X-Pro peptides: synthesis and solution conformation of benzyloxycarbonyl-(Aib-Pro)<SUB>4</SUB>methyl ester. Evidence for a novel helical structure

The synthesis of the octapeptide, benzyloxycarbonyl-(&#945;-aminoisobutyryl-L-prolyl)4-methyl ester [Z-(Aib-Pro)4-OMe] and an analysis of its solution conformation is reported. The octapeptide is shown to possess three strong intramolecular hydrogen bonds on the basis of studies of the solvent and temperature dependence of NH chemical shifts and rates of hydrogen-deuterium exchange. 13C studies are consistent with a structure involving only trans Aib-Pro bonds, while ir experiments support a hydrogen-bonded conformation. The Aib 3, 5, and 7 NH groups are shown to participate in hydrogen bonding. A 310 helical conformation compatible with the spectroscopic data is suggested. The proposed conformation consists of three type III &#946;-turns with Aib and Pro at the corners and stabilized by 4&#8594; 1 intramolecular hydrogen bonds

Gramicidin S: A peptide model for protein glycation and reversal of glycation using nucleophilic amines

Nonenzymatic glycation of proteins has been implicated in various diabetic complications and age-related disorders. Proteins undergo glycation at the N-terminus or at the ε-amino group of lysine residues. Glycation of proteins proceeds through the stages of Schiff base formation, conversion to ketoamine product and advanced glycation end products. Gramicidin S, which has two ornithine residues, was used as a model system to study the various stages of glycation of proteins using electrospray ionization mass spectrometry. The proximity of two ornithine residues in the peptide favors the glycation reaction. Formation of advanced glycation end products and diglycation on ornithine residues in gramicidin S were observed. The formation of Schiff base adduct is reversible, whereas the Amadori rearrangement to the ketoamine product is irreversible. Nucleophilic amines and hydrazines can deglycate the Schiff base adduct of glucose with peptides and proteins. Hydroxylamine, isonicotinic acid hydrazide and aminoguanidine effectively removed glucose from the Schiff base adduct of gramicidin S. Hydroxylamine is more effective in deglycating the adduct compared with isonicotinic acid hydrazide and aminoguanidine. The observation that the hydrazines are effective in deglycating the Schiff base adduct even in the presence of high concentrations of glucose, may have a possible therapeutic application in preventing complications of diabetes mellitus. Hydrazines may be used to distinguish between the Schiff base and the ketoamine products formed at the initial stages of glycation

Stereochemistry of Schellman motifs in peptides: crystal structure of a hexapeptide with a C-terminus 6 →1 hydrogen bond

The Schellman motif is a widely observed helix terminating structural motif in proteins, which is generated when the C-terminus residue adopts a left-handed helical (&#945;L) conformation. The resulting hydrogen-bonding pattern involves the formation of an intramolecular 6&#8594;1 interaction. This helix terminating motif is readily mimicked in synthetic helical peptides by placing an achiral residue at the penultimate position of the sequence. Thus far, the Schellman motif has been characterized crystallographically only in peptide helices of length 7 residues or greater. The structure of the hexapeptide Boc-Pro-Aib-Gly-Leu-Aib-Leu-OMe in crystals reveal a short helical stretch terminated by a Schellman motif, with the formation of 6 &#8594; 1 C-terminus hydrogen bond. The crystals are in the space group P212121 with a = 18.155(3) &#197;, b = 18.864(8) &#197;, c = 11.834(4) &#197;, and Z = 4 . The final R1 and wR2 values are 7.68 and 14.6%, respectively , for 1524 observed reflections [Fo &#8805; 3&#962;(Fo)]. A 6 &#8594;1 hydrogen bond between Pro(1)CO &#183; &#183; &#183; Leu(6)NH and a 5 &#8594;2 hydrogen bond between Aib(2)CO &#183; &#183; &#183; Aib(5)NH are observed. An analysis of the available oligopeptides having an achiral Aib residue at the penultimate position suggests that chain length and sequence effects may be the other determining factors in formation of Schellman motifs

Spermidine as a potential biosynthetic precursor to the 1,5-diazabicyclo[4:3:0]nonene residue in the efrapeptins

