Molecular orbital studies on the conformation of the terminal aminoacyladenosine moieties of tRNA

Saran, Anil; Pullman, Bernard; Pérahia, David

doi:10.1016/0014-5793(72)80309-0

Cited by 9 publications

(11 citation statements)

References 14 publications

(15 reference statements)

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“…S~m/Iar considerations are likely to apply to tryptophanyl-adenosi~e, so that the intramoleCular'stacked configuration is unlikely, and this is supported by our fluorescence data_ Molecular orbital calculations also favour an "open" structure, thou~h they suggest that amknoacybadenosine moeities may have somewhat more eonformational freedom t|mn puromycin [9] _ A stacking interaction in Trp-tRNAT~ would favour models ~qth the 3'-terminus rather close to one loop, or a sugar-phosphate backbone conformation in the termir~aI regi~xn which brings ~he amino acid ~to proximity with other bases in the acceptor stem. There is experimental evidence in favour of an interaction be-…”

Section: Resutts Mad D~cussionsupporting

confidence: 61%

Fluorescence of tryptophanyl‐tRNA^Trp from E. coli; An interaction between the indole and tRNA and its dependence on tRNA conformation

Buckingham

Danchin

1973

FEBS Letters

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Section: Resutts Mad D~cussionsupporting

confidence: 61%

Fluorescence of tryptophanyl‐tRNA^Trp from E. coli; An interaction between the indole and tRNA and its dependence on tRNA conformation

Buckingham

Danchin

1973

FEBS Letters

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“…X-Ray (30-35), p.m.r. (18)(19), and theorktical calculations (36) consistently predict a correlation between puckering and the C4.-C,, conformer population. (The consistent prediction is that for pyrimidine nucleosides with features a, b, and c, the gg conformation is favored if the ring assumes a C,, endo pucker but is destabilized by a C,, endo p~c k e r .~)…”

Section: Discussionmentioning

confidence: 81%

A Nuclear Magnetic Resonance Study of Nucleoside Conformation in Solution. The Effect of Structure and Conformation on the Magnetic Nonequivalence of the 5′-Methylene Hydrogens

Hruska¹,

Wood²,

McCaig³

et al. 1974

Can. J. Chem.

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The relative chemical shift between the 5'-methylene hydrogens of a number of purine and pyrimidine nucleosides and nucleotides in solution are presented. For structurally related pyrimidine nucleosides in aqueous solution a good correlation between this relative shift and the sum of the 4'-5' hydrogen-hydrogen vicinal coupling constants is noted. For this series of related molecules arguments are presented that the variation in the magnetic nonequivalence of this pair of hydrogens is a consequence of conformational changes about the C4'-C5' bond. Deviations from the correlation plot a r e observed for purine derivatives, nucleoside monophosphates etc. and discussed in terms of the effect of the specific chemical modification upon the nucleoside conformation and upon the intrinsic chemical shift nonequivalence of the 5'-methylene hydrogens.On presente les deplacements chimiques relatifs des hydrogenes appartenant aux groupes mCthylenes-5' pour plusieurs nuclCosides et nuclCotides dCrivCs de la purine et de la pyrimidine en solution. O n remarque un bon accord entre ce deplacement chimique relatif et la somme des constantes de couplage vicinal hydrogene-hydrogene 4'-5' pour les nucleosides dCrivCs de la pyrimidine qui sont relies par leur structure.On apporte des preuves visant a demontrer que la variation de la non-Cquivalence magnetique d' e cette paire d'hydrogenes est une consiquence de changements de conformation autour du lien C4'-C5' pour cette skrie de molCcules. On observe et on discute des Ccarts par rapport a cette relation dans le cas des derives de la purine, des monophosphates de nuclCoside etc. Ces Ccarts seraient d i s a l'effet d e rnodification chimique spCcifique a u niveau de la conformation du nuclkoside et a u niveau de la non-Cquivalence intrinseque des dtplacements chimiques des hydrogenes appartenant aux groupes methylenes-5'.[Traduit par le journal]Can. J . Chem., 52,497 (1974)

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“…These two rotamers are coupled and mutually stabilized by a combination of ionic, dipolar and, in special cases, hydrogen bonding forces to which the C-5' groups contribute a decisive fraction. These data offer a valuable experimental verification of the quantum-mechanical coniputations predicting a similar interdependence [7]. It must be envisaged that stabilizing forces determine the typical conformation of a ribonucleoside to a much higher degree than do small steric barriers of rotation (H-2') destabilizing certain base torsion angles.…”

Section: Non-classical Base Con Formationsmentioning

confidence: 78%

“…Although these forces must be small they should still contribute substantially to a selective energetic stabilisation of the anti-conformation if this is only slightly favored over the syn-conformation. For example, refined computations [6,7] indicate that the type of sugar ring puckering may intricately direct base and C-5' conformations and it is clear that in such a case additional interactions, however weak, could greatly affect the individual structure of a nucleoside molecule.…”

