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PubMed1997

The polymorphic drug substances of the European pharmacopoeia. Part 9. Physicochemical properties and crystal structure of acetazolamide crystal forms.

The crystal structure of acetazolamide modification I (mod. I) was determined, and its differences compared with the already known crystal structure of the triclinic modification II (mod. II) are discussed. The monoclinic mod. I crystallizes in space group P2(1)/n with four molecules in the unit cell: a = 4.7674, b = 21.956, and c = 8.186 A, beta = 104.23 degrees. In both modifications, the molecules form hydrogen-bonded centrosymmetric dimers. The two modifications differ distinctly in the spatial arrangement of these pairs and in the hydrogen bonds formed between them. The thermodynamic relationship between the two modifications is demonstrated by a semischematic energy/temperature diagram, based on the results of thermal analysis and solubility experiments. Mod. II is the thermodynamically stable modification at 20 degrees C and enantiotropically related to mod. I. The thermodynamic transition point lies between 120 and 148 degrees C. The solid-state properties of acetazolamide are mainly directed by the strong intermolecular hydrogen bond forces. Thus, the metastable mod. I exhibits a higher density than mod. II and a very high kinetic stability at 20 degrees C. Both modifications can be crystallized from water and the solubility differences are very small, so, in addition to mod. II, the metastable but extremely resistant mod. I is suggested to be suitable for use in solid pharmaceutical formulations.

Acetazolamide↗
PubMed1997

1H and 15N NMR assignment and solution structure of the SH3 domain of spectrin: comparison of unrefined and refined structure sets with the crystal structure.

The assignment of the 1H and 15N nuclear magnetic resonance spectra of the Src-homology region 3 domain of chicken brain alpha-spectrin has been obtained. A set of solution structures has been determined from distance and dihedral angle restraints, which provide a reasonable representation of the protein structure in solution, as evaluated by a principal component analysis of the global pairwise root-mean-square deviation (rmsd) in a large set of structures consisting of the refined and unrefined solution structures and the crystal structure. The solution structure is well defined, with a lower degree of convergence between the structures in the loop regions than in the secondary structure elements. The average pairwise rmsd between the 15 refined solution structures is 0.71 +/- 0.13 A for the backbone atoms and 1.43 +/- 0.14 A for all heavy atoms. The solution structure is basically the same as the crystal structure. The average rmsd between the 15 refined solution structures and the crystal structure is 0.76 A for the backbone atoms and 1.45 +/- 0.09 A for all heavy atoms. There are, however, small differences probably caused by intermolecular contacts in the crystal structure.

Amino Acid Sequence↗
PubMed2005

Effect of pressure on the crystal structure of L-serine-I and the crystal structure of L-serine-II at 5.4 GPa.

The crystal structure of L-serine has been determined at room temperature at pressures between 0.3 and 4.8 GPa. The structure of this phase (hereafter termed L-serine-I), which consists of the molecules in their zwitterionic tautomer, is orthorhombic, space group P212121. The least compressible cell dimension (c), corresponds to chains of head-to-tail NH...carboxylate hydrogen bonds. The most compressible direction is along b, and the pressure-induced distortion in this direction takes the form of closing up voids in the middle of R-type hydrogen-bonded ring motifs. This occurs by a change in the geometry of hydrogen-bonded chains connecting the hydroxyl groups of the -CH2OH side chains. These hydrogen bonds are the longest conventional hydrogen bonds in the system at ambient pressure, having an O...O separation of 2.918 (4) A and an O...O...O angle of 148.5 (2) degrees ; at 4.8 GPa these parameters are 2.781 (11) and 158.5 (7) degrees . Elsewhere in the structure one NH...O interaction reaches an N...O separation of 2.691 (13) A at 4.8 GPa. This is amongst the shortest of this type of interaction to have been observed in an amino acid crystal structure. Above 4.8 GPa the structure undergoes a single-crystal-to-single-crystal phase transition to a hitherto uncharacterized polymorph, which we designate L-serine-II. The OH...OH hydrogen-bonded chains of L-serine-I are replaced in L-serine-II by shorter OH...carboxyl interactions, which have an O...O separation of 2.62 (2) A. This phase transition occurs via a change from a gauche to an anti conformation of the OH group, and a change in the NCalphaCO torsion angle from -178.1 (2) degrees at 4.8 GPa to -156.3 (10) degrees at 5.4 GPa. Thus, the same topology appears in both crystal forms, which explains why it occurs from one single-crystal form to another. The transition to L-serine-II is also characterized by the closing-up of voids which occur in the centres of other R-type motifs elsewhere in the structure. There is a marked increase in CH...O hydrogen bonding in both phases relative to L-serine-I at ambient pressure.

