Nano theoretical studies of fMet-tRNA structure in protein synthesis of prokaryotes and its comparison with the structure of fAla-tRNA

It is generally accepted that initiation of protein synthesis in Escherichia coli starts with formyl-methionine, directed by the codons AUG or GUG. Protein synthesis proceeds by transfer of the growing polypeptide chain from the tRNA bound to the ribosomal P site to the incoming aminoacyl-tRNA in the adjacent A site. After translocation of the ribosome in the 30 direction of the mRNA, by the action of elongation factor G, the A site again becomes empty and the next codon exposed so that a new aminoacyl-tRNA ternary complex can be selected (Ogle and Ramakrishnan, 2005). Synthetic polynucleotide containing AUG and/or GUG codons as well as natural mRNA have been used extensively in order to elucidate the mechanism of initiation of protein synthesis (Grunberg-Manago, 1977). In all these studies it has been assumed that binding of fMet-tRNA to ribosome’s is the polynucleotide in bacteria the start codon AUG is recognized by fMet-tRNA. This tRNA does not recognize internal AUG codons. Initiation of protein biosynthesis requires the correct positioning of charged initiator tRNA, fMet-tRNA in the ribosomal P-site of the mRNA-programmed 70S ribosome’s (Gualerzi and Pon, 1990; La Teana et al., 1996; Monajjemi et al., 2008; Spurio et al., 1993; Forster et al., 1999). The rapid development of molecular biology in recent years has been mirrored by the rapid development of


INTRODUCTION
It is generally accepted that initiation of protein synthesis in Escherichia coli starts with formyl-methionine, directed by the codons AUG or GUG.Protein synthesis proceeds by transfer of the growing polypeptide chain from the tRNA bound to the ribosomal P site to the incoming aminoacyl-tRNA in the adjacent A site.After translocation of the ribosome in the 30 direction of the mRNA, by the action of elongation factor G, the A site again becomes empty and the next codon exposed so that a new aminoacyl-tRNA ternary complex can be selected (Ogle and Ramakrishnan, 2005).
Synthetic polynucleotide containing AUG and/or GUG codons as well as natural mRNA have been used extensively in order to elucidate the mechanism of initiation of protein synthesis (Grunberg-Manago, 1977).
In all these studies it has been assumed that binding of fMet-tRNA to ribosome's is the polynucleotide in bacteria the start codon AUG is recognized by fMet-tRNA.This tRNA does not recognize internal AUG codons.Initiation of protein biosynthesis requires the correct positioning of charged initiator tRNA, fMet-tRNA in the ribosomal P-site of the mRNA-programmed 70S ribosome's (Gualerzi and Pon, 1990;La Teana et al., 1996;Monajjemi et al., 2008;Spurio et al., 1993;Forster et al., 1999).
The rapid development of molecular biology in recent years has been mirrored by the rapid development of *Corresponding author.E-mail: smollaamin@gmail.com.computer hardware and software.This improvement leaded to the development of sophisticated computational techniques and a wide range of computer simulations involving such methods among the areas It is well observed that fMet-tRNA is the pharmacological targets of many of the drugs that are currently in clinical use or in advanced clinical trials.Therefore, the implication throughout this paper has been profound is the modeling of fMet-tRNA structure and function, the chemical behavior of fMet-tRNA within drug design and also understanding at a molecular level of the role of solvents in biotechnological applications (Agris et al., 1997;Monajjemi et al., 2010).We selected adenine of tRNA structure (first nucleotide in acceptor arm of tRNA structure) and then perform modeling of fMet-tRNA, during the process we formylized alanine and then attached it to the adenine of tRNA and then designed the structure of fAla-tRNA to compare it with fMet-tRNA, (Figure 1).

