Crystallization of a complex between ribonuclease Ms and 3'-guanylic acid

The crystals of a complex between ribonuclease Ms, the extracellular ribonuclease from Aspergillus saitoi, and 3'-guanylic acid were obtained from 2-methyl-2,4-pentanediol solution by vapor diffusion technique in the hanging drop mode. The crystals belong to orthorhombic space group P2(1)2(1)2(1) with dimensions a = 47.0 A, b = 62.8 A, c = 37.9 A. The crystals diffract strongly up to at least 2.0 A resolution.     

Crystallization of a complex between ribonuclease T1 and 2'-guanylic acid

Ribonuclease T1 was crystallized under various conditions. Form I crystals were produced by microdialysis against 53% (v/v) 2-methyl-2,4-pentanediol in 0.01 M sodium acetate, 0.05% 2'-guanylic acid (2'GMP) and 0.02% NaN3 (pH 6.2-7.2). These crystals are tetragonal, space group P41212 and contain two molecules per asymmetric unit; cell dimensions are a = b = 5.86 nm, c = 13.28 nm. Form IIa and form IIb crystals were obtained by microdialysis from a buffer of 0.01-0.05 M sodium acetate, 0.25-0.5% 2'GMP, 0.02% NaN3 and 2-5 mM calcium acetate (pH 4.0-4.4) in the presence of 50-75% (v/v) 2-methyl-2,4-pentanediol. These crystals are orthorhombic, space group P212121, and contain one molecule per asymmetric unit; cell dimensions are a = 4.66 nm, b = 5.02 nm, c = 4.04 nm (form I) and alpha = 4.44 nm, b = 5.00 nm, c = 4.03 nm (form II). Using high-performance liquid chromatography, it could be shown for all crystal forms that 2'-GMP is bound in the crystals. The molecular ratio between RNase T1 and 2'GMP was 0.9 for form II crystals and thus agreed with a 1:1 enzyme-nucleotide complex. Heavy-atom derivatives were produced with lead acetate for form IIa crystals and with uranyl acetate for from IIb crystals. Three-dimensional X-ray analysis of the RNase-T1 x 2'GMP complex is under way.     

Structural and conformational studies of polyriboadenylic acid in neutral and acid solution

Raman spectra of solutions of polyriboadenylic acid have been studied in the pH range of 7.2–5.2. Bands are identified which are sensitive to the characteristics of poly(rA) in the single-and double-stranded helical forms. Thermal melting profiles were obtained as a function of pH to monitor simultaneously the changes in (1) the phosphodiester backbone, (2) the base-stacking interactions, (3) the perturbation of the PO unit, and (4) the degree of protonation at the N-1 position in the adenine base. The temperature dependence of the intensity ratio of the bands at 725 and 705 cm^?1 appears to be sensitive to the noncooperative and the cooperative thermal-melting process for the single-and double-stranded forms of poly(rA), respectively. Concurrently, bands diagnostic of the degree of protonation reveal that the cooperative melting process for the “acid” poly(rA) clearly involves deprotonation. The progressive perturbation of the 1100 cm^?1 band with an increasing degree of protonation of poly(rA) is consistent with earlier suggestions regarding a PO-(6)-NH₂ interaction in the double-helical form of poly(rA). The stability of the double-helix parallels the degree of protonation over the pH range studied as reflected in the t_m values, which increase linearly with decreasing pH.     

Formation of the double helix: a mutational study

To investigate the mechanisms by which oligonucleotides hybridize to target molecules, the binding of two oligodeoxynucleotide probes to RNA targets was measured over a broad range of temperatures. Mutations were then scanned across each DNA/RNA hybrid to map, at single base resolution, sequences important for hybridization. Despite being unrelated in sequence, each hybrid formed by a similar mechanism. In the absence of secondary structure, two stretches of bases, termed nucleation regions, cooperated with one another by a looping mechanism to nucleate hybridization. Mutations inside each nucleation region strongly decreased hybridization rates, even at temperatures well below the melting temperature (T_m) of the hybridized duplex. Surprisingly, nucleation regions were detected in a RNA target but not a corresponding DNA target. When either nucleation region was sequestered in secondary structure, the hybridization rate fell and the mechanism of hybridization changed. Single-stranded bases within the nucleation region of the probe and target first collided to form a double helix. If sufficiently G + C rich, the double helix then propagated throughout the oligonucleotide by a strand invasion process. On the basis of these results, general mechanisms for the hybridization of oligonucleotides to complementary and mutant targets are proposed.     