Crystallography↗
PubMed2001

Preferential enrichment: an essential crystal structure.

The crystal structure of (+/-)-[2-[4-(2-hydroxyhexyloxy)phenylcarbamoyl]ethyl]dimethylsulfonium p-chlorobenzenesulfonate [(+/-)-SCC], which failed to effect preferential enrichment due to the chemical modification of the prototype (+/-)-[2-[4-(3-ethoxy-2- hydroxypropoxy)phenylcarbamoyl]ethyl]dimethylsulfonium p-chlorobenzenesulfonate [(+/-)-SC] showing preferential enrichment, has been determined by x-ray crystallographic analysis. The crystalline form of (+/-)-SCC is not a mixed crystal of the two enantiomers, but a racemic compound. In addition, the revised crystal structures of (+/-)-[2-[4-(3-ethoxy-2-hydroxypropoxy)phenylcarbamoyl]ethyl] dimethylsulfonium p-toluenesulfonate [(+/-)-ST] and (+/-)-SC, both of which showed preferential enrichment, are described. The crystal structure of (+/-)-SCC is different from that of (+/-)-SC, but very similar to that of (+/-)-ST. The formation of the crystal phase of the (+/-)-SC type, which can be followed by polymorphic transition to afford the crystal one of (+/-)-ST type if necessary, seems to be essential for successful preferential enrichment.

Journal Article↗
PubMed2002

Observation of an arsenic adduct in an acetyl esterase crystal structure.

The crystal structures of an acetyl esterase, HerE, and its complex with an inhibitor dimethylarsinic acid have been determined at 1.30- and 1.45-A resolution, respectively. Although the natural substrate for the enzyme is unknown, HerE hydrolyzes the acetyl groups from heroin to yield morphine and from phenyl acetate to yield phenol. Recently, the activity of the enzyme toward heroin has been exploited to develop a heroin biosensor, which affords higher sensitivity than other currently available detection methods. The crystal structure reveals a single domain with the canonical alpha/beta hydrolase fold with an acyl binding pocket that snugly accommodates the acetyl substituent of the substrate and three backbone amides that form a tripartite oxyanion hole. In addition, a covalent adduct was observed between the active site serine and dimethylarsinic acid, which inhibits the enzyme. This crystal structure provides the first example of an As-containing compound in a serine esterase active site and the first example of covalent modification of serine by arsenic. Thus, the HerE complex reveals the structural basis for the broad scope inhibition of serine hydrolases by As(V)-containing organic compounds.

Acetylesterase↗
PubMed2005

Same structure, different function crystal structure of the Epstein-Barr virus IL-10 bound to the soluble IL-10R1 chain.

Human IL-10 (hIL-10) is a cytokine that modulates diverse immune responses. The Epstein-Barr virus (EBV) genome contains an IL-10 homolog (vIL-10) that shares high sequence and structural similarity with hIL-10. Although vIL-10 suppresses inflammatory responses like hIL-10, it cannot activate many other immunostimulatory functions performed by the cellular cytokine. These functional differences have been correlated with the approximately 1000-fold lower affinity of vIL-10, compared to hIL-10, for the IL-10R1 receptor chain. To define the structural basis for these observations, crystal structures of vIL-10 and a vIL-10 point mutant were determined bound to the soluble IL-10R1 receptor fragment (sIL-10R1) at 2.8 and 2.7 A resolution, respectively. The structures reveal that subtle changes in the conformation and dynamics of the vIL-10 AB and CD loops and an orientation change of vIL-10 on sIL-10R1 are the main factors responsible for vIL-10's reduced affinity for sIL-10R1 and its distinct biological profile.

