Structure and conformation of linear peptides. XII. Structure of tryptophanyl-glycyl-glycine dihydrate

The crystal structure of a tripeptide, tryptophanyl-glycyl-glycine dihydrate (C15H18N4O4.2H2O, molecular weight = 354) has been determined. The crystals are orthorhombic, space group P2(1)2(1)2(1), with a = 7.875 (1) A, b = 9.009(1), c = 24.307(1) and Z = 4. The final R-index is 0.058 for 1488 reflections [sin theta)/lambda less than or equal to 0.6 A-1) with I greater than 2 sigma (I). The molecule exists as a zwitterion, with terminal NH3+ and COO- groups. The peptide units are trans and nearly perpendicular to the plane of the carboxyl group. The backbone torsion angles are: psi 1 = 132.7 degrees, omega 1 = 174.2 degrees, phi 2 = 88.2 degrees, psi 2 = 8.6 degrees, omega 2 = -179.8 degrees, phi 3 = -85.2 degrees, psi 31 = -178.1 degrees, psi 32 = 5.0 degrees. For the sidechain of tryptophan, chi 1 = -171.6 degrees, chi 2 = 101.0 degrees.     

Structure and conformation of linear peptides. I. Structure of L-tyrosyl-L-tyrosine

L-tyrosyl-L-tyrosine crystallizes as a dihydrate in the orthorhombic system, space group C222(1), with a = 12.105(2), b = 12.789(2), c = 24.492(3) A, Z = 8. The structure was solved by direct methods and refined to a final R-value of 0.059 for 1740 observed reflections. The molecule exists as a zwitterion, the peptide unit is trans planar, and the backbone torsion angles correspond to an extended conformation, with psi 1 = 149.4 degrees, phi 2 = -161.2 degrees, psi 2 = 158.3 degrees. The values of the side-chain torsion angles (chi 1, chi 2) are (-58.8 degrees, -63.1 degrees) for the first tyrosine and (-171.7 degrees, -116.5 degrees) for the second. The planes of the aromatic rings are nearly parallel (dihedral angle of 6.1 degrees), and their centers are separated by 10.9 A. The carboxyl plane forms a dihedral angle of 23.8 degrees with the plane of the peptide bond.     

Structure and conformation of linear peptides. VIII. Structure of t-Boc-glycyl-L-phenylalanine

The crystal structure of t-Boc-glycyl-L-phenylalanine (C14H22N2O5, molecular weight = 298) has been determined. Crystals are monoclinic, space group P2(1), with a = 7.599(1) A, b = 9.576(2), c = 12.841(2), beta = 97.21(1) degrees, Z = 2, Dm = 1.149, Dc = 1.168 g X cm-3. Trial structure was obtained by direct methods and refined to a final R-index of 0.064 for 1465 reflections with I greater than 1 sigma. The peptide unit is trans planar and is nearly perpendicular to the plane containing the urethane moiety. The plane of the carboxyl group makes a dihedral angle of 16.0 degrees with the peptide unit. The backbone torsion angles are omega 0 = -176.9 degrees, phi 1 = -88.0 degrees, psi 1 = -14.5 degrees, omega 1 = 176.4 degrees, phi 2 = -164.7 degrees and psi 2 = 170.3 degrees. The phenylalanine side chain conformation is represented by the torsion angles chi 1 = 52.0 degrees, chi 2 = 85.8 degrees.     

Structure and conformation of linear peptides. V. Structure of L-prolyl-glycyl-glycine

The tripeptide, L-prolyl-glycyl-glycine, crystallizes in the trigonal space group P3(2), with a = b = 8.682(2) A, c = 12.008(2) and Z = 3. The structure was solved by direct methods and refined to an R-value of 0.07 for 727 reflections (I greater than 1.0 sigma). The molecule exists as a zwitterion in the crystal. The peptide units are trans and show significant deviations from planarity (omega 1 = 169.7 degrees, omega 2 = -170.1 degrees). The peptide backbone adopts a left-handed helical conformation similar to that of polyglycine II and polyproline II.     