METHDOLOGY
At first, we have modeled the structure of fMet-tRNA and fAla-tRNA with Chem office package and then optimized at the B3LYP and HF levels of theory with 3-21G* basis set.After fully optimization of those structures , we have calculated NMR parameters and NBO analysis at the levels of HF/3-21G* and B3LYP/3-21G* theory and theoretically explored the solvent effects(GAS ,DMSO ,CHCL3,H2O) on structure of adenine + fMet and adenine + fAla and calculations of NMR parameters and NBO calculation have been Performed on a Pentium-4 based system using GAUSSIAN   (Gaussian et al., 1998).

RESULTS AND DISCUSSION
In this paper we performed quantum calculations on the structure of fMet-tRNA and fAla-tRNA and to perform the action, first we formilized (gave a formyl molecule to the structure) two amino acids methionine and alanin and then we attached them from tRNA to adenine nucleotide and then we performed the quantum calculations on the achieved structures (fMet-tRNA and fAla-tRNA).
In this paper HF and DFT/B3LYP methods with 3-21G * basis set were Employed for investigating the structure optimization and energy minimization of fMet-tRNA and fAla-tRNA (Figure 1) have been summarized in Table 1.The HF and DFT energies are of particular interest because they provide results for interactions appearing in solvent medium considered in this letter, which are in accord with biological behavior of fMet-tRNA and fAla-tRNA.Furthermore, recent papers often tend to ask about the role of water solvent effect on the stability of fMet-tRNA and fAla-tRNA structures.The detailed results of relative energy values for those structures in gas, DMSO, CHCL3 and water solvents optimized at the HF and B3LYP levels of theory with 3-21G * basis set are summarized in Table 1.
In the NBO analysis, in order to compute the span of the valence space, each valence bonding NBO (σ AB ), must in turn, be paired with a corresponding valence anti bonding NBO ( ): Namely, the Lewis σ-type (donor) NBO are complemented by the non-Lewis σ * -type (acceptor) NBO that are formally empty in an idealized Lewis structure picture.Readily, the general transformation to NBO leads to orbitals that are unoccupied in the formal Lewis structure.As a result, the filled NBO of the natural Lewis structure are well adapted to describe covalency effects in molecules.Since the non-covalent delocalization effects are associated with σ → σ * interactions between filled (donor) and unfilled (acceptor) orbitals, it is natural to describe them as being of donoracceptor, charge transfer, or generalized "Lewis base-Lewis acid" type.The anti bonds represent unused valence-shell capacity and spanning portions of the atomic valence space that are formally unsaturated by covalent bond formation.Weak occupancies of the valence anti bonds signal irreducible departures from an idealized localized Lewis picture, that is, true "delocalization effects".As a result, in the NBO analysis, the donor-acceptor (bond-anti bond) interactions are taken into consideration by examining all possible interactions between 'filled' (donor) Lewis-type NBO and 'empty' (acceptor) non-Lewis NBO and then estimating their energies by second-order perturbation theory.
Table 5 shows calculated natural orbital occupancy (number of electron, or ''natural population" of the orbital).It is noted that for σO29 -C30 of fMet-tRNA and σ O30-C44 of fAla-tRNA bond orbital, Decreased or increased occupancy of the localized σO29 -C30 of fMet-tRNA and σ O30-C44 of fAla-tRNA orbital in the idealized Lewis structure, and their subsequent impact on molecular stability and geometry (bond lengths) are also related with the resulting p character of the corresponding O29 natural hybrid orbital (NHO) of σO29 -C30 and O30 natural hybrid orbital (NHO) of σ O30-C44 bond orbital.
Nuclear magnetic Resonance (NMR) is based on the quantum mechanical property of nuclei (Benas et al., 2000).The chemical shielding refers to the phenomenon which associated with the secondary magnetic field created by the induced motions of the electrons that surrounding the nuclei when in the presence of an applied magnetic field.The energy of a magnetic moment µ , in a magnetic field, B, is as follow: (1) Where the shielding σ is the differential resonance shift due to the induced motion of the electrons (Magdalena and Sadlej, 1998).In general, the electron distribution around a nucleus in a molecule is more spherically symmetric.Therefore, the size of electron current around the field, and hence the size of the shielding, will depend on the orientation of the molecule within the applied field B0 (Melinda, 2003).
For chemical shielding (CS) tensor, which describes how the size of shielding varies with molecular Mollaamin et al. 2669 orientation, we often use the following convention for the three principal components: The three values of the shielding tensor are frequently expressed as the isotropic value ( ) iso σ , the anisotropy ( ) σ ∆ , and the asymmetry ( ) η There quantities are defined as follows [Monajjemi et al., 2004]: 1.The isotropic value iso σ : ( ) are the corresponding parameters for calculation with reference solvent.In this case, we may suppose that optimization of solute molecule in solvent and then performing shielding calculations is similar to shielding calculations in the isolated system (Lynden and Rasaiah, 1997).
Self-Consistent Reaction Field (SCRF) method is based on a continuum model with uniform dielectric constant ( ) ε .The simplest SCRF model is the Onsager reaction field model.In this method, the solute occupies a fixed spherical cavity of radius a0 within the solvent field.A dipole in the molecule will induce a dipole in the medium, and the electric field applied by the solvent dipole will in turn in interact with the molecular dipole leading to net stabilization.
The Gauge Including Atomic Orbital (GIAO) approach  47) atoms in structure of fAla-tRNA (Figure 1) have been summarized in Table 6 and O(29),O(32)and C(30) atoms are the connections of adenine of fMet and also O(30), C(44) and O(47) atoms are the connections of adenine to fAla , these atoms are so important to us.

