Molecular dynamics of phenylalanine transfer RNA

Structural Insights into tRNA Dynamics on the Ribosome

High-resolution structures at different stages, as well as biochemical, single molecule and computational approaches have highlighted the elasticity of tRNA molecules when bound to the ribosome. It is well acknowledged that the inherent structural flexibility of the tRNA lies at the heart of the protein synthesis process. Here, we review the recent advances and describe considerations that the conformational changes of the tRNA molecules offer about the mechanisms grounded in translation.

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

Experimental and computational determination of tRNA dynamics

As the molecular representation of the genetic code, tRNA plays a central role in the translational machinery where it interacts with several proteins and other RNAs during the course of protein synthesis. These interactions exploit the dynamic flexibility of tRNA. In this minireview, we discuss the effects of modified bases, ions, and proteins on tRNA structure and dynamics and the challenges of observing its motions over the cycle of translation.

Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A′-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA – namely major groove width, inclination and the number of base pairs in a helical twist – over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A′-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors).

Molecular dynamics applied to nucleic acids

In this Account, we focus on molecular dynamics (MD) simulations involving fully solvated nucleic acids. Historically, MD simulations were first applied to proteins and several years later to nucleic acids. The first MD simulations of DNA were carried out in vacuo, but nowadays fully solvated systems are common practice. Recently, technical improvements have made it possible to conduct accurate MD simulations of highly charged nucleic acids. The state-of-the-art of MD simulations and a number of applications on various nucleic acid systems are discussed.

RNA tertiary structure of the HIV RRE domain II containing non-Watson-Crick base pairs GG and GA: molecular modeling studies

We have used molecular modeling techniques to model the RNA tertiary structure of the viral RNA element (referred to as domain II of Rev responsive element, RRE) bound by the Rev protein of HIV. In this study, the initial three-dimensional model was built from its established RNA secondary structure, including three non-Watson-Crick G:G, G:A and G:U base pairs. Molecular dynamics (MD) simulations were performed with hydrated or unhydrated sodium ions. Our results indicate that the non-Watson-Crick base pairs in the simulation with unhydrated sodium ions and water are more stable than those with hydrated sodium ions only. The RNA can maintain its compact double helical structure throughout the course of the MD simulations with water and unhydrated sodium ions, although the non-Watson-Crick base pairs and two bulge loops show much more flexibility and conformational distortion than the classical RNA helical region. The distinct distortion of the sugar-phosphate backbone significantly widens the RNA major groove so that the major groove is readily accessible for hydrogen bonding by specific Rev binding. This model emphasizes the importance of specific hydrogen bonding in the stabilization of the three-dimensional structure of the HIV Rev core binding element, not only between the nucleotide bases, but also among the ribose hydroxyls, phosphate anionic oxygens, base oxygens and nitrogens, and bridging water molecules. Moreover, our results suggest that sodium ions play an important role in the formation of base pairs G:G and G:A of the RRE by a manner similar to the arginine of the Rev-RRE complex.

Analysis of sequence dependent variations in secondary and tertiary structure of tRNA molecules

The double helical regions of the five tRNA(Phe) and two tRNA(Asp) crystal structures have been analyzed using the local basepair step parameters. The sequence dependent effects in the mini double helices of tRNA are very similar to those observed in the crystal structures of oligonucleotides in the A-form, the purine-pyrimidine and purine-purine steps have small roll angles when compared to the fiber models of A-DNA as well as A-RNA, while the pyrimidine-purine doublet steps have large roll angles. The orientation of the basepairs in the D-stem is unusual and invariant i.e. they are different from the other three stems but are very similar in all the five tRNA(Phe) crystal structures, presumably due to tertiary interaction of the Watson-Crick basepairs with other bases, with all bases being highly conserved. The origin of the differences between the tertiary structures of tRNA(Phe) and tRNA(Asp) from yeast has also been investigated. It is found that even though the angle between the acceptor arm and the D-stem is very similar in the two structures, the angle subtended by the acceptor arm and the anticodon arm is smaller in the tRNA(Phe) structure (by more than 10 degrees). This is due to differences in the orientation of the two mini helices constituting the anticodon arm, which are inclined to each other by approximately 25 degrees in tRNA(Phe) and 16 degrees in tRNA(Asp). In addition, the acceptor arm, the D-stem and the anticodon stem are nearly coplanar in tRNA(Phe), while in tRNA(Asp) the anticodon stem projects out of the plane defined by the acceptor arm and the anticodon stem. These two features together lead to a larger separation between the acceptor and anticodon ends in tRNA(Asp) and indicate that the junction between the D-stem and the anticodon stem is quite variable, with features characteristic of a ball-and-socket type joint and determined for each tRNA molecule by the base sequence at the junction.