Structure and conformation on linear peptides. VI. Structure of D,L-alanyl-L,D-norvaline

The dipeptide, (DL)-alanyl-(DL)-norvaline, crystallizes in the monoclinic space group P2(1)/c, with a = 12.559(2)A, b = 5.265(1), c = 16.003(3), beta = 103.53(2) degrees, Z = 4. The structure was solved by direct methods and refined to an R-value of 0.054 for 871 reflections with I greater than 2 sigma. The molecule exists as a zwitterion in the crystal. The peptide unit is trans and shows significant deviations from planarity (delta omega = 12.4 degrees). The peptide backbone adopts an extended conformation. The unit cell contains D-Ala-L-norval and its enantiomer. The molecular conformation and packing features show a striking resemblance to those for D-Ala-L-Met (1), and leads to the speculation that norvaline might act as an analog of methionine.     

Structure and conformation of linear peptides. XIII. Structure of L-phenylalanyl-glycyl-glycine

The crystal structure of a tripeptide, L-phenylalanyl-glycyl-glycine (C13H17N3O4), molecular weight = 279.3, has been determined. The crystals are orthorhombic, space group P2(1)2(1)2(1), with a = 5.462(1) A, b = 15.285(5), c = 16.056(4), Z = 4, and P (calc) = 1.384 g.cm-3. The final R-index is 0.052 for 866 reflections with sin theta/lambda less than or equal to 0.55 A-1 and I greater than 1 sigma. The molecule exists as a zwitterion, with the N-terminus protonated and the C-terminus in an ionized form. Both the peptide units are in the trans configuration and planar, though one of them shows significant deviations from planarity ([delta w[ = 5.1 degrees). The peptide backbone is folded, with the torsion angles of: psi 1 = 116.2(5) degrees, omega 1 = 178.8(4), phi 2 = -89.7(5). psi 2 = -28.9(6), omega 2 = -174.9(4), phi 3 = 134.9(5), psi 31 = 7.8(6), psi 32 = -172.6(4). The terminal glycine adopts a "D-residue" conformation. For the sidechain of phenylalanine, chi 1 = 175.5(4), chi 2 = -127.0(6).     

Characterization and crystal structure of cadmium(II) halide complexes with amino acids and their derivatives VI. The comparison of crystal structures of cadmium(II) halide complexes with three kinds of piperidine carboxylic acids

Six cadmium(II) halide complexes with dl-piperidine-2-carboxylic acid (DL-Hpipe-2), dl-piperidine-3-carboxylic acid (DL-Hpipe-3), and piperidine-4-carboxylic acid (Hpipe-4), have been prepared and characterized by means of IR and Raman spectra and thermal analysis. The crystal structures of [CdCl2(DL-Hpipe-2)(H2O)], [CdBr2(DL-Hpipe-3)], and [CdCl2(Hpipe-4)] have been determined by X-ray diffraction. These three complexes have one-dimensional polymer structures bridged by halide atoms. The crystal of [CdCl2(DL-Hpipe-2)(H2O)] is orthorhombic with the space group Pca2(1). The cadmium atom is in an octahedral geometry, ligated by a carboxyl oxygen atom, two bridging chlorine atoms, a terminal chlorine atom, a water molecule and a carboxyl oxygen atom of a neighboring molecule. The carboxyl oxygen atoms of DL-Hpipe-2 are coordinated to two cadmium atoms. The unit cell consists of two types of one-dimensional polymer structures: [CdCl2(D-Hpipe-2)(H2O)] and [CdCl2(L-Hpipe-2)(H2O)]. Therefore, it is better to write [CdCl2(DL-Hpipe-2)(H2O)] as [CdCl2(D-Hpipe-2)(H2O)][CdCl2(L-Hpipe-2)(H2O)]. The crystal structure of [CdBr2(DL-Hpipe-3)] is monoclinic with space group P2(1). The cadmium atom is in a distorted octahedral geometry ligated by two carboxyl oxygen atoms and four bridging bromine atoms. This complex consists of either D-Hpipe-3 or L-Hpipe-3. Therefore [CdBr2(DL-Hpipe-3)] is written as [CdBr2(D or L-Hpipe-3)]. The crystal of [CdCl2(Hpipe-4)] is monoclinic with space group P2(1)/n. The structure is similar to that of [CdBr2(D or L-Hpipe-3)].     

Structure of chicken plasma retinol-binding protein.

