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  • Polymer and Materials Science  (9)
  • 1
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Direct x-ray analysis has been used to determine the crystal structure of [D-Hyi2, L-Hyi4]meso-valinomycin {cyclo[-D-Val-D-Hyi-L-Val-L-Hyi-(D-Val-L-Hyi-L-Val-D-Hyi)2-], C60H102N6O18}, which crystallized from acetone with two solvent molecules. The crystals are trigonal, space group P32, number of molecules per unit cell Z = 3, cell parameters a = b = 15.2085 (8) Å, c = 29.3250 (9) Å, γ = 120°. The standard (R)and weighted (Rw) reliability factors after refinement of the atomic coordinates for C, N, and O atoms in the anisotropic thermal motion approximation, allowing for isotropic H atom contributions, were 0.070 and 0.082, respectively. The molecule adopts a distorted bracelet structure which is stabilized by six N—H … O=C 4 → 1 type intramolecular hydrogen bonds. The side chains predominantly occupy external pseudoaxial positions relative to the cylindrical axis of the molecule. In contrast to meso-valinomycin, only four of the six Val carbonyl oxygen atoms are directed inwards to form a coordination centre for the molecule, and the carbonyl oxygen atoms of residues D-Val1 and L-Val3 are twisted outward and point away from the centre of the molecule. Although the analogue has a partially formed ion-binding center, it is inaccessible because the hydrophobic isopropyl groups of the D-Hyi2 and L-Hyi4 residues screen the molecular cavity on both sides.
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  • 2
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure of a synthetic analogue of valinomycin, cyclo [-(D-Val-L-Hyi-L-Val-D-Hyi)2-] (octa-meso-valinomycin) (I) (C40H68N4O12 · 1.5 · C4H8O2, Mr = 937.01 + 88.10), has been determined. Crystals grown from dioxane are monoclinic, space group P21/a, with cell parameters a = 21.487(8), b = 16.836(5), c = 16.089(4) Å, β = 111.70(4), and Z = 4. The atomic coordinates for nonhydrogen atoms were refined in the anisotropic thermal motion approximation. H atom positions were included in the structure factor calculations at their geometrically expected positions. Values of the standard and weighted R factors after refinement are 0.11 and 0.13, respectively. The conformation of the depsipeptide crystallized from dioxane is different from that crystallized from chloroform (II). The molecule adopts a rectangular shape with two type IV β-turns containing a hydrogen bond and possesses pseudorotational symmetry. The side chains are located on the molecular periphery. The orientation of the carbonyl groups of the molecule is not conducive for efficient metal-ion coordination and in the observed conformation cannot behave as an ionophore.In the crystal the molecules form infinite chains parallel to the c axis, and are stabilized by two intermolecular hydrogen bonds that are shorter and have better geometry than the intramolecular hydrogen bonds.A φ/Ψ plot for dodecadepsipeptides with a (DLLD)3 sequence has well-defined areas for Val and Hyi residues only in cases when the crystals have been grown from nonpolar or medium-polar solvents. The Φ/Ψ plot for octadepsipeptides crystallized from chloroform (II) shows this behavior also. There also is a correlation between the polarity of the solvent from which crystals of octa-meso-valinomycin or valinomycin analogues with a (DLLD) sequence of configuration have been grown and the number of the intramolecular hydrogen bonds that are formed. The more polar the solvent the fewer the number of intramolecular hydrogen bonds.Empirical energy calculations on octa-meso-valinomycin indicate that for isolated molecules, the energy of the bracelet form (II) is 4.7 kcal/mole lower than that of the rectangular form (I).
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  • 3
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure of a synthetic analogue of valinomycin, cyclo[-(L-Val-L-Hyi-L-Val-D-Hyi)2-(D-Val-L-Hyi-L-Val-D-Hyi)-] ([L-Val1, L-Val5]meso-valinomycin), C60H102N6O18, has been determined. Crystals grown from petroleum ether are orthorhombic, space group P212121, with cell parameters a = 16.41(1), b = 18.76(1), c = 25.86(1) Å, and Z = 4. The atomic coordinates for nonhydrogen atoms, except those of terminal carbons on one side chain, were refined in the anisotropic thermal motion approximation. The coordinate parameters of the H atoms were incorporated into the structure factor calculations at geometrically expected positions. Values of the standard and weighted R factors after refinement are 0.074 and 0.083, respectively. The crystal structure of the molecule is asymmetric and adopts a conformation with four 4 → 1 type and one 6 → 1 type intramolecular hydrogen bonds between amide nitrogens and carbonyl oxygens. Valinomycin binds potassium more than 100 times strongly than the D,L Stereoisomeric analogue, as a result of a different spatial orientation of potentially interacting carbonyl groups.