Conclusion
In this work, we have summarized: 1. Optimization at the HF and DFT levels of theory Table3.Calculated natural hybrid orbitals (NHOs) and the polarization coefficient for each hybrid in the corresponding NBO (parentheses) for the selected fMet-tRNA (1) and fAla-tRNA (2) using the selected methods.

Phase
Bond provides a suitable computational model in terms of calculated NMR parameters and relative energies.
2. There was an increase in the relative stability of the interested structures through the improvement of basis set and including electron correlations , Hence, the most stable structures are perceived in the CHCL3 solution at the B3LYP/3-21G* level of theory.
3. We observed an increase in values of NMR chemical shielding around O29, O32 By increasing lone pair electrons contribution of oxygen (O29, O32) atoms in resonance Interactions, Hence, O29 atom has the highest chemical shielding among the oxygen atoms (fMet-tRNA).4. We observed a decrease in the bond lengths of the O29-C30 of the structure by the increase of solvent dielectric constant (fMet-tRNA).5. We observed an increase in the relative stability by increasing the LP Os (O29, O32) electrons contribution in the enhancement of π electron clouds (fMet-tRNA).6.In many lab experiments it is proven that the real structure to start protein synthesis in prokaryotes is fMet-tRNA and we studied calculated and worked out the stability and the  real reasons that why this structure is produced in protein synthesis in prokaryotes and fAla-tRNA is not produced there and presented the results and finding in the charts.
As O(29), O(32) and C(30) atoms are the connections of adenine of fMet and also O(30), C(44) and O(47) atoms are the connections of adenine to fAla, these atoms are  7.The largest value of mentioned nuclei of Adenine+ fMet of fMet-tRNA structure observed for O(29), whereas the smallest one belongs to O(32).It is interesting to note that the opposite trend have been observed for asymmetry parameters ( ) η .This usual behavior may be readily understood in accord with biotechnological conceptions.

Figure 1 .
Figure 1.Structure of Adenine + fMet of fMet-tRNA and Adenine + fAla of fAla-tRNA of the PCMoptimized shielding and the PCM shielding of the molecule held at the geometry optimized in vacuum, it can be obtained from the shielding calculated in vacuum for a molecule that is geometry-optimized in solution[Monajjemi et al., 2007].Thus,

Table 1 .
Optimization energy for each method.

Table 4 .
Atomic charge distribution described in terms of natural population analysis (NPA) for the compounds studied.