The crystal structure of the specific carrier of retinol (retinol-binding protein, RBP) purified from chicken plasma has been determined (space group P2(1)2(1)2(1), with a=46.06(5) A, b=53.56(6) A, c=73.41(8) A, and one protein molecule in the asymmetric unit). Despite being obtained from a species phylogenetically distant from mammals, chicken holoRBP has an overall structure that closely resembles the previously determined structures of mammalian holoRBPs. The lack in chicken RBP of eight carboxy-terminal amino acid residues characteristic of mammalian RBPs does not significantly affect the protein structure. A distinctive feature of the avian protein is a better definition of the loop 63-67, close to the opening of the beta-barrel cavity accommodating the retinol molecule, which is rather disordered in the structures of mammalian RBPs.     

Conformation and hydrogen bonding of N-formylpeptides: crystal and molecular structure of N-formyl-L-alanyl-L-aspartic acid.

Crystals of N-formyl-L-alanyl-L-aspartic acid (C8H11N2O6) grown from aqueous methanol solution are orthorhombic, space group, P2(1)2(1)2(1) with cell parameters at 294K of a = 13.619(2), b = 8.567(2), c = 9.583(3)A, V = 1118.1A3, M.W. = 232.2, Z = 4, Dm = 1.38 g/cm3 and Dx = 1.378 g/cm3. The crystal structure was solved by the application of direct methods and refined to an R value of 0.075 for 1244 reflections with I greater than or equal to 3 sigma collected on a CAD-4 diffractometer. The structure contains two short intermolecular hydrogen bonds: (i) between the C-terminal carboxyl OH and the N-acyl oxygen (2.624(3)A), a characteristic feature found in many N-acyl peptides and (ii) between the aspartic carboxyl OH. and the peptide oxygen OP1 (2.623(3)A). The peptide is nonplanar (omega = 165.5(6) degrees). The molecule takes up a folded conformation in contrast to N-formyl peptides which form extended beta-sheets; the values of phi 1, psi 1, phi 2, psi 2(1), and psi 2(2) are, respectively -65.7(6), 152.0(5), -107.2(5), 30.9(5), and -150.3(6). The aspartic acid side chain conformation is g- with chi 1 = 73.1(5). The formyl group, as expected, is transplanar [OF-CF-N1-CA1 = -4.0(8) degrees]. The presence of the short O-H ... O hydrogen bond emerges as a structural feature common to this peptide and several other N-formyl peptides. There are no C-H ... O hydrogen bonds in this structure.     

Modified bases in tRNA: the structures of 5-carbamoylmethyl- and 5-carboxymethyl uridine.

The crystal structures of two nucleosides, 5-carbamoylmethyluridine (1) and 5-carboxymethyluridine (2), were determined from three-dimensional x-ray diffraction data, and refined to R = 0.036 and R = 0.047, respectively. Compound 1 is in the C3'-endo conformation with chi +5.2 degrees (anti), psiinfinity = +63.4 degrees and psialpha = +180.0 degrees (tt); 2 is in the C2'endo conformation with chi +49.4 degrees (anti), psiinfinity -60.5 degrees and psialpha +60.0 degrees (gg). For each derivative, the plane of the side chain substituent is skewed with respect to the plane of the nucleobase; for 1, the carboxamide group is on the same side of the uracil plane vis a vis the ribose ring; for 2, the carboxyl group is on the opposite side of this plane. No base pairing is observed for either structure. Incorporation of structure 1 into a 3'-stacked tRNA anticodon appears to place 08 within hydrogen bonding distance of the 02' hydroxyl of ribose 33, which may limit the ability of such a molecule of tRNA to "wobble".     

