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Journal ArticleDOI

Permanent dipole moment of tRNA's and variation of their structure in solution.

01 Aug 1990-Biophysical Journal (The Biophysical Society)-Vol. 58, Iss: 2, pp 403-411

TL;DR: The structure of six different tRNA molecules has been analyzed in solution by electrooptical measurements and by bead model simulations and these measurements indicate that the structure of some other tRNA's in solution is different, even in cases with the same number of nucleotide residues.

AbstractThe structure of six different tRNA molecules has been analyzed in solution by electrooptical measurements and by bead model simulations. The electric dichroism measured as a function of the field strength shows that tRNA's are associated with substantial permanent dipole moments, which are in the range of 1 x 10(-27) cm(identical to 300 D; before correction for the internal directing field). Rotational diffusion time constants of tRNA molecules in their native state at 2 degrees C show a considerable variation. A particularly large value found for tRNA(Tyr) (50 ns) can be explained by its nine additional nucleotide residues. However, remarkable variations remain for tRNA molecules with the standard number of 76 nucleotide residues (tRNA(Phe) [yeast] 41.6 ns, tRNA(Val) [Escherichia coli] 44.9 ns, tRNA(Glu) [E. coli] 46.8 ns; tRNA(Phe) [E. coli] 48.3 ns). These variations indicate modulations of the tertiary structure, which may be due to a change of the L-hinge angle. Bead models are used to simulate both electric and hydrodynamic parameters of tRNA molecules according to the crystal structure of tRNA(Phe) (yeast). The asymmetric distribution of phosphate charges with respect to the center of diffusion leads, under the assumption of a constant charge reduction to 15% by ion condensation, to a theoretical dipole moment of 7.2 x 10(-28) cm, which is in reasonable agreement with the measurements. The dichroism decay curve calculated for tRNA(Phe) (yeast) is also consistent with the measurements and thus the structure in solution and in the crystal must be very similar in this case. However, our measurements also indicate that the structure of some other tRNA's in solution is different, even in cases with the same number of nucleotide residues.

Topics: Native state (51%)

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Citations
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Book ChapterDOI
Abstract: Publisher Summary This chapter discusses the role of tRNA structure in the recognition process with synthetases and on the implications for aminoacylation efficiency. Many examples are taken from our own research on several specific aminoacylation systems, for example aspartate, histidine, valine, but concepts are presented more globally with reference to the complete set of aminoacylation systems. It emphasizes on the importance of tRNA-like structures for understanding the interaction of canonical tRNAs with synthetase. Although tRNA-like molecules found in some plant viral RNAs do not participate in protein synthesis, they represent interesting natural mutants to be compared to canonical tRNAs. This is also the case of tRNAlike structures found in some messenger RNAs as well as of bizarre tRNAs from mitochondria . In addition, competition and kinetic effects may also contribute to the overall specificity of the various aminoacylation systems; the balance between the concentration of tRNAs and synthetases would be essential for ensuring optimal specificity. According to this view, individual aminoacylation systems do not work at their optimal chemical efficiency, but work instead to assure optimal discrimination among the different aminoacylation systems. Such a balance may be perturbed under certain physiological or pathological conditions. Finally, this chapter discusses a comparison of recent results with previous observations, and show how old concepts established phenomenologically can now be tested more explicitly.

185 citations


Journal ArticleDOI
TL;DR: If the hydrodynamic model for the short DNA is simply a cylindrical rod, the predictions for overall translation and rotation are slightly worse, but the NMR correlation times and the degree of hydration, which depend more on the cross-sectional structure, are more severely affected.
Abstract: Hydrodynamic properties (translational diffusion, sedimentation coefficients and correlation times) of short B-DNA oligonucleotides are calculated from the atomic-level structure using a bead modeling procedure in which each non-hydrogen atom is represented by a bead. Using available experimental data of hydrodynamic properties for several oligonucleotides, the best fit for the hydrodynamic radius of the atoms is found to be approximately 2.8 A. Using this value, the predictions for the properties corresponding to translational motion and end-over-end rotation are accurate to within a few percent error. Analysis of NMR correlation times requires accounting for the internal flexibility of the double helix, and allows an estimation of approximately 0.85 for the Lipari-Szabo generalized order parameter. Also, the degree of hydration can be determined from hydrodynamics, with a result of approximately 0.3 g (water)/g (DNA). These numerical results are quite similar to those found for globular proteins. If the hydrodynamic model for the short DNA is simply a cylindrical rod, the predictions for overall translation and rotation are slightly worse, but the NMR correlation times and the degree of hydration, which depend more on the cross-sectional structure, are more severely affected.