High salt solution structure of a left-handed RNA double helix

Right-handed RNA duplexes of (CG)_n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)₂ determined in 6 M NaClO₄. This is the first nucleic acid motif determined at such high salt. Sequential assignments of non-exchangeable proton resonances of the Z-form were based on the hitherto unreported NOE connectivity path [H6_(n)-H5′/H5″_(n)-H8_(n+1)-H1′_(n+1)-H6_(n+2)] found for left-handed helices. Z-RNA structure shows several conformational features significantly different from Z-DNA. Intra-strand but no inter-strand base stacking was observed for both CpG and GpC steps. Helical twist angles for CpG steps have small positive values (4–7°), whereas GpC steps have large negative values (−61°). In the full-turn model of Z-RNA (12.4 bp per turn), base pairs are much closer to the helix axis than in Z-DNA, thus both the very deep, narrow minor groove with buried cytidine 2′-OH groups, and the major groove are well defined. The 2′-OH group of cytidines plays a crucial role in the Z-RNA structure and its formation; 2′-O-methylation of cytidine, but not of guanosine residues prohibits A to Z helicity reversal.     

Complex between triple helix of collagen and double helix of DNA in aqueous solution

We demonstrate in this paper that one example of a biologically important and molecular self-assembling complex system is a collagen–DNA ordered aggregate which spontaneously forms in aqueous solutions. Interaction between the collagen and the DNA leads to destruction of the hydration shell of the triple helix and stabilization of the double helix structure. From a molecular biology point of view this nano-scale self-assembling superstructure could increase the stability of DNA against the nucleases during collagen diseases and the growth of collagen fibrills in the presence of DNA.     

Diffusion of bovine serum albumin in a neutral polymer solution

The diffusion coefficient D of bovine serum albumin through various solutions (pH 7.0, 0.5M NaCl) of polythylene oxide (M_w ～ 1 × 10⁵, 3 × 10⁵) was studied with quasielastic light scattering. In solutions of the 1 × 10⁵ polymer solution at polymer concentrations above 0.5 g/L, D is considerably greater than would have been expected from the viscosity of water:polymer mixtures, the deviations being larger at low protein concentration that at high protein concentration. With either polymer, D falls with increasing protein concentration.     

Formation of a hydrate structure in the collagen-like triple helix upon hydration

By the IR-spectroscopy method successive stages of hydrate envelope formation of the collagen-like triple-helical structure of the monodisperse synthetic polytripeptide Z-(Gly-Pro-Pro)8-OMe were studied. The multistep-type process is followed by isomorphic transitions of the triple-helical structure and by the increasing of hydrogen bond strength.     

Effect of a single aspartate on helix stability at different positions in a neutral alanine-based peptide.

A single aspartate residue has been placed at various positions in individual peptides for which the alanine-based reference peptide is electrically neutral, and the helix contents of the peptides have been measured by circular dichroism. The dependence of peptide helix content on aspartate position has been used to determine the helix propensity (s-value). Both the charged (Asp-) and uncharged (Asp0) forms of the aspartate residue are strong helix breakers and have identical s-values of 0.29 at 0 degree C. The interaction of Asp- with the helix dipole affects helix stability at positions throughout the helix, not only near the N-terminus, where the interaction is helix stabilizing, and the C-terminus, where it is destabilizing. Comparison of the helix contents at acidic pH (Asp0) and at neutral pH (Asp-) shows that the charge-helix dipole interaction is screened slowly with increasing NaCl concentration, and screening is not complete even at 4.8 M NaCl. Lastly, a helix-stabilizing hydrogen-bond interaction between glutamine and aspartate (spacing i, i + 4) has been found. This side-chain interaction is specific for both the orientation and spacing of the glutamine and aspartate residues and is resistant to screening by NaCl.     