Models for two tRNAs bound to successive codons on mRNA on the ribosome

We have investigated the structural changes necessary to build a model complex of two molecules of phenylalanine transfer RNA (tRNA(Phe) bound to successive codons in a short segment of a model messenger RNA (mRNA), consisting of U6. We keep the mRNA in an ideal helical conformation, deforming the tRNAs as necessary to eliminate steric overlaps while bringing the two 3' termini together. The resulting model has the two tRNAs oriented relative to one another in a manner that is very similar to a model developed by McDonald and Rein (1) in which the tRNAs maintain their ideal crystallographic conformations and all of the deformations are introduced into the mRNA. Consequently, regardless of how one divides the deformations between the tRNAs and the mRNA it is clear that, on the ribosome, the tRNA in the P site has its "front" side (that side with the variable loop) close to the "back" side of the tRNA in the A site (that side with the D loop). The space between the two molecules must be left free on the ribosome, in order to facilitate the transition from the A site to the P site. A detailed pathway is also proposed for changing the anticodon loop structure from that of the A site to that of the P site. The anticodon loop is always kept in a 3'-stacked conformation, since we find that the shift between the 3'-stacked and 5'-stacked structures proposed by Woese (2) is not feasible.

Conformational change of the L-shaped tRNA(Phe) molecule

Fluorophore of proflavine was introduced onto the 3'-terminal ribose moiety of yeast tRNA(Phe). The distance between the fluorophore and the fluorescent Y base in the anticodon of yeast tRNA(Phe) was measured by a singlet-singlet energy transfer. Conformational changes of tRNA(Phe) with binding of tRNA(2Glu), which has the anticodon UUC complementary to the anticodon GAA of tRNA(Phe), were investigated. The distance obtained at the ionic strength of 100 mM K+ and 10 mM Mg2+ is very close to the distance from x-ray diffraction, while the distance obtained in the presence of tRNA(2Glu) is significantly smaller. Further, using a fluorescent probe of 4-bromomethyl-7-methoxycoumarin introduced onto pseudouridine residue psi 55 in the T psi C loop of tRNA(Phe), Stern-Volmer quenching experiments for the probe with or without added tRNA(2Glu) were carried out. The results showed greater access of the probe to the quencher with added tRNA(2Glu). These results suggest that both arms of the L-shaped tRNA structure tend to bend inside with binding of tRNA(2Glu) and some structural collapse occurs at the corner of the L-shaped structure.

Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows

A new procedure for the analysis of the structure and molecular dynamics of duplex DNA is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the values of the conformational and helicoidal parameters for each structure entering the analysis using the method "Curves" developed by Lavery and Sklenar, J. Biomol. Str. Dyn. 6, 63 (1988), followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels, or "dials", for each IUPAC torsional parameter and "windows" on the range of values assumed by the linear and angular helicoidal parameters, and is presented in a form isomorphous with the structure per se. The complete time evolution of the conformational and helicoidal parameters of a DNA double helix can then be depicted in a set of six composite figures. Dynamical aspects of helix bending are also subsumed in this analysis. The procedure is illustrated with an analysis of the structures of canonical A and B forms of DNA and the 300 degrees K native dodecamer duplex d(CGCGAATTCGCG). The "dials and windows" are then used for a comprehensive analysis of 30 psec of molecular dynamics on the dodecamer in the vicinity of a canonical B-DNA energy minimum. This involves presentation of the time evolution of 206 conformational and 230 helicoidal parameters for the dodecamer. A number of interesting structural features can be recognized in the analysis, including crankshaft motions, BI - BII transitions, sugar repuckerings, and a description of spontaneous helix bending at what corresponds to the 1 degrees and 2 degrees "hinge points" indicated in the crystal structure. Our approach is expected to be directly useful for critical analysis of the effects of various assumptions about force field parameters, hydration and electrostatic effects and thus contribute to the development of reliable simulation protocols for nucleic acid systems. Extension of the method to present differential changes in conformational and helicoidal parameters is expected to be valuable for the analysis of structural and molecular dynamics studies of the reorganization and adaptation of DNA on complexation with various drugs and regulatory proteins.

Mobility of individual 5-fluorouridine residues in 5-fluorouracil-substituted Escherichia coli valine transfer RNA. A 19F nuclear magnetic resonance relaxation study

