adopted by the DNA fragment in the crystal.     

The catalytic activity of muscle phosphoglucomutase in the crystalline phase

A suspension of microcrystals of phosphoglucomutase in 60% ammonium sulfate exhibits a maximal catalytic activity in substrate-velocity studies that is about 0.2 of that obtained with the soluble enzyme under the same conditions. The apparent Michaelis constants for the reaction in the crystal phase are altered to an even smaller extent, relative to that in solution, although the parameters for the monophosphate and bisphosphate are increased more than 3 and more than 5 orders of magnitude, respectively, by the sulfate present. The compatibility of larger crystals with a reaction that constitutes part of the catalytic process also is demonstrated.     

Conformation of 4-thio- -lyxono-1,4-lactone in solution and in the crystalline state

The conformation in ²H₂O of 4-thio- -lyxono-1,4-lactone (1) was studied by nuclear magnetic resonance spectroscopy, by means of homonuclear (J_1H,1H) and heteronuclear (J_1H,13C) coupling constants. The couplings were directly measured by a two-dimensional heteronucleus-coupled ω₁ hetero-half-filtered proton-proton correlation (HETLOC) experiment, which does not require ¹³C isotopic enrichment. In solution, the thiolactone ring of 1 adopts preferentially the E₃ conformation, and its hydroxymethyl group populates mainly the gt rotamer. The X-ray diffraction data of a single crystal of 1 indicates that also in the solid state the thiolactone ring adopts an E₃ conformation, with a puckering somewhat larger than that observed for aldono-1,4-lactones and furanose rings. The molecules are linked by hydrogen bonds, which form chains. Particularly, O-5 is fully engaged as donor and acceptor in hydrogen bonding and the rotameric conformation of the hydroxymethyl group of 1 is fixed in the tg form.     

Structure of GlyGly peptide in the crystalline state as studied by X-ray diffraction and solid state 13C-NMR methods

A new type of crystal of glycylglycine (GlyGly) hydrate was crystallized from an aqueous solution, and the structure of the crystal has been determined by x-ray diffraction. The crystal is monoclinic, and the space group is C2/c, with the cell constants of a = 15.941(2) Å, b = 4.774(2) Å, c = 19.428(2) Å and β = 109.884(7)° at 296 K. There are eight GlyGly molecules and six water solvent in the cell. The GlyGly molecules are packed in a parallel β-sheet arrangement. The single crystal was obtained with a maximum size of 10 × 7 × 4 mm and is not stable under atmospheric conditions. The transparent crystal turned to turbid with the elapse of time. The isotropic ¹³C chemical shifts obtained from the ¹³C cross polarization magic angle spinning nmr experiments reveal that GlyGly hydrate was changed into GlyGly (form α) by dehydration. © 1998 John Wiley & Sons, Inc. Biopoly 45: 333–339, 1998     

Dihydroxyacetone phosphate, DHAP, in the crystalline state: monomeric and dimeric forms

It was shown that dihydroxyacetone phosphate may exist in both monomeric DHAP (C₃H₇O₆P) and dimeric DHAP-dimer (C₆H₁₄O₁₂P₂) form. Monomeric DHAP was obtained in the form of four crystalline salts: CaCl(DHAP)·2.9H₂O (7a), Ca₂Cl₃(DHAP)·5H₂O (7b), CaCl(DHAP)·2H₂O (7c), and CaBr(DHAP)·5H₂O (7d) by crystallization from aqueous solutions containing DHAP acid and CaCl₂ or CaBr₂, or by direct crystallization from a solution containing DHAP precursor and CaCl₂. At least one of the salts is stable and may be stored in the crystalline state at room temperature for several months. The dimeric form was obtained by slow saturation of free DHAP syrup with ammonia at −18 °C and isolated in the form of its hydrated diammonium salt (NH₄)₂(DHAP-dimer)·4H₂O (8). The synthesis of the compounds, their crystallization, and crystal structures determined by X-ray crystallography are described. In all 7a-d monomeric DHAP exists in the monoanionic form in an extended (in-plane) cisoid conformation, with both hydroxyl and ester oxygen atoms being synperiplanar to the carbonyl O atom. The crucial structural feature is the coordination manner, in which the terminal phosphate oxygen atoms act as chelating as well as bridging atoms for the calcium cations. Additionally, the DHAP monoanions chelate another Ca²⁺ by the α-hydroxycarbonyl moiety, in a manner observed previously in dihydroxyacetone (DHA) calcium chloride complexes. In dimeric 8 the anion is a trans isomer with the dioxane ring in a chair conformation with the hydroxyl groups in axial positions and the phosphomethyl group in an equatorial position.