Section: The Nature Of Base-ribose Interactionsmentioning

confidence: 99%

“…We initially focussed our attention on adenine nucleosides because of the wide natural occurrence of adenine derivatives and because of the synthetic availability of a large number of suitable analogs. In the adenosine series, PCILO ("perturbative configuration interaction using localized orbitals") computations, as well as the inspection of space-filling models, suggest that the anti and syn-conformation ranges [6] and the gaucheltrans rotamers [7] are separated by rather low energy barriers but that a different situation may exist in adenosine phosphates [8]. The anti-con formation is preferred in most crystalline compounds [I] but some others have been found to crystallize with a syn-base conformation, e.g.…”

mentioning

confidence: 99%

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Adenine Nucleosides in Solution: Stabilisation of the anti‐Conformation by C‐5′ Substituents

Follmann

Gremels

1974

European Journal of Biochemistry

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Proton magnetic resonance spectra of 30 adenine nucleosides have been obtained in dilute (0.001 to 0.05 M) aqueous or dimethyl sulfoxide solutions and have been analysed with respect to structuredependent variations of the purine proton chemical shifts. In 2Hz0 the resonance signal of H-8 shows a marked dependence upon the nature of substituents linked to C-4' of adenine ribofuranoside derivatives and upon the presence of a 2': 3'-O-isopropylidene group while H-2 is relatively unaffected.Therefore the chemical shift difference, 6H-8 -6H-2 = Ad, may serve as an indicator of intramolecular ribose-base interact ons. d6 varies with the chemical nature of C-4' or C-5' substituents in the order: ammonium, sulfonium (0 ppm) < hydrogen < hydroxyl amino < thio < halogen < phosphate, carboxylate (0.4 ppm), and decreases with increasing chain length of these substituents. These results suggest the existence of electrostatic and dipolar repulsion or, in the majority of cases, attractive forces between the C-5' and C8-H regions of adenine nucleosides which have been previously demonstrated for 5'-nucleotides only. They imply a strong preference of most adenosine derivatives with unsubstituted 2' and 3'-hydroxyl groups for the anti-conformation range and the gauche, gauche C-5' conformation. In dimethyl sulfoxide, basically the same situation exists but different substituents exhibit smaller individual A6 variations than in water, indicating different solvation shells. In this solvent two additional conformation-stabilizing contributions can be recognized, viz. an interaction of the bridge oxygen (0-4') of ribose with adenine, and a hydrogen bond between H-8 and a 5'-carboxylate anion. This energetic stabilisation of the anti and g,g-conformers by most types of adenosine C-5' substituents supports the "rigidity" concept of nucleotides, extending it to the nucleoside level. The only exception found is 5'-nitromethyladenosine in which ultraviolet, circular dichroism and magnetic resonance spectra suggest rotation of the adenine base to a "non-classical" conformation due to base-chain n-electron interaction. The anti-conformation of the adenosine derivatives used in this study can in some cases be correlated with their enzymatic deamination by adenosine and AMP aminohydrolase.The biochemical function of nucleosides and nucleotides as substrates or effectors of the degrading and polymerizing enzymes of nucleic acid metabolism depends critically upon the molecular conformation which they assume in solution. The three substructures of a typical nucleoside, viz. the heterocyclic base, the pentofuranose ring and the exocyclic 5'-carbon atom carrying various substituents, are known to be arranged in certain relative orientations which have been Part 1 of a series entitled Forces Stabilizing the Conformation of Nucleosides in Solution.

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Molecular orbital studies on the conformation of the terminal aminoacyladenosine moieties of tRNA

Cited by 9 publications

References 14 publications

Fluorescence of tryptophanyl‐tRNA^Trp from E. coli; An interaction between the indole and tRNA and its dependence on tRNA conformation

Fluorescence of tryptophanyl‐tRNA^Trp from E. coli; An interaction between the indole and tRNA and its dependence on tRNA conformation

A Nuclear Magnetic Resonance Study of Nucleoside Conformation in Solution. The Effect of Structure and Conformation on the Magnetic Nonequivalence of the 5′-Methylene Hydrogens

Adenine Nucleosides in Solution: Stabilisation of the anti‐Conformation by C‐5′ Substituents

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Molecular orbital studies on the conformation of the terminal aminoacyladenosine moieties of tRNA

Cited by 9 publications

References 14 publications

Fluorescence of tryptophanyl‐tRNATrp from E. coli; An interaction between the indole and tRNA and its dependence on tRNA conformation

Fluorescence of tryptophanyl‐tRNATrp from E. coli; An interaction between the indole and tRNA and its dependence on tRNA conformation

A Nuclear Magnetic Resonance Study of Nucleoside Conformation in Solution. The Effect of Structure and Conformation on the Magnetic Nonequivalence of the 5′-Methylene Hydrogens

Adenine Nucleosides in Solution: Stabilisation of the anti‐Conformation by C‐5′ Substituents

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Fluorescence of tryptophanyl‐tRNA^Trp from E. coli; An interaction between the indole and tRNA and its dependence on tRNA conformation

Fluorescence of tryptophanyl‐tRNA^Trp from E. coli; An interaction between the indole and tRNA and its dependence on tRNA conformation