Amino Acid Sequence↗
PubMed1992

Alpha-beta-dehydro-amino acid residues in the design of peptide structures. Molecular and crystal structures of two folded dehydro peptides.

The molecular and crystal structures of two N alpha-protected tripeptide amides, containing in the central position the alpha-beta-dehydro-amino acid residue delta Phe (Z-configurational isomer), were determined by X-ray diffraction. While Z-Gly-delta Phez-L-Pro-NH2 is characterized in the crystal state by the presence of a type I beta-bend conformation (at the delta Phez-L-Pro sequence), Z-D-Ala-delta Phez-Gly-NH2 is folded into two consecutive beta-bends (type II' followed by type I), at the D-Ala-delta Phez and delta Phez-Gly sequences, respectively. In both cases the achiral delta Phez residue adopts a set of phi, psi angles typical of the right-handed helical conformation. The delta Phe residue may be exploited to design aromatic peptides with preferred secondary structures.

Amino Acid Sequence↗
PubMed1987

Crystal structure of two crystal forms of 9 alpha-fluorocortisol acetate: variation of the conformation of the A ring of steroids due to crystal packing.

This paper reports the crystal structure of the propanol solvate of 9 alpha-fluorocortisol acetate, which crystallizes in the monoclinic space group P21 [a = 7.470 (6), b = 14.78 (1), c = 12.310 (9), beta = 105.2 degrees, Z = 2, R = 0.061, and the tetragonal unsolvated crystal form (a = b = 9.208 (2), c = 49.284 (9), P4(1)2(1)2, Z = 8, R = 0.050)]. The molecular structure of fluorocortisol acetate in the two crystal forms differs primarily in the A ring and acetoxy orientation. The A ring of the steroid in the tetragonal crystal was found to be disordered, and exists in both a normal and inverted conformation. The A ring of the steroid in the monoclinic propanol solvate has the normal (1 alpha, 2 beta half-chain) conformation. The differences in the conformation of the side chain and the A ring appear to reflect the conformational variability in 9 alpha-fluorocortisol acetate.

Fludrocortisone↗
PubMed2001

Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction.

The crystal structure of a novel Cre-Lox synapse was solved using phases from multiple isomorphous replacement and anomalous scattering, and refined to 2.05 A resolution. In this complex, a symmetric protein trimer is bound to a Y-shaped three-way DNA junction, a marked departure from the pseudo-4-fold symmetrical tetramer associated with Cre-mediated LoxP recombination. The three-way DNA junction was accommodated by a simple kink without significant distortion of the adjoining DNA duplexes. Although the mean angle between DNA arms in the Y and X structures was similar, adjacent Cre trimer subunits rotated 29 degrees relative to those in the tetramers. This rotation was accommodated at the protein-protein and DNA-DNA interfaces by interactions that are "quasi-equivalent" to those in the tetramer, analogous to packing differences of chemically identical viral subunits at non-equivalent positions in icosahedral capsids. This structural quasi-equivalence extends to function as Cre can bind to, cleave and perform strand transfer with a three-way Lox substrate. The structure explains the dual recognition of three and four-way junctions by site-specific recombinases as being due to shared structural features between the differently branched substrates and plasticity of the protein-protein interfaces. To our knowledge, this is the first direct demonstration of quasi-equivalence in both the assembly and function of an oligomeric enzyme.

Attachment Sites, Microbiological↗
PubMed2006

A crystal structure study when crystallized only in d(CG)3 + methylamine and a d(CG)3 + metal ion.

