Design of peptides using alpha,beta-dehydro-residues: synthesis, crystal structure and molecular conformation of Boc-L-Val-delta Phe-delta Phe-L-Val-OCH3

The peptide Boc-L-Val-delta Phe-delta Phe-L-Val-OCH3 was synthesized by the azlactone method in solution phase, and its crystal and molecular structures were determined by x-ray diffraction method. Single crystals were grown by slow evaporation from a methanol/water solution at 6 degrees C. The crystals belong to an orthorhombic space group P212121 with a = 10.478 (6) A, b = 13.953 (I), c = 24.347 (2) and Z = 4. The structure was determined by direct methods and refined by least squares procedure to an R value of 0.052. The structure consists of a peptide and a water molecule. The peptide adopts two overlapping beta-turn conformations of Types II and I' with torsion angles: phi 1 = -54.8 (6) psi 1 = 130.5 (4), phi 2 = 65.8 (5), psi 2 = 12.8 (6), phi 3 = 79.4 (5), psi 3 = 3.9 (7) degrees. The conformation is stabilized by intramolecular hydrogen bonds involving Boc CO and NH of delta Phe3 and CO of Val1 and NH of Val4. The molecules are tightly packed in the unit cell. The crystal structure is stabilized by hydrogen bonds involving NH of delta Phe2 and CO of a symmetry related (x-1/2, 1/2-y, -z) delta Phe2. The solvent-water molecule forms two hydrogen bonds with peptide molecule involving NH of Val1 as an acceptor and another with CO of a symmetry related (1-x, y-1/2, 1/2 -z) delta Phe3 as a donor. These studies indicate that a tetrapeptide with two consecutive delta Phe residues sequenced with valines on both ends adopts two overlapping beta-turns of Types II and I'.     

Structure and conformation of helical nucleic acids: rebuilding program (SCHNArP)

We present a program, SCHNArP, for rebuilding double-helical nucleic acid structures from a set of helical parameters. The parameter sets are based on mathematically reversible schemes that allow direct comparison of data from experimental X-ray crystal structures analyzed using the analysis program, SCHNAaP (see accompanying paper), and structures built using the rebuilding program, SCHNArP. The program uses either local CEHS helical parameters or global helical parameters. A number of standard parameter sets from the literature are included that allow comparison of oligomer and polymer structures generated using different models for sequence-dependent DNA bending. Exact atomic models are provided for the bases. Schematic models that trace the path of the backbone and use rectangular blocks for the bases can be generated.     

Accommodation of insertions in helices: the mutation in hemoglobin Catonsville (Pro 37 alpha-Glu-Thr 38 alpha) generates a 3(10)-->alpha bulge

Hemoglobin Catonsville is a mutation of human hemoglobin (an alpha 2 beta 2 tetramer) in which a glutamate residue is inserted into the first turn of a highly conserved 3(10) helix (the C helix) of each alpha subunit. In theory, amino acid insertions (or deletions) in protein helices can be accommodated via two distinct mechanisms. One, termed the register shift mechanism, preserves the geometry of the helix while requiring all of the residues on one flank of the insertion site to rotate by 100 degrees in the case of an alpha helix or by 120 degrees in the case of a 3(10) helix. The other, termed the bulge (or indentation) mechanism, distorts the local geometry of the helix but does not alter the helix register. High-resolution X-ray diffraction analysis of deoxyhemoglobin Catonsville shows that the inserted residue is accommodated as a bulge, demonstrating that this is a viable mechanism. (In contrast, no such evidence is yet available for the register shift mechanism.) More specifically, the insertion converts one turn of the C helix from 3(10) geometry to alpha helix-like geometry, raising the possibility that a common mechanism for accommodating insertions and deletions within helices may involve localized interconversions between 3(10), alpha, and pi helical structures.     

A proteinase K inhibitor using alpha,beta-unsaturated (dehydro) residues: a presumptive model

PURPOSE: To quantify age-related changes in products of lipid oxidation in human lenses and to relate these changes to membrane hydrocarbon chain structure. Deviation from a well-defined membrane-lipid composition and structure could result in alterations in membrane function and disruption of the homeostasis of the cell. METHODS: Infrared spectroscopy was used to detect lipid compositional and structural changes in human lens membranes associated with age and cataracts. RESULTS: Lipid oxidation increased linearly threefold relative to total phospholipids in subjects ranging in age between 1 and 85 years, as was evident by increases in trans double bonds, lipid carbonyls, and secondary products. There was no statistical difference between the levels of lipid oxidation in the cortex or nucleus. Lipid hydrocarbon chain order (rigidity) increased from approximately 40% at birth to 70% at 80 years of age. Changes in lipid order correlated with changes in the relative content of membrane phosphatidylcholine and sphingomyelin, and with the level of lipid oxidation. CONCLUSIONS: Lipid oxidation increased linearly and uniformly throughout the human lens with age. The change in lipid oxidation with age correlated to a change in lipid order.     