X-Ray Studies on Crystalline Complexes Involving Amino Acids and Peptides XXXI. Effect of Chirality on Ionization State,Stoichiometry and Aggregation in the Complexes of Oxalic Acid with L-and DL-histidine

Abstract

Crystals of the oxalic acid complex of L-histidine (orthorhombic P2₁2₁2₁; a=5.535(4), b=6.809(4), c=26.878(3) Å) R= 3.6% for 1188 observed reflections) contain histidine molecules and semi-oxalate ions in the 1:1 ratio, while the ratio is 1:2 in the crystals of the DL-histidine complex (monoclinic P2₁ lc; a=6.750(7), b=10.139(2), c=19.352(2) Å, β= 90.8°; R= 3.7% for 3176 observed reflections). The histidine molecule in the latter has an unusual ionization state with positively charged amino and imidazole groups and a neutral carboxyl group. The molecule has the sterically least favourable allowed conformation with the side chain imidazole ring staggered between the α-amino and the α- carboxyl (carboxylate) groups, in both the structures. The unlike molecules aggregate into separate alternating layers in both of them. There are elements of similarity in the aggregation patterns in the semi-oxalate layers in the two complexes, but the patterns in the amino acid layers are entirely different. Interestingly, the crystal structure of L-histidine semi-oxalate has broad similarities with that of DL-histidine glycolate, demonstrating how broad features of aggregation could be retained inspite of changes in chirality and composition. The unusual ionization state of the amino acid molecule in the DL-histidine complex is reflected in a hitherto unobserved aggregation pattern in its crystal structure.     

Structure and conformation of peptides containing the sulphonamide junction. III. Synthesis, crystal and molecular structure of a taurine containing peptidic oxa-cyclol

The insertion of the (S)-lactyl residue into the cyclodipeptide cyclo (-Tau-Pro-) 3 leads in good yields to the first example of a stable tetrahedral adduct (oxa-cyclol) 5 containing the sulphonamide junction. Compound 5 does not show a significant tendency towards tautomeric equilibria and possesses an unexpected syn-orientation involving the hydroxyl group and the Pro-H alpha. The crystal structure and molecular conformation of 5 has been determined. Crystals are orthorhombic, s.g. P2(1)2(1)2(1), with a = 6.607, b = 12.297, c = 16.622 A. The cisoidal conformation around the S-N bond is very similar to that found in the previously studied linear and cyclic peptides containing a sulphonamide junction. The taurine nitrogen is practically planar whereas the proline nitrogen, bound to the SO2 group, is highly pyramidal. In the tricyclic system of 5 the seven-membered ring adopts a twist-chair conformation while the pyrrolidine and oxazolidinone rings show an envelope conformation. The crystal packing is characterized by three hydrogen bonds all formed by means of a water molecule.     

Metal-phenoxyalkanoic acid interactions. Part 15. The crystal structures of diaquabis(phenoxyacetato)cadmium(II) and catena-μ-[aquabis(phenoxyacetato-O)lead(II)-bis(phenoxyacetato)lead(II)]

The crystal structures of the cadmium(II) and lead(II) complexes of phenoxyacetic acid (PAH) have been determined by single crystal X-ray diffraction techniques. The cadmium complex, [Cd(PA)₂(H₂O)₂] (1), space group C2, with Z = 2 in a cell of dimensions, a = 11.801(2), b = 5.484(1), c = 13.431(3) Å, β = 100.87(2)°, possesses a distorted trapezoidal bipyramidal coordination around the metal atom, involving two water oxygens [2.210(5) Å] and four carboxyl oxygens from two symmetrical bidentate phenoxyacetate ligands [2.363(4), 2.365(4) Å] with Cd lying on the crystallographic two- fold axis. The lead complex, [Pb₂(PA)₄(H₂O)]_n(2) is triclinic, space group P$\text{1}$, Z = 2, with a cell of dimensions, a = 10.135(4), b = 10.675(3), c = 19.285(9) Å, α = 114.66(3), β = 91.94(3) and γ = 114.99(3)°. (2) is a two-dimensional polymer with a repeating dimer sub-unit. The first lead [Pb(1)] has an irregular MO₈ coordination [2.34?2.96(2) Å: mean, 2.63(2) Å] involving the water molecule, two oxygens from an asymmetric bidentate carboxylate group, two from a bidentate chelate [O(ether), O(carboxylate)] group and three from bridging oxygens, one of which also provides a polymer link to another symmetry generated lead. The second lead [Pb(2)] is irregular seven-coordinate [PbO, 2.48?2.73(2) Å: mean, 2.61(2) Å] with three bonds from the bridging groups, two from an unsymmetrical bidentate carboxylate (O, O′) group and one from a second carboxyl group which also bridges two Pb(2) centres in the polymer.     