76 citations


Journal ArticleDOI
TL;DR: The method is intended to provide data that may be compared to the results of transient electric dichroism experiments on protein solutions to give hydrodynamic and electrical parameters for proteins in good agreement with experimental data.
Abstract: A simple and computationally feasible procedure for the calculation of net charges and dipole moments of proteins at arbitrary pH and salt conditions is described. The method is intended to provide data that may be compared to the results of transient electric dichroism experiments on protein solutions. The procedure consists of three major steps: (i) calculation of self energies and interaction energies for ionizable groups in the protein by using the finite-difference Poisson-Boltzmann method, (ii) determination of the position of the center of diffusion (to which the calculated dipole moment refers) and the extinction coefficient tensor for the protein, and (iii) generation of the equilibrium distribution of protonation states of the protein by a Monte Carlo procedure, from which mean and root-mean-square dipole moments and optical anisotropies are calculated. The procedure is applied to 12 proteins. It is shown that it gives hydrodynamic and electrical parameters for proteins in good agreement with experimental data.

68 citations


Cites background from "Permanent dipole moment of tRNA's a..."

  • ...Dipole moments are also important for proper interpretation of the results of electrooptical relaxation experiments in terms of macromolecular structures (O'Konsky et al., 1959; Porschke, 1987; Porschke and Antosiewicz, 1990)....

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Journal ArticleDOI
TL;DR: This method uses a convex hull model to estimate the hydrodynamic volume of the molecule and is orders of magnitude faster than common methods and works well for both folded proteins and ensembles of conformationally heterogeneous proteins and for nucleic acids.
Abstract: Hydrodynamic properties are useful parameters for estimating the size and shape of proteins and nucleic acids in solution. The calculation of such properties from structural models informs on the solution properties of these molecules and complements corresponding structural studies. Here we report, to our knowledge, a new method to accurately predict the hydrodynamic properties of molecular structures. This method uses a convex hull model to estimate the hydrodynamic volume of the molecule and is orders of magnitude faster than common methods. It works well for both folded proteins and ensembles of conformationally heterogeneous proteins and for nucleic acids. Because of its simplicity and speed, the method should be useful for the modification of computer-generated, intrinsically disordered protein ensembles and ensembles of flexible, but folded, molecules in which rapid calculation of experimental parameters is needed. The convex hull method is implemented in a Python script called HullRad. The use of the method is facilitated by a web server and the code is freely available for batch applications.

56 citations


Cites methods from "Permanent dipole moment of tRNA's a..."

  • ...RNA molecules in isolation are flexible (37,38), so we used two different protein-RNA complexes—histidinyl-tRNA synthetase (39,40) and bacterial 50s ribosomal subunit—to test the method on known structures containing RNA that are expected to be less flexible....

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Journal ArticleDOI
TL;DR: The translational and rotational diffusion coefficients of very short DNA fragments have been calculated using a double-helical bead model in which each nucleotide is represented by one bead, indicating that the internal motion of the bases has a remarkable amplitude.
Abstract: The translational and rotational diffusion coefficients of very short DNA fragments have been calculated using a double-helical bead model in which each nucleotide is represented by one bead. The radius of the helix is regarded as an adjustable parameter. The translational coefficient and the perpendicular rotation coefficient agree very well with experimental values for oligonuclotides with 8, 12, and 20 base pairs, for a single value of the helical radius of about 10 A. We have also calculated a nuclear magnetic resonance relaxation time in which the coefficient for rotation about the main axis is involved. As found previously with cylindrical models, the results deviate from experimental values, indicating that the internal motion of the bases has a remarkable amplitude. An attempt to quantify the extent of internal motions is presented.

37 citations


Cites background from "Permanent dipole moment of tRNA's a..."

  • ...However, bead models at a molecular scale, even with atomic resolution, were later used successfully for various biopolymers (Venable and Pastor, 1988; Porschke and Antosiewicz, 1990; Tirado et al., 1990)....

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References
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Book
01 Jan 1973

483 citations


Journal ArticleDOI
Abstract: Single-stranded polynucleotides are used as model systems for the investigation of conformational changes induced by electric fields. It is demonstrated that the single-strand helix–coil transition in poly(A), poly(dA), and poly(C) can be induced by application of high electric fields. The transition is measured by UV absorbance using polarized light at an angle of 54.8° with respect to the vector of the electric field and by electrodichroism. A linear increase of the absorbance, reflecting the helix-to-coil transition, is observed at increasing field strength. When ions are added to the polymer, electric fields do not induce conformation changes, unless a threshold value of the electric field strength E0 is exceeded. At field strengths above this threshold, the degree of transition is a linear function of the increase in field strength. The threshold values E0 show a linear increase with the logarithm of the ion concentration. Bivalent ions cause thresholds at much lower ion concentrations than mo-novalent ions. The shielding efficiency of ions is correlated to the binding affinity of these ions to the polymer. The conformation changes induced by the field and the existence of thresholds can be explained on the basis of dissociation field effects. Similar threshold effects may be expected for other macromolecules as well as for membrane structures and may be important in the regulation of bioelectricity.

29 citations