Cr(III)-mediated crosslinks of glutathione or amino acids to the DNA phosphate backbone are mutagenic in human cells

Carcinogenic Cr(VI) compounds were previously found to induce amino acid/glutathione-Cr(III)-DNA crosslinks with the site of adduction on the phosphate backbone. Utilizing the pSP189 shuttle vector plasmid we found that these ternary DNA adducts were mutagenic in human fibroblasts. The Cr(III)-glutathione adduct was the most potent in this assay, followed by Cr(III)-His and Cr(III)-Cys adducts. Binary Cr(III)-DNA complexes were only weakly mutagenic, inducing a significant response only at a 10 times higher number of adducts compared with Cr(III)-glutathione. Single base substitutions at the G:C base pairs were the predominant type of mutations for all Cr(III) adducts. Cr(III), Cr(III)-Cys and Cr(III)-His adducts induced G:C-->A:T transitions and G:C-->T:A transversions with almost equal frequency, whereas the Cr(III)-glutathione mutational spectrum was dominated by G:C-->T:A transversions. Adduct-induced mutations were targeted toward G:C base pairs with either A or G in the 3' position to the mutated G, while spontaneous mutations occurred mostly at G:C base pairs with a 3' A. No correlation was found between the sites of DNA adduction and positions of base substitution, as adducts were formed randomly on DNA with no base specificity. The observed mutagenicity of Cr(III)-induced phosphotriesters demonstrates the importance of a Cr(III)-dependent pathway in Cr(VI) carcinogenicity.     

Accommodation of a D-Phe residue into a right-handed 3(10)-helix: structure of Boc-D-Phe-(Aib)4-Gly-L-Leu-(Aib)2-OMe, an analogue of the amino terminal segment of antiamoebins and emerimicins

Recently an unstable trinucleotide CTG repeat, located within the 3' untranslated region of a gene on 19q13.3 was discovered in kindreds with myotonic dystrophy (DM). The age-of-onset/severity of DM shows a good correlation with CTG repeat size, and pedigrees and data reported to date have shown a striking trend toward amplification of the size of the CTG repeat during transmission from parent to child. The amplification has been accepted as the biological explanation for anticipation in the clinical severity observed in many families with DM. In this paper we report on 3 families where CTG amplification decreased during transmission from parent to child. In one case there was a gene conversion event, while in the remaining 2 there was a simpler reduction in the size of the repeat length. The changes appear to have been accompanied by a reduction in clinical severity in the child when compared to the parent. These observations are discussed in terms of their clinical implications and the biases that may exist in much of the reported data.     

Comparative studies on Y(III) and Dy(III) extraction from hydrochloric and nitric acids by Cyanex 572 as a novel extractant

Extraction of Y(III) and Dy(III) from hydrochloric and nitric acids by Cy-572 in kerosene was studied. The factors affecting the extraction were separately investigated. The stoichiometry of the extracted species was deduced on the basis of slope analysis method. Evaluation of extraction equilibrium and stripping investigation was studied as well as saponification effect of Cy-572. The composition of the extracted metal species in the organic phase was found to be $\overline{{[\text{MA}}_3·{\left(\text{HA}\right)}_3]}$ for Y(III) or Dy(III) in both media. 1.0 mol/L HCl is the best stripping agent for each metal ion from the studied acidic media in one step. Saponified Cy-572 does not exhibit any selectivity towards the extraction of Y(III) or Dy(III) from both HCl and HNO₃ solutions. Based on the obtained results, the data were compared and the separation feasibility between lanthanides and Y(III) in the two media was discussed.     

Comparison between the phi distribution of the amino acids in the protein database and NMR data indicates that amino acids have various phi propensities in the random coil conformation

It has been indicated that amino acids have various intrinsic phi and psi propensities, as demonstrated from the comparison between experimental secondary structure propensities and their relative statistical distribution in the protein database for the appropriate region of the Ramachandran plot. However, this does not eliminate the possibility that these experimental propensities are the result of context effects due to the secondary structure environment of the mutated position. To demonstrate that there are at least real intrinsic phi propensities, independent of context effects, we have used two different nuclear magnetic resonance parameters related to the phi dihedral angle (J3 alpha HN coupling constants and the chemical shift of the C alpha H proton), determined in random-coil tetra- and pentapeptides, and/or in proteins. Comparison of the experimentally determined values for these parameters with the theoretical ones determined from the analysis by different empirical and theoretical equations of the phi dihedral angle statistical distribution of the amino acids in the protein database, supports the idea that each amino acid has, at least, different phi intrinsic propensities. Consideration of all conformations, or only coil conformations, in the protein database produces similar results. The reasonable correlation between these experimental and theoretical data and the hydrogen-exchange data in random-coil peptides suggests that maximisation of hydrophobic surface-buried and hydrogen-bond formation with the solvent could be responsible for these different random-coil conformational preferences. Analysis of the intrinsic propensities for beta-strand, alpha-helix and polyproline II dihedral angles of the 20 amino acids in coil conformations, indicates that the side-chain of the amino acids is mainly determining the relative preferences for the phi angle.