Conformationally restricted formyl methionyl tripeptide chemoattractants: a three-dimensional structure-activity study of analogs incorporating a C alpha,alpha-dialkylated glycine at position 2

The conformationally restricted CHO-L-Met-Xxx-L-Phe-OY (where Xxx = Aib, Ac3c, Ac5c, Ac6c, and Ac7c; Y = H, Me) tripeptides, analogs of the chemoattractant CHO-L-Met-L-Leu-L-Phe-OH, have been synthesized in solution by classical methods and fully characterized. Compounds were compared to determine the combined effect of backbone conformational preferences and side-chain bulkiness on the relation of three-dimensional structure to biological activity. Each peptide was tested for its ability to induce granule enzyme secretion from rabbit peritoneal polymorphonuclear leukocytes. In parallel, a conformational analysis on the CHO-blocked peptide and their tertbutyloxycarbonylated synthetic precursors was performed in the crystal state and in solution using X-ray diffraction, infrared absorption, and 1H nuclear magnetic resonance. The biological and conformational data are discussed in relation to the proposed model of the chemotactic peptide receptor of rabbit neutrophils.

Peptide mimics for structural features in proteins. Crystal structures of three heptapeptide helices with a C-terminal 6-->1 hydrogen bond.

The crystal structure determination of three heptapeptides containing alpha-aminoisobutyryl (Aib) residues as a means of helix stabilization provides a high-resolution characterization of 6-->1 hydrogen-bonded conformations, reminiscent of helix-terminating structural features in proteins. The crystal parameters for the three peptides, Boc-Val-Aib-X-Aib-Ala-Aib-Y-OMe, where X and Y are Phe, Leu (I), Leu, Phe (II) and Leu, Leu (III) are: (I) space group P1, Z = 1, a = 9.903 A, b = 10.709 A, c = 11.969 A, alpha = 102.94 degrees, beta = 103.41 degrees, gamma = 92.72 degrees, R = 4.55%; (II) space group P21, Z = 2, a = 10.052 A, b = 17.653 A, c = 13.510 A, beta = 108.45 degrees, R = 4.49%; (III) space group P1, Z = 2 (two independent molecules IIIa and IIIb in the asymmetric unit), a = 10.833 A, b = 13.850 A, c = 16.928 A, alpha = 99.77 degrees, beta = 105.90 degrees, gamma = 90.64 degrees, R = 8.54%. In all cases the helices form 3(10)/alpha-helical (or 3(10)helical) structures, with helical columns formed by head-to-tail hydrogen bonding. The helices assemble in an all-parallel motif in crystals I and III and in an antiparallel motif in II. In the four crystallographically characterized molecules, I, II, IIIa and IIIb, Aib(6) adopts a left-handed helical (hL) conformation with positive phi, psi values, resulting in 6-->1 hydrogen-bond formation between Aib(2) CO and Leu(7)/Phe(7) NH groups. In addition a 4-->1 hydrogen bond is seen between Aib(3) CO and Aib(6) NH groups. This pattern of hydrogen bonding is often observed at the C-terminus of helices proteins, with the terminal pi-type turn being formed by four residues adopting the hRhRhRhL conformation.

Conformation of the flexible bent helix of Leu1-zervamicin in crystal C and a possible gating action for ion passage

The membrane channel-forming polypeptide, Leu(1)-zervamicin, Ac-Leu-Ile-Gln-Iva-Ile(5)-Thr-Aib-Leu-Aib-Hyp(10) -Gln-Aib-Hyp-Aib-Pro(15)-Phol (Aib: alpha-aminoisobutyric acid; Iva: isovaline; Hyp: 4-hydroxyproline; Phol: phenylalininol) has been analyzed by x-ray diffraction in a third crystal form. Although the bent helix is quite similar to the conformations found in crystals A and B, the amount of bending is more severe with a bending angle approximate to 47 degrees, The water channel formed by the convex polar faces of neighboring helices is larger at the mouth than in crystals A and B, and the water sites have become disordered. The channel is interrupted in the middle by a hydrogen bond between the OH of Hyp(10) and the NH2 of the Gln(11) of a neighboring molecule. The side chain of Gln(11) is wrapped around the helix backbone in an unusual fashion in order that it can augment the polar side of the helix. In the present crystal C there appears to be an additional conformation for the Gln(11) side chain (with approximate to 20% occupancy) that opens the channel for possible ion passage. Structure parameters for C85H140N18O22.xH(2)O.C2H5OH are space group P2(1)2(1)2(1), a = 10.337 (2) Angstrom, b = 28.387 (7) Angstrom, c = 39.864 (11) Angstrom, Z = 4, agreement factor R = 12.99% for 3250 data observed > 3 sigma(F), resolution = 1.2 Angstrom. (C) 1994 John Wiley & Sons, Inc.

