Influence of Conterions on the Radius of Gyration of Phenylalanine Specific Transfer RNA as Determined by Small Angle X‐Ray Studies

Abstract

The influence of the ion and water cloud shell on the structure of polyelectrolytes is very important especially for small angle studies. I n the present work the change in the radius of gyration of phenylalanine specific tRNA under the influence of various counterions was investigated. tRNAPhe(yeast) was studied in different solutions at pH 7.5, each containing only one certain kind of cation. As cations lithium, cesium, barium and spermidin were used. The influence of the ions on the radius of gyration of tRNAPhe (yeast) . As a rule it is not absolutely necessary t o use the coordinates of the single atoms [6] for the calculation and often the coordinates are assigned only t o the scattering centers of base, sugar and phosphate groups. This approximation has no decisive influence on the calculated value of the radius of gyration or on the inner portion of the scattering curve.The comparison of the experimental small angle X-ray data with those calculated for a particular model involves another problem. The experimental studies are carried out in solution and the influence of the solvent, the counterions and additional electrolytes on the radius of gyration is not well known.Since the problem of the structure of the water shell could not be completely clarified even with simple ions [7], the theoretical treatment of the water shell and hydration presents very great difficulties with a polyelectrolyte such as tRNA.Therefore the influence of the water and ion cloud shell is frequently ignored; some authors [3,4] assign one univalent ion to each phosphate group of the tRNA molecule for the calculation.Theoretically, polyions have discrete charged groups, and for many calculations it is assumed that counterions are bound only to these discrete groups. I n real polyions, however, a m u s e atmosphere of counterions in which the distribution of the counterions fluctuates must be assumed [7]. A theoretical treatment of this problem, based upon a geometric concept, was given by Luzzati et al. [S].I n order t o compare the experimental data with the data calculated for the various suggested models it seemed important to discover more about the influence of both hydration and the binding of counterions. Consequently we investigated tRNAPhe in solution in several cationic forms. Similar studies were effected by Luzzati et al.[S] and Bram [9] on DNA molecules; the authors determined the mass per unit length and the radius of gyration of the cross-section of DNA by using various counterions. The results obtained by the two groups are not in mutual agreement, as is discussed in detail by Eisenberg and Cohen [lo]. EXPERIMENTAL PROCEDURE MATERJAL.SPreparation of tRNAPhe( Yeast) with a Certain Cation 77 mg of tRNAPhe from yeast prepared as described earlier [l] was dissolved in 20 ml of double-distilled water. 5 ml aliquots were dialyzed once against 0.4 M sodium phosphate pH 7.0, twice

Mg2+-Dependent Compaction and Folding of Yeast tRNAPhe and the Catalytic Domain of the B. subtilis RNase P RNA Determined by Small-Angle X-ray Scattering

“…(i) The R g and the P(r) function of the tRNA Phe are in excellent agreement with those calculated from the crystal structure (Figure 1D). (ii) The R g values at tRNA concentrations of 0.3-0.5 mg/mL are in agreement with earlier studies conducted over a more extensive concentration range [up to 20 mg/mL (26,27)], including a study where the correct monomolecular weight of tRNA was obtained from the absolute scattering intensity (28). (iii) The normalized scattering intensity, I(0)/C, is independent of concentration 5) for both unmodified (Figure 1C) and modified tRNA Phe (data not shown) at 0.3 and 0.5 mg/mL.…”

Structure of phenylalanine-accepting transfer ribonucleic acid and of its environment in aqueous solvents with different salts

“…Before the publication of the crystal structure of tRNAPhe by Kim et al (1974) and Robertus et al (1974), considerable effort was directed toward finding the structure of the molecule by various solution methods [for example, the X-ray smallangle studies of Pilz et al (1971) and Ninio et al (1972)]. Since, and especially following the crystal structures of a number of tRNAs, all showing a characteristic L shape (Shevitz et al, 1979;Woo et al, 1980;Moras et al, 1980), the question has shifted to the relationship between solution and crystal structures and to conformational changes in different conditions [review by Schimmel & Redfield (1980) and Favre & Thomas (1981)].…”

Tertiary structure and function of transfer-RNA

“…This is especially low-angle X-ray scattering [19,50,70]. This method measures in addition to the t-RNA structure the unknown, but in this case important amount of bound water molecules and cations [75]; thus limiting the value of this method.…”