Structural and functional roles of the N1- and N3-protons of psi at tRNA's position 39.

Pseudouridine at position 39 (Psi(39)) of tRNA's anticodon stem and loop domain (ASL) is highly conserved. To determine the physicochemical contributions of Psi(39)to the ASL and to relate these properties to tRNA function in translation, we synthesized the unmodified yeast tRNA(Phe)ASL and ASLs with various derivatives of U(39)and Psi(39). Psi(39)increased the thermal stability of the ASL (Delta T (m)= 1.3 +/- 0.5 degrees C), but did not significantly affect ribosomal binding ( K (d)= 229 +/- 29 nM) compared to that of the unmodified ASL (K (d)= 197 +/- 58 nM). The ASL-Psi(39)P-site fingerprint on the 30S ribosomal subunit was similar to that of the unmodified ASL. The stability, ribosome binding and fingerprint of the ASL with m(1)Psi(39)were comparable to that of the ASL with Psi(39). Thus, the contribution of Psi(39)to ASL stability is not related to N1-H hydrogen bonding, but probably is due to the nucleoside's ability to improve base stacking compared to U. In contrast, substitutions of m(3)Psi(39), the isosteric m(3)U(39)and m(1)m(3)Psi(39)destabilized the ASL by disrupting the A(31)-U(39)base pair in the stem, as confirmed by NMR. N3-methylations of both U and Psi dramatically decreased ribosomal binding ( K (d)= 1060 +/- 189 to 1283 +/- 258 nM). Thus, canonical base pairing of Psi(39)to A(31)through N3-H is important to structure, stability and ribosome binding, whereas the increased stability and the N1-proton afforded by modification of U(39)to Psi(39)may have biological roles other than tRNA's binding to the ribosomal P-site.

Unconventional structure of tRNA(Lys)SUU anticodon explains tRNA's role in bacterial and mammalian ribosomal frameshifting and primer selection by HIV-1.

Transfer RNA(Lys)SUU, with a 5-modified-2-thiouridine at wobble position 34, facilitates -1 frameshifts for correct translation of the Escherichia coli DNA polymerase gamma subunit and retroviral polymerases. Peptidyl-tRNA(Lys)SUU prematurely terminates translation more often than other tRNAs. In order to determine if the anticodon structures of bacterial and mammalian tRNA(Lys)SUU species explain these observations, oligonucleotides corresponding to the anticodon regions of mammalian and E. coli tRNA(Lys)SUU were synthesized and their physicochemical properties compared with that of E. coli tRNA(Glu)SUC. The anticodon region of tRNA(Lys)SUU was stabilized by an unusual interaction between the side chains of the 5-modified-s(2)U34 and N-6-threonylcarbamoyl-adenosine-37 (t(6)A37), a combination of modified nucleosides unique to tRNA(Lys)SUU species. This first observation of modified nucleoside side-chain interactions is analogous to the interactions of amino acid side chains in proteins. The tRNA(Lys)SUU anticodon structure was determined from NMR restraints on model oligonucleotides. With only two of three anticodon bases available for codon pairing, this unconventional anticodon structure is a reasonable explanation for the bacterial and mammalian tRNA(Lys)SUU tendency to frameshift. A two-out-of-three reading of coding triplets also explains the increased rate at which peptidyl-tRNA(Lys)SUU prematurely terminates translation. In addition, modified nucleoside interaction distorts the anticodon loop. The distorted loop is a possible structural determinant for the preferential selection of tRNA(Lys3)SUU as primer of HIV-1 reverse transcriptase in vivo.

Design, biological activity and NMR-solution structure of a DNA analogue of yeast tRNA(Phe) anticodon domain.

Design of biologically active DNA analogues of the yeast tRNA(Phe) anticodon domain, tDNAPheAC, required the introduction of a d(m5C)-dependent, Mg(2+)-induced structural transition and the d(m1G) disruption of an intra-loop dC.dG base pair. The modifications were introduced at residues corresponding to m5C-40 and wybutosine-37 in tRNA(Phe). Modified tDNAPheAC inhibited translation by 50% at a tDNAPheAC:ribosome ratio of 8:1. The molecule's structure has been determined by NMR spectroscopy and restrained molecular dynamics with an overall r.m.s.d. of 2.8 A and 1.7 A in the stem, and is similar to the tRNA(Phe) anticodon domain in conformation and dimensions. The tDNAPheAC structure may provide a guide for the design of translation inhibitors as potential therapeutic agents.