There is not an example of the crystallization only of d(CG)(3) and a metallic cation without putting the amine in addition in there is no example of the crystallization d(CG)(3) with methylamine that is the mono-amine so far either. We were able to obtain a very beautiful crystal with all sides of 0.3mm by the sitting drop method that had done the crystallization of d(CG)(3)+ methylamine and d(CG)(3)+ Mg(2 +). The crystal was diffracted up to 1.0 A by using the synchrotron radiation. As a result of the X-ray crystal structure analysis, methylamine was not seen while d(CG)(3)+ methylamine was crystallizing mysteriously. d(CG)(3) had stabilized with five Mg(2+) ions. d(CG)(3) had stabilized similarly with five Mg(2+) ions in the crystal of d(CG)(3)+ Mg(2+). The position of these five Mg(2+) ions understood that I agreed on superimpose in a crystal of d(CG)(3) + methylamine, a crystal of d(CG)(3)+Mg(2+), a crystal of d(CG)(3) + spermidine, and crystals of d(CG)(3) + PA (24) which was already analyzed so as to cut it and stabilized d(CG)(3) at an about the same position.

Cations↗
PubMed2000

Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B<-->A intermediate crystal structure.

The crystal structure of d(CATGGGCCCATG)(2) shows unique stacking patterns of a stable B<-->A-DNA intermediate. We evaluated intrinsic base stacking energies in this crystal structure using an ab initio quantum mechanical method. We found that all crystal base pair steps have stacking energies close to their values in the standard and crystal B-DNA geometries. Thus, naturally occurring stacking geometries were essentially isoenergetic while individual base pair steps differed substantially in the balance of intra-strand and inter-strand stacking terms. Also, relative dispersion, electrostatic and polarization contributions to the stability of different base pair steps were very sensitive to base composition and sequence context. A large stacking flexibility is most apparent for the CpA step, while the GpG step is characterized by weak intra-strand stacking. Hydration effects were estimated using the Langevin dipoles solvation model. These calculations showed that an aqueous environment efficiently compensates for electrostatic stacking contributions. Finally, we have carried out explicit solvent molecular dynamics simulation of the d(CATGGGCCCATG)(2) duplex in water. Here the DNA conformation did not retain the initial crystal geometry, but moved from the B<-->A intermediate towards the B-DNA structure. The base stacking energy improved in the course of this simulation. Our findings indicate that intrinsic base stacking interactions are not sufficient to stabilize the local conformational variations in crystals.

Base Composition↗
PubMed1991

Refined crystal structure of ytterbium-substituted carp parvalbumin 4.25 at 1.5 A, and its comparison with the native and cadmium-substituted structures.

The crystal structure of carp parvalbumin 4.25 containing a 1:1 molar ratio of ytterbium chloride to protein has been refined at 1.5 A resolution by restrained least-squares methods to a crystallographic R value of 0.199. The crystal structure confirms the NMR studies, which suggest that low concentrations of ytterbium cause an extensive displacement of calcium from the EF metal binding site. A comparison of the ytterbium-substituted model with the native and cadmium-substituted structure show no significant differences, except around the substituted EF metal-binding region. The displacement of calcium by ytterbium at the EF site has caused a movement in the polypeptide backbone of Ser-91 and Asp-92. This movement resulted in an increase in the number of oxygen ligands bound to ytterbium in the EF site from seven to eight.

Amino Acid Sequence↗
PubMed1996

Inter-ring communication is disrupted in the GroEL mutant Arg13 --> Gly; Ala126 --> Val with known crystal structure.

The crystal structures of the chaperonin GroEL Arg13 --> Gly; Ala126 --> Val double mutant, without and in complex with ATP gamma S, have been determined at atomic resolution. Here, we show that the double mutation Arg13 --> Gly; Ala126 --> Val disrupts negative co-operativity between GroEL rings, with respect to ATP, but has little effect on the positive co-operativity within each ring. Our results help to explain why the double mutation facilitated the crystallization of GroEL and why breaking of dyad symmetry between rings is not observed in crystal structures of this mutant. Our results may also help to explain why the observed structural differences between the GroEL double mutant and its ATP gamma S-bound form are small.