Pre-steady-state currents in neutral amino acid transporters induced by photolysis of a new caged alanine derivative

Na+-Dependent transmembrane transport of small neutral amino acids, such as glutamine and alanine, is mediated, among others, by the neutral amino acid transporters of the solute carrier 1 [SLC1, alanine serine cysteine transporter 1 (ASCT1), and ASCT2] and SLC38 families [sodium-coupled neutral amino acid transporter 1 (SNAT1), SNAT2, and SNAT4]. Many mechanistic aspects of amino acid transport by these systems are not well-understood. Here, we describe a new photolabile alanine derivative based on protection of alanine with the 4-methoxy-7-nitroindolinyl (MNI) caging group, which we use for pre-steady-state kinetic analysis of alanine transport by ASCT2, SNAT1, and SNAT2. MNI-alanine has favorable photochemical properties and is stable in aqueous solution. It is also inert with respect to the transport systems studied. Photolytic release of free alanine results in the generation of significant transient current components in HEK293 cells expressing the ASCT2, SNAT1, and SNAT2 proteins. In ASCT2, these currents show biphasic decay with time constants, tau, in the 1-30 ms time range. They are fully inhibited in the absence of extracellular Na+, demonstrating that Na+ binding to the transporter is necessary for induction of the alanine-mediated current. For SNAT1, these transient currents differ in their time course (tau = 1.6 ms) from previously described pre-steady-state currents generated by applying steps in the membrane potential (tau approximately 4-5 ms), indicating that they are associated with a fast, previously undetected, electrogenic partial reaction in the SNAT1 transport cycle. The implications of these results for the mechanisms of transmembrane transport of alanine are discussed. The new caged alanine derivative will provide a useful tool for future, more detailed studies of neutral amino acid transport.     

Three-dimensional structure of ribonuclease Ms*3'-guanylic acid complex at 2.5 A resolution.

The crystal structure of ribonuclease Ms*3'-guanylic acid complex has been determined by molecular replacement methods based on the known structure of ribonuclease T1. The pattern of hydrogen-bonds between the enzyme and the guanine base is similar to that discovered by Arni et al. [( 1988) J. Biol. Chem. 263, 15358-15368] in the crystal structure of ribonuclease T1*2'-guanylic acid complex. As for the possible general base in the trans-phosphorylation step of the catalysis, 0 epsilon 1 of Glu57 is within the hydrogen-bond distance (2.7 A) of the 2'-0 of the nucleotide while N epsilon 2 of His39 is significantly more distant (3.4 A) from the 2'-0.     

Formation of thomasidioic acid from dehydrosinapinic acid dilactone under neutral conditions, and a remaining inhibitory activity against peroxynitrite-mediated protein nitration

Dehydrosinapinic acid dilactone (1) was converted to thomasidioic acid (3) and (E,E)-2,3-bis(3,5-dimethoxy-4-hydroxybenzylidene)succinic acid (4) via an alpha,beta-unsaturated gamma-lactone type dimer (2) in phosphate buffer (pH 7.4). A study of the reaction mechanism was accomplished by observing the reaction of methyl ester of 2. The lignans (3, 4) were also prevented the peroxynitrite-mediated protein nitration.     