Efrapeptins (1±3

Effect of amino acid substitutions at the subunit interface on the stability and aggregation properties of a dimeric protein: role of Arg 178 and Arg 218 at the dimer interface of thymidylate synthase

The significance of two interface arginine residues on the structural integrity of an obligatory dimeric enzyme thymidylate synthase (TS) from Lactobacillus casei was investigated by thermal and chemical denaturation. While the R178F mutant showed apparent stability to thermal denaturation by its decreased tendency to aggregate, the Tm of the R218K mutant was lowered by 5°C. Equilibrium denaturation studies in guanidinium chloride (GdmCl) and urea indicate that in both the mutants, replacement of Arg residues results in more labile quaternary and tertiary interactions. Circular dichroism studies in aqueous buffer suggest that the protein interior in R218K may be less well-packed as compared to the wild type protein. The results emphasize that quaternary interactions may influence the stability of the tertiary fold of TS. The amino acid replacements also lead to notable alteration in the ability of the unfolding intermediate of TS to aggregate. The aggregated state of partially unfolded intermediate in the R178F mutant is stable over a narrower range of denaturant concentrations. In contrast, there is an exaggerated tendency on the part of R218K to aggregate in intermediate concentrations of the denaturant. The 3 Å crystal structure of the R178F mutant reveals no major structural change as a consequence of amino acid substitution. The results may be rationalized in terms of mutational effects on both the folded and unfolded state of the protein. Site specific amino acid substitutions are useful in identifying specific regions of TS involved in association of non-native protein structures

Interactions of linear dicationic molecules with lipid A: structural requisites for optimal binding affinity

The structural determinants of the binding affinity of linear dicationic molecules toward lipid A have been examined with respect to the distance between the terminal cationic functions, the basicity, and the type of cationic moieties using a series of spermidine derivatives and pentamidine analogs by fluorescence spectroscopic methods. The presence of two terminal cationic groups corresponds to enhanced affinity. A distinct sigmoidal relationship between the intercationic distance and affinity was observed with a sharp increase at 11 Å, levelling off at about 13 Å. The basicity (pK) and nature of the cationic functions are poor correlates of binding potency, since molecules bearing primary amino, imidazolino, or guanido termini are equipotent. The interaction of pentamidine, a bisamidine drug, with lipid A, characterized in considerable detail employing the putative intermolecular excimerization of the drug, suggests a stoichiometry of 1:1 in the resultant complex. The binding is driven almost exclusively by electrostatic forces, and is dependent on the ionization states of both lipid A and the drug. Under conditions when lipid A is highly disaggregated, pentamidine binds specifically to bis-phosphoryl- but not to monophosphoryl-lipid A indicating that both phosphate groups of lipid A are necessary for electrostatic interactions by the terminal amidininium groups of the drug. Based on these data, a structural model is proposed for the pentamidine-lipid A complex, which may be of value in designing endotoxin antagonists from first principles

Geochemistry and magnetostratigraphy of Deccan flows at Anjar, Kutch

Chemical analysis of nine Deccan flow basalts at Anjar, Kutch, western India, indicates that all, except the uppermost flow F-9, are alkaline. In their major and trace element composition, the alkali basalts resemble Ocean island basalts (OIB). Similarities of many diagnostic trace element ratios (e.g. Sm/Nd, Ba/Nb,Y/Nb and Zr/Nb) are similar to those found in the Reunion Island basalts. The uppermost basalt is tholeiitic and chemically resembles the least contaminated Deccan basalt (Ambenali type). The Anjar basalts have iridium concentration ranging between 2 and 178 pg/g. Some of these values are higher by about an order of magnitude compared to the Ir concentration in other basalts of the Deccan. A synthesis of chemical, palaeomagnetic and geochronologic data enables us to construct a chemical and magnetic stratigraphy for these flows. The three flows below the iridium enriched intertrappean bed (IT III) show normal magnetic polarity whereas all except one of the upper basalts show reversed magnetic polarity. The sequence seems to have started in polarity zones 31N and probably continued up to 28R or 27R. The results presented here support the view that Deccan volcanism in Kutch occurred on a time span of a few million years