19F nuclear magnetic resonance (n.m.r.) relaxation parameters of 5-fluorouracil-substituted Escherichia coli tRNA(Val)1 were measured and used to characterize the internal mobility of individual 5-fluorouridine (FUrd) residues in terms of several models of molecular motion. Measured relaxation parameters include the spin-lattice (T1) relaxation time at 282 MHz, the 19F(1H) NOE at 282 MHz, and the spin-spin (T2) relaxation time, estimated from linewidth data at 338 MHz, 282 MHz and 84 MHz. Dipolar and chemical shift anisotropy contributions to the 19F relaxation parameters were determined from the field-dependence of T2. The results demonstrate a large chemical shift anisotropy contribution to the 19F linewidths at 282 and 338 MHz. Analysis of chemical shift anisotropy relaxation data shows that, relative to overall tumbling of the macromolecule, negligible torsional motion occurs about the glycosidic bond of FUrd residues in 19F-labeled tRNA(Val)1, consistent with the maintenance of base-base hydrogen-bond and/or stacking interactions at all fluorouracil residues in the molecule. The dipolar relaxation data are analyzed by using the "two-state jump" and "diffusion in a cone" formalisms. Motional amplitudes (theta) are interpreted as being due to pseudorotational fluctuations within the ribose ring of the fluorinated nucleoside. These amplitudes range from approximately 30 degrees to 60 degrees, assuming a correlation time (tau i,2) of 1.6 ns. By using available 19F n.m.r. assignment data for the 14 FUrd residues in 5-fluorouracil-substituted tRNA(Val)1, these motional amplitudes can be correlated directly with the environmental domain of the residue. Residues located in tertiary and helical structural domains show markedly less motion (theta approximately equal to 30 to 35 degrees) than residues located in loops (theta approximately equal to 45 to 60 degrees). A correlation between residue mobility and solvent exposure is also demonstrated. The amplitudes of internal motion for specific residues agree quite well with those derived from X-ray diffraction and molecular dynamics data for yeast tRNA(Phe).

A molecular dynamics computer simulation of an eight-base-pair DNA fragment in aqueous solution: comparison with experimental two-dimensional NMR data

The structure and dynamics of an 8-base-pair DNA fragment (dCGCAACGC/dGCGTTGCG) in aqueous solution (14 Na+ ions, 1231 water molecules) have been simulated by using the molecular-dynamics method. Interproton distances have been calculated for various structures and are compared with a set of 174 distances which have been derived from 2D NOE experiments. The averaged MD structures are compared with ideal A-DNA and B-DNA structures in terms of helix parameters, dihedral angles, and so forth. The hydration of various atoms of the DNA fragment and of the Na+ ions is analyzed by calculating coordination numbers and first-neighbor shell residence times.

Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions

We present the results of molecular dynamics simulations on d(C-G-C-G-A) X d(T-C-G-C-G) with fully charged phosphates with and without inclusion of counterions. The average structures found in the two simulations are similar, but the simulation with counterions does give an average helix repeat, tilt, and twist in better agreement with those found in the x-ray structure of d(C-G-C-G-A-A-T-T-C-G-C-G)2. The average sugar pucker phases and amplitudes are in qualitative agreement with those found in NMR studies of double-helical DNA, and a number of examples of sugar repuckering from C2' endo to C3' endo carbon conformations in the sugar ring are found. The hydrogen bond correlations as well as torsion correlations are analyzed, and some interesting long-range correlations between dihedral angles are found.

Aqueous hydration of nucleic acid constituents: Monte Carlo computer simulation studies

Monte Carlo computer simulations were performed on dilute aqueous solutions of thymine, cytosine, uracil, adenine, guanine, the dimethyl phosphate anion in the gauche-gauche conformation and a ribose and deoxyribose derivative. The aqueous hydration of each molecule was analysed in terms of quasi-component distribution functions based on the Proximity Criterion, and partitioned into hydrophobic, hydrophilic and ionic contributions. Color stereo views of selected hydration complexes are also presented. A preliminary discussion of the transferability of functional group coordination numbers is given. The results enable to comment on two current problems related to the hydration of nucleic acids: a) the theory of Dickerson and coworkers on the role of water in the relative stability of the A and B form of DNA and b) the idea of water bridges and filaments emerging from the computer simulation results on the hydration of DNA fragments by Clementi.

A molecular mechanical model to predict the helix twist angles of B-DNA

We present here a model for the prediction of helix twist angles in B-DNA, a model composed of a collection of torsional springs. Statistically averaged conformational energy calculations show that, for a specified basepair step, the basepair-basepair conformational energy is quadratically dependent on the helix twist angle, so the calculations provide the spring parameters for the basepair-basepair interactions. Torsional springs can also be used to model the effects of the backbone on the helix twist, and the parameters for those springs are derived by fitting the model to experimental data. The model predicts a macroscopic torsional stiffness and a longitudinal compressibility (Young's modulus) which are both in good agreement with experiment. One biological consequence of the model is examined, the sequence specificity of the Eco RI restriction endonuclease, and it is shown that the discriminatory power of the enzyme receives a substantial contribution from the energetic cost of torsional deformations of the DNA when wrong sequences are forced into the enzyme binding site.

Phenylalanine transfer RNA: molecular dynamics simulation

Yeast phenylalanine transfer RNA was subjected to a 12-picosecond molecular dynamics simulation. The principal features of the x-ray crystallographic analysis are reproduced, and the amplitudes of atomic displacements appear to be determined by the degree of exposure of the atoms. An analysis of the hydrogen bonds shows a correlation between the average length of a bond and the fluctuation in that length and reveals a rocking motion of bases in Watson-Crick guanine X cytosine base pairs. The in-plane motions of the bases are generally of larger amplitude than the out-of-plane motions, and there are correlations in the motions of adjacent bases.