5-Hydroxylevulinic acid,a new intermediate in the biosynthesis of protoanemonin

Administration of 5-hydroxy[1-¹⁴C]-and [4-¹⁴C]levulinic acid to Helleborus foetidus led to the isolation of [1-¹⁴C]- and [4-¹⁴C]protoanemonin, respectively. There was also incorporation of radioactivity into the four glucosides ranunculin, isoranunculin, ranuncoside and ranunculoside. Acid hydrolysis of radioactive ranuncoside gave labelled 5-hydroxylevulinic acid (HKV). A study of the incorporation of various ¹⁴C-labelled tracers into protoanemonin suggested that HKV is formed in higher plants by a new reduction of 2-ketoglutarate (2-KG) without free 4,5-dioxovalerate (DOVA) as an intermediate. A scheme for the biosynthesis of the antibiotic protoanemonin and its glucosidic precursors is proposed. It is shown that 5-(β-d-glucopyranosyloxy)levulinic acid could be the genuine precursor of all the compounds studied.     

Chemical behaviour of cytidine 5'-monophospho-N-acetyl-beta-D-neuraminic acid under neutral and alkaline conditions

The chemical behaviour of CMP-N-acetylneuraminic acid under neutral and different alkaline conditions has been investigated. The products formed were isolated by ion-exchange chromatography and gel filtration and analysed by colorimetric methods, thin-layer chromatography, combined gas-liquid chromatography/mass spectrometry and/or 360-MHz 1H-NMR spectroscopy. A maximum stability of CMP-N-acetylneuraminic acid was observed at pH8-11. In the tested pH range of 6-13, CMP and N-acetylneuraminic acid were formed in variable amounts as decomposition products. 2-Deoxy-2,3-dehydro-N-acetylneuraminic acid was produced at pH greater than 7; the amount of this substance increased with increasing pH. In anhydrous triethylamine its yield was 50%. A new neuraminic acid derivative, N-acetyl-beta-D-neuraminic acid 2-phosphate, could be isolated from the mixture of alkaline decomposition products of CMP-N-acetylneuraminic acid. The yield of this compound was maximum 22% in anhydrous triethylamine. Because 2-deoxy-2,3-dehydro-N-acetylneuraminic acid was formed under simulated physiological conditions, it is assumed that this compound, which occurs in tissues and fluids of man and animals, is derived from CMP-N-acetylneuraminic acid non-enzymically also under conditions in vivo.     

Oligopeptide-mediated helix stabilization of model peptides in aqueous solution.

Oligopeptide-mediated helix stabilization of peptides in hydrophobic solutions was previously found by NMR and CD spectroscopic studies. The oligopeptide included the hydrophobic amino acids found in its parent peptide and were interposed by relevant basic oracidic amino acids. The strength of the interactions depended on the amino acid sequences. However, no helix-stabilizing effect was seen for the peptides in phosphate buffer solution, because the peptides assumed a random-coil structure. In order to ascertain whether the helix-stabilizing effect of an oligopeptide on its parent peptide could operate in aqueous solution, model peptides EK17 (Ac-AEAAAAEAAAKAAAAKA-NH2) and IFM17 (Ac-AEAAAAEIFMKAAAAKA-NH2) that may assume an alpha-helix in aqueous solutions were synthesized. Interactions were examined between various oligopeptides (EAAAK, KAAAE, EIFMK, KIFME, KIFMK and EYYEE) and EK17 or IFM17 in phosphate buffer and in 80% trifluoroethanol (TFE)-20% H2O solutions by CD spectra. EAAAK had little effect on the secondary structures of EK17 in both buffer and TFE solutions, while KAAAE, which has the reverse amino acid sequence of EAAAK, had a marked helix-destabilizing effect on EK17 in TFE. EIFMK and KIFME were found to stabilize the alpha-helical structure of EK17 in phosphate buffer solutions, whereas KIFMK and EYYEE destabilized the alpha-helical structure of EK17. EIFMK and KIFME had no effect on IFM17, because unexpectedly, IFM17 had appreciable amounts of beta-sheet structure in buffer solution. It was concluded that in order for the helix-stabilizing (1) the model peptide, the alpha-helical conformation of which is to be stabilized, should essentially assume an alpha-helical structure by nature, and (2) the hydrophobicity of the side-chains of the oligopeptide should be high enough for the oligopeptide to perform stable specific side chain-side chain intermolecular hydrophobic interactions with the model peptide.