Adenosine Triphosphate↗
PubMed2000

Analysis of the kinetic and redox properties of the NADH peroxidase R303M mutant: correlation with the crystal structure.

The crystal structure of the flavoprotein NADH peroxidase shows that the Arg303 side chain forms a hydrogen bond with the active-site His10 imidazole and is therefore likely to influence the catalytic mechanism. Dithionite titration of an R303M mutant [E(FAD, Cys42-sulfenic acid)] yields a two-electron reduced intermediate (EH(2)) with enhanced flavin fluorescence and almost no charge-transfer absorbance at pH 7.0; the pK(a) for the nascent Cys42-SH is increased by over 3.5 units in comparison with the wild-type EH(2) pK(a) of </=4.5. NADH titration of the mutant peroxidase yields the same EH(2) intermediate, but in contrast to the behavior of wild-type enzyme, this species can be reduced directly to an EH(4).NAD(+) complex. Kinetic analyses demonstrate that the R303M mutant is severely compromised, although active, with k(cat) = 3 s(-)(1) at pH 7.0, 5 degrees C; enzyme-monitored turnover results indicate that the steady-state consists predominantly of an E-FADH(2).NAD(+) species. When the oxidized mutant is reacted anaerobically with 0.9 equiv of NADH/FAD, a clearly biphasic pattern is observed at 450 nm; relatively rapid flavin reduction is followed by reoxidation at 2.6-2.7 s(-)(1) ( approximately k(cat)). Thus replacement of Arg303 with Met leads to an altered peroxidase form in which the rate-limiting step in turnover is the intramolecular transfer of electrons from FADH(2) --> Cys42-SOH. The crystal structure of the R303M peroxidase has been refined at 2.45 A resolution. In addition to eliminating the Arg303 interactions with His10 and Glu14, the mutant exhibits a significant change in the conformation of the Cys42-SOH side chain relative to FAD and His10 in particular. These and other results provide a detailed understanding of Arg303 and its role in the structure and mechanism of this unique flavoprotein peroxidase.

Amino Acid Substitution↗
PubMed2005

Hydrothermal single-crystal growth in the systems Ag/Hg/X/O (X = VV, AsV): crystal structures of (Ag3Hg)VO4, (Ag2Hg2)3(VO4)4, and (Ag2Hg2)2(HgO2)(AsO4)2 with the unusual tetrahedral cluster cations (Ag3Hg)3+ and (Ag2Hg2)4+ and crystal structure of AgHgVO4.

Single crystals of (Ag3Hg)VO4 (I), (Ag2Hg2)3(VO4)4 (II), AgHgVO4 (III), and (Ag2Hg2)2(HgO2)(AsO4)2 (IV) were grown under hydrothermal conditions (250 degrees C, 5 d) from starting mixtures of elementary mercury, silver nitrate, ammonium vanadate, and disodium hydrogenarsenate, respectively. All crystal structures were determined from X-ray diffraction data, and their chemical compositions were confirmed by electron microprobe analysis. I crystallizes in the tillmannsite structure, whereas II-IV adopt new structure types: (I) I4, Z = 2, a = 7.7095(2) A, c = 4.6714(2) A, 730 structure factors, 24 parameters, R[F2 > 2sigma(F2)] = 0.0365; (II) I42d, Z = 4, a = 12.6295(13) A, c = 12.566(3) A, 1524 structure factors, 55 parameters, R[F2 > 2sigma(F2)] = 0.0508; (III) C2, Z = 4, a = 9.9407(18) A, b = 5.5730(8) A, c = 7.1210(19) A, beta = 94.561(10) degrees , 1129 structure factors, 48 parameters, R[F2 > 2sigma(F2)] = 0.0358; (IV) P31c, Z = 2, a = 6.0261(9) A, c = 21.577(4) A, 1362 structure factors, 52 parameters, R[F2 > 2sigma(F2)] = 0.0477. The most striking structural features of I, II, and IV are the formation of tetrahedral cluster cations (Ag3Hg)3+ and (Ag2Hg2)4+, respectively, built of statistically distributed Ag and Hg atoms with a metal-metal distance of about 2.72 A. The electronic structure of these clusters can formally be considered as two-electron-four-center bonding. The crystal structure of III differs from the protrusive structure types insofar as silver and mercury are located on distinct crystallographic sites without a notable metal-metal interaction >3.55 A. All crystal structures are completed by tetrahedral oxo anions XO4(3-) (X = VV, AsV) and for IV additionally by a mercurate group, HgO2(2-).

