The Conformation of Ribonucleosides in Solution. The Effect of Structure on the Orientation of the Base<sup>*</sup>

Wa, Klee; Sh, Mudd

doi:10.1021/bi00856a006

Cited by 48 publications

(12 citation statements)

References 42 publications

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“…This situation was not recognized earlier because the literature contains only scattered information about the influence of exocyclic groups (e. g . , acetyl, alkylthio, and 5'-deoxy derivatives of uridine [3] and adenosine [13][14][15][16]), and also because many of the earlier ORD and CD spectra were subject to much larger experimental errors (up to k 207J than the spectra obtained with present-day instrumentation. Our systematic studies clearly establish that the circular dichroism of adenosines is quite strongly influenced by C-5' substituents which are neither directly linked to the chromophore nor to the chiral furanose moiety.…”

Section: '-Iodoadenosine (Xi) (-)mentioning

confidence: 99%

Adenine Nucleosides in Solution: Circular Dichroism Studies and Base Conformation

Follmann

Kuntz

Zacharias

1975

European Journal of Biochemistry

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Adenosine, AMP, S-adenosylhomocysteine, S-adenosylmethionine, aristeromycin and 25 other synthetic adenosine analogs modified in the 4' or 5' positions show certain groups of different circular dichroism (CD) spectra. Both positive and negative Cotton effects can occur in the long-wavelength part (250-270 nm) of the spectra. Molar ellipticities [O] range from -6000 (in adenosine 5'-carboxylate) to + 4000 deg. cm2 dmol-l (in 5'-deoxy-5'iodoadenosine), including some compounds with small, polar 5'-substituents in which low-intensity bands are found in signed pairs. Most of these adenosine derivatives that have the same adenine chromophore and a ribofuranose moiety unsubstituted in the 2' and 3' positions prefer an anti-conformation of the adenine base, as evidenced by proton magnetic resonance spectroscopy. In the majority of cases, electronic perturbations of the chromophore or major alterations of the assymmetric sugar residue can be excluded as sources of the C D variations. Therefore a correlation of the long-wavelength C D bands with the glycosyl torsion angle bCN is suggested, where the gauche, gauchelanti combination which is typical of AMP in the crystal and in solution (&.N zz -40 ', [el negative) is one reference point and a region for &N = 0 'is assigned to compounds with space-filling substituents such as S-adenosylmethionine. Both negative and positive Cotton effects can be associated with the anti conformation range. Within this series, the base conformation of novel nucleoside structures could be predicted from CD measurements. The C D spectrum gives no indication, however, of whether a certain torsion angle is the result of a rigid structure (as in AMP) or the average value of a molecule with high rotational freedom (as in 5'-deoxyadenosine). The conformations of aristeromycin and 4'-thioadenosine are discussed in relation to adenosine, and a structure-determining effect of the 4' bridge atom is noted. Circular dichroism (CD) and, in earlier years, optical rotatory dispersion (ORD) spectroscopy have become useful tools for the study of conformation changes in nucleic acids, pol ynucleotides, and nucleosides or mononucleotides [l]. Like nuclear magnetic resonance, these techniques are valuable because they provide information about the state of the molecules in dilute solutions resembling physiological conditions of pH, ionic strength, and concentration. Several authors have described correlations of the sign of Cotton effects in pyrimidine and purine nucleosides with the sugar-base torsion angle &N [2] about the glycosidic bond, based upon empirical assignments important result of these studies is the reversion of long-wavelength Cotton effects found in compounds in which the base is forced out of its regular anticonformation by bulky substituents at the 6 or 8 position of a pyrimidine or purine ring, respectively [9]. The ORD and C D spectra of anomeric pentofuranosides have also been well documented [lo, 111. Studies of magnetic circular dichroism (the Faraday effect) have provided precise resolu...