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  • 4
    ISSN: 0006-3525
    Keywords: x-ray crystallography ; ionophore ; valinomycin analogue ; crystal and molecular structure ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal and molecular structure of the valinomycin analogue, cyclo [(D-Val-L-Lac-L-Ala-D-Hyi)2 (D-Val-L-Lac-L-Val-D-Hyi)] has been solved by x-ray direct methods using the “Shake and Bake” procedure. The crystals, grown from a mixture of octane/CH2Cl2, belong to space group P21 (Z = 4 ) with cell parameters a = 10.29, b = 32.08, c = 18.73 Å β = 97.05°, and contain two molecules per asymmetric unit. After anisotropic refinement the standard reliability factor was R1 = 0.058. The conformations of both independent molecules is similar to that observed for isoleucinomycin, cyclo [-(D-Ile-L-Lac-L-Ile-D-Hyi)3] [V. Z. Pletnev et al. (1980) Biopolymers, Vol. 19, pp. 1517-1534]. The structure has an asymmetric conformation stabilized by six intramolecular H bonds, five bonds being of the 4 → 1 type and one bond being of the 5 → 1 type. One water molecule is caged in the internal cavity of each cyclodepsipeptide. This conformation could represent an intermediate state between free and complexed forms of valinomycin. © 1997 John Wiley & Sons, Inc. Biopoly 42: 651-658, 1997
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  • 5
    ISSN: 0006-3525
    Keywords: valinomycin analogue ; ionophore ; x-ray direct methods ; structure and function ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation and intermolecular association of [D-Hyi2, L-Hyi4]meso-valinomycin {cyclo[-D-Val-D-Hyi-L-Val-L-Hyi- (D-Val-L-Hyi-L-Val-D-Hyi)2-], C60H102N6O18} in a crystal form obtained from ethanol solution has been determined by x-ray crystallography. Two depsipeptides and one ethanol molecule per asymmetric unit crystallize in space group P21 (Z = 4); a - 14.579, b = 39.795, c = 13.928 Å, β = 116.90, R1 = 0.0757. The molecular conformation is very similar to that observed in the trigonal P32 crystal form obtained from acetone solution [V. Z. Pletnev et al. (1991) Biopolymers, Vol. 31, pp. 409-415]. Both independent molecules in the crystal adopt a similar distorted bracelet structure with a sterically inaccessible, partially formed, ion-binding center that is stabilized by six 4 → 1 type H bonds. The observed conformation accounts for the inability of the molecule to complex ions. Close examination of the three crystallographically independent molecules reveals that differences in the backbone conformation associated with solvent interaction are significantly larger than those associated with hydrophobic van der Waals interactions of crystal packing.© 1997 John Wiley & Sons, Inc. Biopoly 42: 645-650, 1997
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  • 6
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure of a synthetic analog of valinomycin, cyclo[-(D-Ile-Lac-Ile-D-Hyi)3-] (C60H102N6O18), has been determined by x-ray diffraction procedures. The crystals are orthorhombic, space group P212121, with cell parameters a = 11.516, b = 15.705, c = 39.310 Å, and Z = 4. The atomic coordinates for the C, N, O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation. Values of standard (R) and weighted (Rw) reliability factors after refinement are 0.073 and 0.056, respectively. The structure is completely asymmetric. The cyclic molecular backbone is stabilized by six intramolecular hydrogen bonds N—H…O=C, five bonds being of the 4→1 type and one being of the 5→1 type. The side chains are located on the molecular periphery. The conformational state of isoleucinomycin in the crystal is intermediate between the corresponding crystalline states of valinomycin and meso-valinomycin. The observed conformation suggests that complexation could proceed via entry of the ion at the face possessing the L-Lac residues, the less crowded face.