Journal Article↗
PubMed2005

Exhaustively methylated azacalix[4]arene: preparation, conformation, and crystal structure with exclusively CH/pi-controlled crystal architecture.

[structure: see text]. Described are the preparation, conformation, and crystal structure of exhaustively methylated azacalix[4]arene involving nitrogen atoms as bridging units. NMR and X-ray crystallographic analysis have demonstrated that this novel azacalix[4]arene adopts a 1,3-alternate conformation both in solution and in the solid state. The crystal structure has been characterized solely by intermolecular CH/pi interactions, by which the azacalix[4]arenes mutually interact with each other outside the cavity to furnish a two-dimensional network structure.

Journal Article↗
PubMed1984

Human alpha 1-proteinase inhibitor. Crystal structure analysis of two crystal modifications, molecular model and preliminary analysis of the implications for function.

Two closely related crystal structures of alpha 1-proteinase inhibitor modified at the reactive site peptide bond Met358--Ser359 have been analysed. The crystal structure has been obtained from diffraction data at 3 A resolution, with phases originally from isomorphous replacement. The electron density map was substantially improved by cyclic averaging of the electron densities of the two crystal forms and allowed the chain to be traced in terms of the known chemical amino acid sequence. Energy restrained crystallographic refinement was initiated and resulted in conventional R-values of 0.251 for the tetragonal crystal form (6 to 3 A resolution) and 0.247 for the hexagonal crystal form (6 to 3.2 A resolution). The polypeptide chain is almost completely arranged in well-defined secondary structural elements: three beta-sheets and eight alpha-helices. The helices are preferentially formed by the first 150 residues. They are in proximity underneath sheet A. The chain ends Met358 and Ser359 of the nicked species are arranged in strands on opposite ends of the molecule indicating a major structural rearrangement upon modification of the intact inhibitor. It is suggested that the Met358 strand is in a different conformation removed from sheet A and approaches Ser359 in the intact inhibitor species. Glu342, which is exchanged by a lysine in the Z-variant is in a strategic position for such a rearrangement. The three carbohydrate chains of alpha 1-proteinase inhibitor have partly defined electron density close to their attachment sites at asparagine residues. The anti-thrombin and ovalbumin amino acid sequences can be accommodated in the alpha 1 inhibitor molecular structure. The intron-exon junctions of the ovalbumin and the alpha 1-proteinase inhibitor gene are all in surface loops of the mature protein.

Amino Acid Sequence↗
PubMed1987

Crystal structures of [Met5] and [(4-bromo)Phe4,Met5]enkephalins: formation of a dimeric antiparallel beta-structure.

The crystal structure of [(4-bromo)Phe4,Met5]enkephalin (Tyr-Gly-Gly-(4-bromo)-Phe-Met) shows two independent molecular conformations. The molecules are arranged in parallel in a head-to-tail fashion and form an antiparallel beta-sheet structure involving intermolecular hydrogen bonds. This dimeric beta-structure is also observed in the [Met5]enkephalin crystal, in spite of their different crystal packing environments, which shows the energetic stability of this molecular conformation. The three-dimensional similarity between the dimeric beta-structure and the beta-turn form is discussed in the relation to the opioid delta and mu receptors.

Crystallography↗