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Section: '-Iodoadenosine (Xi) (-)mentioning

confidence: 99%

Adenine Nucleosides in Solution: Circular Dichroism Studies and Base Conformation

Follmann

Kuntz

Zacharias

1975

European Journal of Biochemistry

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“…This confirms prior studies showing that the r 1=6 averaging of the NOE signal obtained experimentally is most sensitive to changes in the proton-proton distance distribution at short distances and not sensitive to capture notorious changes in the populations of more than one conformation when present [38][39][40]. Additional experimental observations based on IR and UV spectroscopy, Circular Dichronism and NMR spectroscopy conclude that the glycosidic bond might also adopt an anti conformation beside the syn conformation found in some protein crystals [11][12][13]. In terms of the experimental intramolecular NOE distances the distances H42-H44 and H42-H46 are most sensitive to changes in the glycosidic angle.…”

Section: Resultsmentioning

confidence: 93%

“…The D-HI charges with the optimized parameters for the CT-CT-S-CT dihedral angle constitutes a set of parameters which reproduces the experimental NOE distances and experimentally observed conformations in aqueous solution obtained by other spectroscopy techniques as UV, IR and Circular Dichronism [11][12][13]. These charges will reflect the average molecular electrostatic potential (MEP) of the polarized molecule due to the presence of the solvent, since the Hirshfeld-I method has been shown to reproduce the molecular electrostatic potential in vacuum (see above) and the inclusion of the solvent as point charges in the molecular dynamics simulations should take into account the average polarization.…”

Section: Resultsmentioning

confidence: 94%

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A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation

Sáez

Vöhringer‐Martinez

2015

J Comput Aided Mol Des

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S-Adenosylmethionine (AdoMet) is involved in many biological processes as cofactor in enzymes transferring its sulfonium methyl group to various substrates. Additionally, it is used as drug and nutritional supplement to reduce the pain in osteoarthritis and against depression. Due to the biological relevance of AdoMet it has been part of various computational simulation studies and will also be in the future. However, to our knowledge no rigorous force field parameter development for its simulation in biological systems has been reported. Here, we use electronic structure calculations combined with molecular dynamics simulations in explicit solvent to develop force field parameters compatible with the AMBER99 force field. Additionally, we propose new dynamic Hirshfeld-I atomic charges which are derived from the polarized electron density of AdoMet in aqueous solution to describe its electrostatic interactions in biological systems. The validation of the force field parameters and the atomic charges is performed against experimental interproton NOE distances of AdoMet in aqueous solution and crystal structures of AdoMet in the cavity of three representative proteins.

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“…It was reported by Arnott & Hukins (1969) and Sundaralingam (1969)that the conformational angles in the monomers of the nucleic acid are confined to narrow ranges, no matter what their environment in crystals may be. However, the conformations of nucleotides in the solid state determined by X-ray analysis and in solution, which were investigated by means of n.m.r, or o.r.d., are not always in good agreement with each other (Schrimer, Davis, Noggle & Hart, 1972;Klee & Mudd, 1967). These differences in conformation indicate that there is considerable flexibility in the sugar-base conformation and ribose puckering.…”

Section: Introductionmentioning

confidence: 89%

The crystal and molecular structure of inosine-5'-phosphate

Nagashima¹,

Wakabayashi²,

Matsuzaki³

et al. 1974

Acta Crystallogr Sect B

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The crystal and molecular structure of inosine-5'-phosphate has been determined by the symbolic addition method. The crystal obtained from an aqueous methanol solution contains one water and one methanol molecule per nucleotide and belongs to space group P2,212, with a=23.33, b=4.788, c= 15"44/~, Z=4. The phosphate oxygen atoms are distributed at the two rotational positions around the P-O ester bond. The torsion angle of the base with respect to the sugar, ~bcN is -20 °, in the anti conformation. The ribose puckering is C(3")-endo, which is different from the molecule of inosine-5'-phosphate in the salt crystals. The conformation about the C(4')-C(5') bond is gauche-gauche. Large tunnels run through the structure parallel to the b axis. Water and methanol molecules fill the tunnels, but their positions are considerably disordered.

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The Conformation of Ribonucleosides in Solution. The Effect of Structure on the Orientation of the Base^*

Cited by 48 publications

References 42 publications

Adenine Nucleosides in Solution: Circular Dichroism Studies and Base Conformation

Adenine Nucleosides in Solution: Circular Dichroism Studies and Base Conformation

A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation

The crystal and molecular structure of inosine-5'-phosphate

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The Conformation of Ribonucleosides in Solution. The Effect of Structure on the Orientation of the Base*

Cited by 48 publications

References 42 publications

Adenine Nucleosides in Solution: Circular Dichroism Studies and Base Conformation

Adenine Nucleosides in Solution: Circular Dichroism Studies and Base Conformation

A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation

The crystal and molecular structure of inosine-5'-phosphate

Contact Info

Product

Resources

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The Conformation of Ribonucleosides in Solution. The Effect of Structure on the Orientation of the Base^*