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  • 7
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure of a synthetic depsipeptide ionophore hexadecaisoleucinomycin, cyclo[-(D-Ile-L-Lac-L-Ile-D-Hyi)4-] (C80H136N8O24), has been determined by single crystal x-ray diffraction techniques. The crystals are orthorhombic, space group P212121, number of molecules per unit cell z = 4, and cell parameters a = 11.195, b = 17.853, c = 54.835 Å. The values of the standard ( R) and weighted ( Rw ) discrepancy factors after refinement are 0.122 and 0.135, respectively. The structure is characterized by an elongated bracelet form with a twofold axis of pseudosymmetry. It is stabilized by eight intramolecular 4 → 1 hydrogen bonds between the amide C=O and N—H groups. The ester carbonyls are directed toward the inside of the molecule, their oxygen atoms forming an ellipsoidal internal cavity. The side chains are located on the molecular periphery. The conformational states of hexadecaisoleucinomycin in solution are discussed in the light of the data obtained.
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  • 8
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure of cyclo (D-Val-D-Hyi-D-Val-L-Hyi-L-Val-D-Hyi-L-Val-L-Hyi-L-Val-D-Hyi-L-Val-L-Hyi)-2H2O has been solved by x-ray direct methods. The crystals (grown from a mixture of octane / CH2C12) are an orthorhombic, centrosymmetric space group Pbca, cell parameters a = 11.458(2). b = 25.613(3). c = 23.691(3) Å. Z = 4; therefore the molecule lies on a center of inversion in the cell. The atomic coordinates for the C, N, and O atoms were refined in the anisotropic thermal motion approximation (allowing for II-atom contribution to Fcal) to a standard R- factor value of 0.081. In contrast to meso-valinomycin, the analogue under study does not adopt an octahedral cage bracelet conformation. It has an unusual centrosymmetric elongated form with two type II terminal β-bends formed by N—H-C=O 4 → 1 type intramolecular H bonds. Two symmetry-related water molecules reside in the elongated molecular cavity of the centrosymmetric depsipeptide ring. © 1995 John Wiley & Sons, Inc.
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  • 9
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ionophores are antibiotics that induce ion transport across natural and artificial membranes. The specific function of a given ionophore depends upon its selectivity and the kinetics of ion capture, transport, and release. Systematic studies of complexed and uncomplexed forms of linear and cyclic ionophores provide insight into molecular mechanisms of ion capture and release and the basis for ion selectivity. The cyclic dodecadepsipeptide valinomycin, cyclo[(L-Val-D-Hyi-D-Val-L-Lac)3-]. transports potassium ions across cellular membrane bilayers selectively. The x-ray crystallographic and nmr spectroscopic data concerning the structures of Na+, K+, and Ba+2 complexes are consistent and provide a rationale for the K+ selectivity of valinomycin. Three significantly different conformations of valinomycin are observed in anhydrous crystals, in hydrated crystals grown from dimethylsulfoxide, and in crystals grown from dioxane. Each of these conformations suggests a different mechanism of ion capture. One of the observed conformations has an elliptical structure stabilized by four 4 ← 1 intramolecular hydrogen bonds and two 5 ← 1 hydrogen bonds. Ion capture could be readily achieved by disruption of the 5 ← 1 hydrogen bonds to permit coordination to a potassium ion entering the cavity. The conformation found in crystals obtained from dimethyl sulfoxide is an open flower shape having three petals and three 4 ← 1 hydrogen bonds. Complexation could proceed by a closing up of the three petals of the flower around the desolvating ion. In the third form, water molecules reside in the central cavity of a bracelet structure having six 4 ← 1 hydrogen bonds. Two of these bracelets stack over one another with their valine-rich faces surrounding a dioxane molecule. The stacked molecules form a channel approximately 20 Å in length, suggesting that under certain circumstances valinomycin might function as a channel. A series of analogues of valinomycin differing in ring composition and size have been synthesized and their transport properties tested. Peptide substitution and chiral variation in the dodecadepsipeptide can result in stabilization or modification of the different conformers. While contraction of the ring size results in loss of ion transport properties, expansion of the ring size permits complexation of larger ions and small positively charged molecules.Gramicidin A is a pentadecapeptide that functions as a transmembrane channel for transporting monovalent cations. Crystal structures of the cesium chloride complex and two uncomplexed forms of gramicidin A have been reported. In all three structures the gramicidin A molecule is a left-handed, antiparallel, double-stranded helical dimer. In the cesium complex the β7.2-helix has 6.4 residues per turn with an internal cavity large enough to accommodate cesium ions. In the uncomplexed structures the channel is 31 Å long and has 5.6 amino acids per turn. Because the helix is too tightly wound to permit ion transport, ion transport would require breaking and reforming of hydrogen bonds. © 1996 John Wiley & Sons, Inc.
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