Peptide-lanthanide interactions. Crystal structure of a europium(III)-triglycine complex

Crystals of Eu-(Gly-Gly-Gly).(H2O)5.(ClO4)3 are triclinic, spacegroup P1BAR with a = 9.123 (2), b = 11.185 (5), c = 11.426 (2) angstrom; alpha = 90.79 (2), beta = 98.08 (1), gamma = 98.57 (2)-degrees; Z = 2. The europium cation is surrounded by four oxygens from three different peptide units and four oxygens from water molecules. The geometry around the metal is a distorted bi-capped trigonal prism. The peptide backbone conformation in this complex is compared with those in the free peptide and in various metal complexes. Considerable differences are observed between Eu(III) and Ca(II) complexes of triglycine. (C) Munksgaard 1994.

Hydration and distortion of peptide helices in crystals. α-Helical structure of a dodecapeptide, Boc-(Ala-Leu-Aib)4-OMe

The dodecapeptide Boc-(Ala-Leu-Aib)(4)-OMe crystallized with two independent helical molecules in a triclinic cell. The two molecules are very similar in conformation, with a 3(10)-helix turn at the N-terminus followed by an alpha-helix, except for an elongated N(7)...O(3) distance in both molecules. All the helices in the crystal pack in a parallel motif. Eleven water sites have been found in the head-to-tail region between the apolar helices that participate in peptide-water hydrogen bonds and a network of water-water hydrogen bonds. The crystal parameters are as follows: 2(C58H104N12O15)+ca. 10H(2)O, space group P1 with a = 12.946(2), b = 17.321(3), c = 20.465(4) Angstrom, alpha = 103.12(2), beta = 105.63(2), gamma = 107.50(2)degrees, Z = 2, R = 10.9% for 5152 data observed > 3 sigma(F), resolution 1.0 Angstrom. In contrast to the shorter sequences [Karle et al. (1988)Proc. Natl. Acad. Sci. USA 85, 299-303] and Boc-(Ala-Leu-Aib)(2)-OMe [Karle et al. (1989) Biopolymers 28, 773-781], no insertion of a water molecule into the helix is observed. However, the elongated N---O distance between Ala(7) NH and Aib(3) CO in both molecules (molecule A, 3.40 Angstrom; molecule B, 3.42 Angstrom) is indicative of an incipient break in the helices. (C) Munksgaard 1994.

Family of Mixed-Valence Oxovanadium(IV/V) Dinuclear Entities Incorporating N4O3-Coordinating Heptadentate Ligands: Synthesis, Structure, and EPR Spectra

Dinuclear ((VVV)-V-IV) oxophenoxovanadates of general formula [V2O3L] have been synthesized in excellent yields by reacting bis(acetylacetonato)oxovanadium(IV) with H3L in a 2:1 ratio in acetone under an N-2 atmosphere. Here L3- is the deprotonated form of 2,6-bis[{{(2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L1), 2,6-bis[{{(5-methyl-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L2) 2,6-bis[ {{(5-tert-butyl-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenoI (H3L3), 2,6-bis[{{(5-chloro-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L4) , 2,6-bis[{{(5-bromo-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L5), or 2,6-bis[{{(5-methoxy-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L6). In [V2O3L1], both the metal atoms have distorted octahedral geometry. The relative disposition of two terminal V=O groups in the complex is essentially cis. The O=V...V=O torsion angle is 24.6(2)degrees. The V-O-oxo-V and V-O-phenoxo-V angles are 117.5(4) and 93.4(3)degrees, respectively. The V...V bond distance is 3.173(5) Angstrom. X-ray crystallography, IR, UV-vis, and H-1 and V-51 NMR measurements show that the mixed-valence complexes contain two indistinguishable vanadium atoms (type 111). The thermal ellipsoids of O2, O4, C10, C14, and C15 also suggests a type III complex in the solid state. EPR spectra of solid complexes at 77 K display a single line indicating the localization of the odd electron (3d(xy)(1)). Valence localization at 77 K is also consistent with the V-51 hyperfine structure of the axial EPR spectra (3d(xy)(1) ground state) of the complexes in frozen (77 K) dichloromethane solution: S = 1/2, g(parallel to) similar to 1.94, g(perpendicular to) similar to 1.98, A(parallel to) similar to 166 x 10(-4) cm(-1), and A(perpendicular to) similar to 68 x 10(-4) cm(-1). In contrast isotropic room-temperature solution spectra of the family have 15 hyperfine lines (g(iso) similar to 1.974 and A(iso) similar to 50 x 10(-4) cm(-1)) revealing that the unpaired electron is delocalized between the metal centers. Crystal data for the [V2O3L1].CH2Cl2 complex are as follows: chemical formula, C32H43O6N4C12V2; crystal system, monoclinic; space group, C2/c; a = 18.461(4), b = 17.230(3), c = 13.700(3) Angstrom; beta = 117.88(3)degrees; Z = 8.

