Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography

The hepatitis delta virus (HDV) ribozyme uses a cytosine to facilitate general acid-base catalysis. Biochemical studies suggest that C75 has a pKa perturbed to near neutrality. To measure this pKa directly, Raman spectra were recorded on single ribozyme crystals using a Raman microscope. A spectral feature arising from a single neutral cytosine was identified at 1528 cm(-1). At low pH, this mode was replaced with a new spectral feature. Monitoring these features as a function of pH revealed pKa values for the cytosine that couple anticooperatively with Mg2+ binding, with values of 6.15 and 6.40 in the presence of 20 and 2 mM Mg2+, respectively. These pKa values agree well with those obtained from ribozyme activity experiments in solution. To correlate the observed pKa with a specific nucleotide, crystals of C75U, which is catalytically inactive, were examined. The Raman difference spectra show that this mutation does not affect the conformation of the ribozyme. However, crystals of C75U did not produce a signal from a protonatable cytosine, providing strong evidence that protonation of C75 is being monitored in the wild-type ribozyme. These studies provide the first direct physical measurement of a pKa near neutrality for a catalytic residue in a ribozyme and show that ribozymes, like their protein enzyme counterparts, can optimize the pKa of their side chains for proton transfer.     

Pi-pi stacking assisted binding of aromatic amino acids by copper(II)-aromatic diimine complexes. Effects of ring substituents on ternary complex stability

Ternary Cu(ii) complexes containing an aromatic diimine (DA = di(2-pyridylmethyl)amine (dpa), 4,4'-disubstituted 2,2'-bipyridine (Y(2)bpy; Y = H (bpy), Me, Cl, N(Et)(2), CONH(2) or COOEt) or 2,2'-bipyrimidine) and an aromatic amino acid (AA = l-phenylalanine (Phe), p-substituted phenylalanine (XPhe; X = NH(2), NO(2), F, Cl or Br), l-tyrosine (Tyr), l-tryptophan (Trp) or l-alanine (Ala)) were characterized by X-ray diffraction, spectroscopic and potentiometric measurements. The structures of [Cu(dpa)(Trp)]ClO(4).2H(2)O and [Cu((CONH(2))(2)bpy)(Phe)]ClO(4).H(2)O in the solid state were revealed to have intramolecular pi-pi interactions between the Cu(ii)-coordinated aromatic ring moiety, Cu(DA) (Mpi), and the side chain aromatic ring of the AA (Lpi). The intensities of Mpi-Lpi interactions were evaluated by the stability constants of the ternary Cu(ii) complexes determined at 25 degrees C and I = 0.1 M (KNO(3)), which revealed that the stability enhancement of the Cu(DA)(AA) systems due to the interactions is in the order (CONH(2))(2)bpy < bpy < Me(2)bpy < (Et(2)N)(2)bpy with respect to DA. The results indicate that the electron density of coordinated aromatic diimines influences the intensities of the stacking interactions in the Cu(DA)(AA) systems. The Mpi-Lpi interactions are also influenced by the substituents, X, of Lpi and are in linear relationship with their Hammett sigma(p) values with the exception of X = Cl and Br.     

Photoinduced diastereoselective addition of perfluoroalkyl iodides to acrylic acid derivatives for the synthesis of fluorinated amino acids

Photoinduced diastereoselective addition of perfluoroalkyl iodides in the presence of an aqueous solution of Na2S2O3 was an excellent method for iodoperfluoroalkylation of acrylic acid derivatives bearing a chiral auxiliary, with moderate to good stereoselectivities and with no detectable side products. The iodoperfluoroalkylation of N-acyloylcamphorsultam provided a convenient route for preparing chiral fluorine-containing amino acids.     

Syntheses of the four stereoisomers of Phytophthora mating hormone α2 and a concise synthesis of mating hormone α1

Four stereoisomers of Phytophthora mating hormone α2 were synthesized using both enantiomers of citronellol as starting materials. The absolute configuration of the natural product was determined to be 7S,11R,15R by oospore-inducing assays of the synthetic isomers. A concise synthetic procedure of α1 was also established using a common synthetic intermediate of α2.     

Synthesis of (±)-cyclic dehypoxanthine futalosine, the biosynthetic intermediate in an alternative biosynthetic pathway for menaquinones

The first synthesis of (±)-cyclic dehypoxanthine futalosine (cyclic DHFL), a biosynthetic intermediate in the futalosine pathway for menaquinones operating in microorganisms, has been achieved. Efficient growth of the Streptomyces coelicolor mutant, which lacks the cyclic DHFL synthetase gene (mqnC gene) was observed in the presence of synthetic (±)-cyclic DHFL.     

Molecular origin for helical winding of fibrils formed by perfluorinated gelators

A chiral low-molecular weight gelator, N,N'-diperfluoroheptanoyl-1,2(R,R)- or -1,2(S,S)-diaminocyclohexane, was prepared to form a gel of acetonitrile. The conformation of the gelator in fibrils was determined by vibrational circular dichroism spectra, providing a molecular model for self-assembly in a helical fibril.     

Biological selection of peptides for poly(l-lactide) substrates

Short peptides that recognize the alpha form of poly( l-lactide) (PLLA) crystalline films were identified from a phage-displayed peptide library. An enzyme-linked immunosorbent assay (ELISA) revealed that the apparent binding constants of the phage clones for the alpha form of PLLA were greater than those of the unselected phage library. The specificity index for the alpha form of PLLA referred to a structurally similar atactic poly(methyl methacrylate) (at-PMMA), supporting the alpha form of PLLA specific binding of the selected phage. Amino acid residues with proton-donor lateral groups and hydrophobic alkyl groups were relatively enriched in a sequence of heptapeptides on the specific phage clones, thereby suggesting the presence of hydrogen bonding as well as hydrophobic interactions between the alpha form of PLLA and the peptides. Surface plasmon resonance (SPR) analysis revealed that the binding constant of the freed c22 heptapeptide (Gln-Leu-Met-His-Asp-Tyr-Arg) for the alpha form of PLLA was greater than those for reference at-PMMA, amorphous PLLA, and the beta form of PLLA. It was found that c22 peptide can recognize slight differences in PLLA polymorphs such as a crystalline state and an arrangement of PLLA functional groups.     

On Lp boundedness of wave operators for 4-dimensional Schrodinger operators with threshold singularities

Let H=–+V(x) be a Schrödinger operator on L²(R⁴),H₀=–. Assume that |V(x)|+| V(x)|C x ^– for some>8. Let be the wave operators. It is known that W_± extend to bounded operators in L^p(R⁴)for all 1p, if 0 is neither an eigenvalue nor a resonance ofH. We show that if 0 is an eigenvalue, but not a resonance ofH, then the W_± are still bounded in L^p(R⁴) for all psuch that 4/3<p<4.     

Color Formation and Gelation of Xyloglucan Upon Addition of Iodine Solutions

Summary: We developed a novel thermo‐reversible gelation system by mixing xyloglucan with an iodine solution. Xyloglucan dissolves in water to produce a colorless solution. However, the addition of iodine solution induces color and gelation; heating causes the gel to melt and become colorless. According to results from spectroscopic and small‐angle X‐ray scattering experiments, the gelation mechanism was proposed to involve two xyloglucan chains that associate side‐by‐side and incorporate iodine and/or iodide ions.

Xyloglucan gel prepared by mixing xyloglucan and iodine solution and heating to 60 °C, followed by cooling.