Complexation of arsenic species in rabbit erythrocytes.

The binding of arsenite, As(III), and arsenate, As(V), by molecules in the intracellular compartment of rabbit erythrocytes has been studied by 1H- and 31P-NMR spectroscopy, uptake of 73As, and ultrafiltration experiments. For intact erythrocytes to which 0.1-0.4 mM arsenite was added, direct evidence was obtained for entry of 76% within 1/2 h and subsequent binding of As(III) by intracellular glutathione and induced changes in the hemoglobin structure (NMR), likely due to binding of As(III). These results were compared with the effect of addition of As(V) on intact erythrocytes and revealed that a smaller amount of As(V) (approximately 25%) enters the cells; the main fraction of As(V) enters the phosphate pathway, depletes ATP, and increases Pi. In contrast, As(III) did not affect the ATP level. Both 1H- and 31P-NMR data indicated striking differences between As(III) and As(V) behavior when incubated with rabbit erythrocytes. These differences were confirmed by 73As uptake and binding experiments. meso-2,3-Dimercaptosuccinic acid (DMSA), a dithiol ligand, released glutathione from its arsenite complexes in erythrocytes.

Reduction and binding of arsenate and dimethylarsinate by glutathione: a magnetic resonance study.

By observing the chemical shifts of the proton and carbon-13 nuclei of reduced glutathione, the interactions of arsenate, arsenite and dimethylarsinate with this tripeptide have been characterized. These spectral studies show the reduction and complexation of arsenic to be a two-step process. Initially, the oxidation of 2 mol of glutathione reduces arsenate to arsenite. Then, 3 mol of glutathione are consumed in the formation of a glutathione-arsenite complex. Similar experiments with arsenite identified a (glutathione)3-arsenite complex; however, no oxidized glutathione was detected. The arsenite binding site in the glutathione-arsenite complex is the cysteinyl sulfhydryl. The glutathione-arsenite complex is stable over the pH range from 1.5 to 7.0-7.5. At higher pH, dissociation occurs releasing reduced glutathione. For a glutathione to dimethylarsinate ratio of 3, oxidized glutathione is also coupled with a reduction to trivalent dimethylarsinous acid, prior to the formation of a 1:1 glutathione-dimethylarsinite complex. The role of reduced glutathione in the metabolism of arsenic is consistent with the previously described effects of this agent on the organismic toxicity of arsenic.

Transfer of arsenite from glutathione to dithiols: a model of interaction.

The interactions of arsenate and arsenite with meso-2,3-dimercaptosuccinic acid (DMSA) have been characterized using carbon-13 nuclear magnetic resonance. These studies show that DMSA reduces arsenate to arsenite and complexes arsenite. Monitoring the carbon-13 signals of complexed DMSA and liberated glutathione shows that DMSA readily extracts arsenite from a (glutathione)3-arsenite complex, proving the affinity of arsenite for dithiols is greater than that for monothiols. Competition between DMSA (vicinal thiols) and dithioerythritol (1,4-dimercapto-2,3-butanediol) for binding of arsenite indicates that the binding affinity is inversely related to the distance between the two thiol groups. On the basis of these findings, a model for the interaction of arsenic with mono- and dithiol-containing molecules is proposed.

1H-, 13C- and 31P-NMR studies of dioctanoylphosphatidylcholine and dioctanoylthiophosphatidylcholine.

Coupling constants and chemical shifts were measured for dioctanoylphosphatidylcholine and its thio analogue in a CDCl3/CD3OD solvent mixture. Replacing the bridging oxygen atom of the CH-CH2-O-P portion of the phosphatidylcholine molecule with a sulfur atom affects chemical shifts and coupling constants in the glycerol backbone portion of the molecule as well as in the choline head group region. Preferred conformations about selected bonds in the phospholipids were determined from the vicinal 1H-1H, 31P-1H and 31P-13C coupling constants. A reduction of the 31P T2* (effective spin-spin relaxation time) for the thio analogue, as well as changes in the relative chemical shifts of 13C nuclei in the acyl chains, suggest a somewhat greater degree of aggregation for the thio analogue. The quadrupolar coupling constant 1J(14N-13C) for the choline methyls of either analogue, however, indicates that aggregation of these phospholipids in the CDCl3/CD3OD solvent mixture is not significant. Differences in conformation between dioctanoylphosphatidylcholine and its thio analogue may be responsible for their differences in chemical and physical properties.