Molecular size and symmetry of the bacterioferritin of Escherichia coli. X-ray crystallographic characterization of four crystal forms

X-ray crystallographic data from four crystal forms of Escherichia coli bacterioferritin show that the molecule has a diameter in the range 119 to 128 A. Molecules are composed of 24 subunits arranged in 432 symmetry. In both size and symmetry the molecule resembles ferritin from eukaryotes. The four crystal forms are monoclinic, space group P2(1) with unit cell dimensions a = 118.7 A, b = 211.6 A, c = 123.3 A and beta = 119.1 degrees; orthorhombic, C222(1), a = 128.7 A, b = 197.1 A, c = 202.8 A; tetragonal, P4(2)2(1)2, a = b = 210.6 A, c = 145.0 A and cubic, I432, a = 146.9 A.     

Structure of the fibrinogen binding sequence: arginylglycylaspartic acid (RGD)

The crystal structure of a tetrahydrated form of L-arginyl-glycyl-L-aspartic acid (RGD), the consensus sequence for binding of fibrinogen to cell surface receptors, has been determined from diffractometer data. The tripeptide was crystallized in double zwitterionic form via hanging drop vapor diffusion experiments at a pH near 6.5. The orthorhombic unit cell contains four formula units in space group P2(1)2(1)2(1) with lattice parameters a = 4.852(4), b = 11.376(3), c = 34.083(8)A at RT. The structure was solved by direct methods and refined to a final R = 0.067 based upon 1345 observations with I greater than or equal to 2 sigma(I). Peptide bonds both are trans, omega 2 = 174.2(6) degrees and omega 3 = -169.3(6) degrees. The backbone bends at glycine with phi 2 = -85.5(8) degrees. One of the water molecules sits between the arginyl side chain and the C-terminal carboxylate, forming an intramolecular hydrogen bond to the glycyl carboxyl and linking adjacent molecules through two other H-bond interactions. Comparison of the structure to RGD sequences extracted from 3-D protein structures reveals a diversity of conformations for this tripeptide sequence.     

Crystal structures of 1 : 1 complexes of meclofenamic acid with choline and ethanolamine

The hydrated 1:1 complex of meclofenamic acid with choline crystallizes in the orthorhombic space group Pna2(1) with a = 9.637(1), b = 12.962(5), c = 33.099(4) A and Z = 8. Crystals of the corresponding anhydrous complex with ethanolamine are triclinic, space group P1, with a = 9.232(3), b = 12.287(5), c = 17.033(3) A, alpha = 70.21(2), beta = 76.72(2), gamma = 68.21(3) degrees and Z = 4. The structures have been solved by direct methods and refined to R values of 0.062 and 0.079, respectively for 1942 and 2852 observed reflections. The four crystallographically independent meclofenamate anions in the complexes have nearly the same molecular geometry which in turn is very similar to that found in the crystal structure of free meclofenamic acid. The choline and ethanolamine molecules assume a gauche conformation with respect to the central C-C bond. The invariant structural features observed in the crystals of the free fenamates are retained by the meclofenamate ions in the complexes. These features are the rigid coplanar geometry of the six-membered ring carrying the carboxyl group, the carboxyl group and the imino nitrogen atom, and the internal hydrogen bond connecting the imino and the carboxyl groups. The crystal structures are stabilised by ionic interactions between the carboxylate groups of meclofenamate ions and choline or ethanolamine cations, and hydrogen bonds. The choline complex exhibits pseudosymmetry and the distribution of molecules in it is nearly centrosymmetric although the space group is noncentrosymmetric. The packing of molecules in the crystals is such that the polar columns are surrounded by non-polar regions. The core of each column in the choline complex is made up of water molecules connected by hydrogen bonds involving disordered protons. The results of the X-ray structure analysis of fenamates and their crystalline complexes provide some insights into structure-function relationships in this family of drugs.     

The crystal structure of the 1:1 inclusion complex of beta-cyclodextrin with benzamide

The 1:1 inclusion complex of beta-cyclodextrin and benzamide was prepared and characterized by single crystal X-ray diffraction, PXRD, TGA, and IR. This complex crystallizes in the monoclinic P2(1) space group with unit cell constants a=15.4244(16), b=10.1574(11), c=20.557(2)A, beta=110.074(2) degrees , V=3025.1(6)A(3). The guest molecule projects into the beta-cyclodextrin cavity from the primary hydroxyl side. The amide group protrudes from the primary hydroxyl side and forms hydrogen bonds with the adjacent beta-cyclodextrin molecule. There are six crystallized water molecules, which play crucial roles in crystal packing.     