Structure of 5-methyl-2'-deoxycytidine 5'-monophosphate dihydrate

CloHI6N307P.2H20 , Mr = 357.2, triclinic, P1, a = 4-8520 (8), b = 8"3703 (8), c = 10.0199 (12) A, a= 104.578 (9),/3= 102.332 (13), 7=93.670(11) o, V = 381"75 A 3, Z = 1, Dx = 1"55, Dm = 1"53 Mg m -3, a(Cu Ka) = 1.5418 A,/z = 2.01 mm- l, F(000) = 188, T= 290 K, R = 0-049 for 1568 unique reflections.

Solution structure of O-glycosylated C-terminal leucine zipper domain of human salivary mucin (MUC7)

Solution structures of a 23 residue glycopeptide II (KIS* RFLLYMKNLLNRIIDDMVEQ, where * denotes the glycan Gal-beta-(1-3)-alpha-GalNAc) and its deglycosylated counterpart I derived from the C-terminal leucine zipper domain of low molecular weight human salivary mucin (MUC7) were studied using CD, NMR spectroscopy and molecular modeling. The peptide I was synthesized using the Fmoc chemistry following the conventional procedure and the glycopeptide II was synthesized incorporating the O-glycosylated building block (N alpha-Fmoc-Ser-[Ac-4,-beta-D-Gal-(1,3)-Ac(2)alpha-D-GalN(3)]-OPfp) at the appropriate position in stepwise assembly of peptide chain. Solution structures of these glycosylated and nonglycosylated peptides were studied in water and in the presence of 50% of an organic cosolvent, trifluoroethanol (TFE) using circular dichroism (CD), and in 50% TFE using two-dimensional proton nuclear magnetic resonance (2D H-1 NMR) spectroscopy. CD spectra in aqueous medium indicate that the apopeptide I adapts, mostly, a beta-sheet conformation whereas the glycopeptide II assumes helical structure. This transition in the secondary structure, upon glycosylation, demonstrates that the carbohydrate moiety exerts significant effect on the peptide backbone conformation. However, in 50% TFE both the peptides show pronounced helical structure. Sequential and medium range NOEs, C alpha H chemical shift perturbations, (3)J(NH:C alpha H) couplings and deuterium exchange rates of the amide proton resonances in water containing 50% TFE indicate that the peptide I adapts alpha-helical structure from Ile2-Val21 and the glycopeptide II adapts alpha-helical structure from Ser3-Glu22. The observation of continuous stretch of helix in both the peptides as observed by both NMR and CD spectroscopy strongly suggests that the C-terminal domain of MUC7 with heptad repeats of leucines or methionine residues may be stabilized by dimeric leucine zipper motif. The results reported herein may be invaluable in understanding the aggregation (or dimerization) of MUC7 glycoprotein which would eventually have implications in determining its structure-function relationship.

Role of the environment in the interaction of nonintercalators with Z-DNA

Interaction of the DNA binding nonintercalators Netropsin, Distamycin and the mPD derivative with Z-DNA has been studied. It has been found that environmental factors like the solvent and added cations significantly modulate the interaction of these ligands with Z-DNA. However no definite Z to B transition in presence of these ligands was found in any case, in contrast to previously reported results (Ch. Zimmer, C. Marck and W. Guschlbauer, FEBS Lett. 154, 156-160 (1983)).

Structure and dynamics of benzene in one-dimensional channels

Molecular dynamics investigation of benzene in one-dimensional channel systems A1PO(4)-5, VPI-5, and carbon nanotube is reported. The results suggest that, in all the three host systems, the plane of benzene is almost perpendicular to the channel axis when the molecule is near the center of the channel and the plane of benzene is parallel to the channel axis when the molecule is near the wall of the channel. The density distribution of benzene as a function of channel length, z and the radial distance, r, from the channel axis is also different in the three host structures. Anisotropy in translational diffusion coefficient, calculated in body-fixed frame of benzene, suggests that benzene prefers to move with its plane parallel to the direction of motion in A1PO(4)-5 and VPI-5 whereas in carbon nanotube the motion occurs predominantly with the plane of the benzene perpendicular to the direction of motion.;Anisotropy associated with the rotational motion is seen to alter significantly in confinement as compared to liquid benzene. In A1PO(4)-5, the rotational anisotropy is reversed as compared to liquid benzene thereby suggesting that anisotropy arising out of molecular geometry can be reduced. Reorientational correlation times for C-6 and C-2 axes Of benzene are reported. Apart from the inertial decay of reorientational correlation function due to free, rotation, two other distinct regimes of decay are observed in narrower channels (AIPO(4)-5 and carbon nanotube): (i) an initial fast decay (0.5-2 ps) and (ii) a slower decay (>2 ps) of reorientational correlation function where C-6 decays slower than C-2 Similar to what is observed in liquid benzene. In the initial fast decay, it is seen that the decay for C-6 is faster than C-2 which is in contrast to what is observed in liquid benzene or for benzene confined in VPI-5.