Structure of inclusion complexes of cyclomaltoheptaose (cycloheptaamylose): crystal structure of the 1-adamantanemethanol adduct

Cyclomaltoheptaose (cycloheptaamylose) has been crystallized with 1-adamantanemethanol as the guest molecule. The complex crystallized in space group C222(1), with unit-cell dimensions a = 19.162 (13), b = 23.965 (17), and c = 32.597 (27) A. The structure was solved by rotation-translation search-methods. The cyclomaltoheptaose exists as a dimer in the crystal by means of extensive hydrogen-bonding across the secondary hydroxyl ends of two cyclomaltoheptaose molecules. The two halves of the dimer are related by a crystallographic two-fold axis. The primary hydroxyl ends of two adjacent cyclomaltoheptaose molecules are also related by a crystallographic two-fold axis, but do not directly hydrogen bond to one another. Instead, they are held in place by a strong hydrogen bond from the hydroxyl group of the 1-adamantanemethanol to a primary hydroxyl group on an adjacent cyclomaltoheptaose molecule. Other stabilizing hydrogen bonds are formed via three water molecules which are situated at the primary hydroxyl interface, and others that form parallel columns stabilizing the crystal structure. A unique feature of this complex is the presence of trapped water in the cavity at the secondary hydroxyl interface. This water is distributed over 3 disordered sites. Its presence blocks one possible site for the 1-adamantanemethanol, which, instead, binds near the primary hydroxyl end, with its hydroxyl group and part of the adamantane moiety protruding from the cyclomaltoheptaose.     

Conformation and hydrogen bonding of N-formylmethionyl peptides. II. Crystal and molecular structure of N-formyl-L-methionyl-L-phenylalanine

Crystals of N-formyl-L-methionyl-L-phenylalanine (C15H20N2O4S), grown from aqueous methanol solution are orthorhombic, space group, P2(1)2(1)2(1), with cell parameters at 294K of a = 4.900(2), b = 17.947(4), c = 18.726(4)A, V = 1646.8A3, M.W. = 324.4, Z = 4 and Dm = 1.308 g/cc, and as expected, all nearly identical to that of N-f-D-Met-D-Phe studied by Jeffs, Heald, Chodosh & Eggleston (Int. J. Peptide Protein Res. 24, 442-446, 1984). The crystal structure was solved and refined using CAD-4 data (1095 reflections greater than or equal to 3 sigma) to a final R value of 0.042. Molecules related by the alpha-translation form a parallel beta-sheet rather than anti-parallel sheet as stated in the earlier study of Jeffs et al. The formation of the parallel rather than the anti-parallel beta-sheet structure, the use of the C-H ...O hydrogen bonds to stabilize the beta-sheet and the very short O-H ...O hydrogen bond between the carboxyl OH and the N-acyl oxygen atom emerge as the main structural features of the chemotactic N-formyl methionyl peptides.     

Complexation of trivalent lanthanide cations by galactitol in the solid state. The crystal structure and an FT-IR study of 2NdCl3.galactitol.14H2O

The crystal structure of 2NdCl3.galactitol.14H2O has been determined. The crystal system is triclinic, space group: -1, with unit-cell dimensions: a = 9.736(2), b = 10.396, c = 8.027 A; alpha = 108.05(3), beta = 92.68(3), gamma = 88.44(3) degrees, V= 771.6(3) A3, Z = 2. Each Nd atom is coordinated to nine oxygen atoms, three from the alditol and six from water molecules, with Nd-O distances from 2.461 to 2.552 A. The seventh water molecule is hydrogen-bonded by the hydroxyl hydrogen on O-1 (O-1-H-ll...O-10, 2.639 A). The FT-IR spectra of 2NdCl3.galactitol.14H2O and 2PrCl3.galactitol.14H2O are analogous, and show that Pr and Nd have the same coordination mode. The IR results are consistent with the crystal structures.