X-Ray structure of a ternary complex, copper(II)–lnosine 5-monophosphate–benzimidazole. The first example for the absence of direct metal–nucleotide interaction

The unprecedented absence of direct metal–nucleotide interaction has been observed in the X-ray structure of the ternary metal nucleotide system [Cu(bzim)(H2O)5]2+[IMP]2–·3H2O [IMP = inosine 5-monophosphate(2–), bzim = benzimidazole). The complex crystallizes in the space group P21 with a= 7.013(2), b= 13.179(9), c= 14.565(9)Å, = 94.82(4)°, and Z= 2. The structure was solved by the heavy-atom method and refined by full-matrix least squares on the basis of 1 761 observed (I? 3i) reflections to final R and R values of 0.034 and 0.036 respectively. The CuII has a distorted octahedral co-ordination with a nitrogen of the bzim ligand [Cu–N 1.947(5)Å] and three oxygens of water molecules in the basal plane [mean Cu–O 2.017(3)Å] and two more water oxygens at axial positions [Cu–O 2.194(6) and 2.732(5)Å]. The nucleotide base stacks with the bzim ligand at an average distance of 3.5 Å and an angle of 22°. In the lattice, N(7) of the base is linked to a lattice water through a hydrogen bond, while all the phosphate oxygens are involved in hydrogen bonds with co-ordinated as well as lattice water molecules. The co-ordination behaviour of IMP to CuII is compared in structures containing different -aromatic amines in order to assess the influence of the ternary ligand in complex formation. The present results indicate that, apart from the commonly observed phosphate binding, other modes of co-ordination are possible, these being influenced mainly by the -accepting properties of the ternary ligand.

Crystal structure of L-lysyl-L-glutamic acid dihydrate

L-Lysyl-L-glutamic acid dihydrate, C11N3O5H21·2H2O, crystallizes in the monoclinic space group P21 with a = 12.474(2), b = 5.020(1), c = 13.157(2) Å, β= 114.69(1)° and Z = 2. The crystal structure was solved by direct methods and refined to an R value of 0.037 using full matrix least-squares method. The molecule exists as a double zwitterion with both the amino and carboxyl groups ionised. The peptide has a folded conformation with its Lys residue trans and Glu residue gauche−gauche+. The side chains of the Lys and Glu residues correspond to all trans and folded (g−g−g−) conformations respectively. The terminal carboxyl group forms hydrogen bonds with the ξ-amino group of the lysine side chain. The head-to-tail interaction often seen in peptide crystals is absent in the present structure. In the extended crystal structure water molecules form channels along the b direction and are enclosed within helically arranged hydrogen bonds formed by the lysine side chain and the peptide backbone.

Structure of columbin, a diterpenoid furanolactone from Tinospora cordifolia Miers

(1S,4R,5R,8S, IOR,12S)-4-Hydroxy-15,16-epoxycleroda-2,13 (16), 14-trieno- 17,12:18,1-biscarbolactone,C20H2206, Mr = 358.2, m.p. = 453-454 K,orthorhombic, P212121, a = 7.3869 (6), b = 11.986 (1),c=19.896(2) A, V=1761.65A 3, Z=4, D x=1.351, Din(by flotation)= 1.349gem -3, 2(CuKa)=1.5418 A, /l = 8.36 cm -1, F(000) = 760, T= 295 K,R = 0.0432 for 1662 observed reflections. Two terpenerings, two ~-lactones, two methyl groups, a tertiary hydroxyl group and a fl-substituted furan ring are present in the structure. The H atoms at C(12) and C(8) are a- and fl-oriented. The terpene ring A is locked into a boat conformation by the C(1)-C(4) lactone bridge. The furan ring is attached equatoriaUy at atom C(12). The hydroxyl group is involved in intramolecular hydrogen bonding.

Crystal structure and ionic conductivity of a new bismuth tungstate,Bi3W2O10.5

The compound Bi3W2O10.5 was synthesized by the solid-state technique from Bi2O3 and WO3 in stoichiometric quantities. Single crystals were grown by the melt-cooling technique and the crystal structure was solved in the tetragonal 141in space group with a = 3.839 (1) A, c = 16-3S2 (5) A, V = 241.4 (1) angstrom(3), Z = 4 and was refined to an R index of 0.0672. The structure represents a modification of the Aurivillius phase and consists of [Bi2O2](2+) units separated by WO8 polyhedra. a.c. impedance studies indicate oxide ion conductivity of 2.91 10(-5) cm(-1) at 600 degrees C.