Idiosyncratic recognition of UUG/UUA codons by modified nucleoside 5-taurinomethyluridine, τm5U present at 'wobble' position in anticodon loop of tRNALeu: A molecular modeling approach

tRNA Modifications and Modifying Enzymes in Disease, the Potential Therapeutic Targets

tRNA is one of the most conserved and abundant RNA species, which plays a key role during protein translation. tRNA molecules are post-transcriptionally modified by tRNA modifying enzymes. Since high-throughput sequencing technology has developed rapidly, tRNA modification types have been discovered in many research fields. In tRNA, numerous types of tRNA modifications and modifying enzymes have been implicated in biological functions and human diseases. In our review, we talk about the relevant biological functions of tRNA modifications, including tRNA stability, protein translation, cell cycle, oxidative stress, and immunity. We also explore how tRNA modifications contribute to the progression of human diseases. Based on previous studies, we discuss some emerging techniques for assessing tRNA modifications to aid in discovering different types of tRNA modifications.

Structural Significance of Conformational Preferences and Ribose-Ring-Puckering of Hyper Modified Nucleotide 5'-Monophosphate 2-Methylthio Cyclic N6-Threonylcarbamoyladenosine (p-ms2ct6A) Present at 37th Position in Anticodon Loop of tRNALys

Structural significance of conformational preferences and ribose ring puckering of newly discovered hyper modified nucleotide, 5'-monophosphate 2-methylthio cyclic N⁶-threonylcarbamoyladenosine (p-ms²ct⁶A) have been investigated using quantum chemical semi-empirical RM1 and molecular dynamics simulation techniques. Automated geometry optimization of most stable structure of p-ms²ct⁶A has also been carried out with the help of abinitio (HF SCF, DFT) as well as semi empirical quantum chemical (RM1, AM1, PM3, and PM6) methods. Most stable structure of p-ms²ct⁶A is stabilized by intramolecular interactions between N(3)…HC(2'), N(1)…HC(16), O(13)…HC(15), and O(13)…HO(14). The torsion angles alpha (α) and beta (β) show the significant characteristic patterns with the involvement of intramolecular hydrogen bonding to provide stability to the p-ms²ct⁶A. Further, molecular dynamics simulations of p-ms²ct⁶A revealed the role of ribose sugar ring puckering i.e. C2'-endo and C3'-endo on the structural dynamics of ms²ct⁶A side chain. The modified nucleotide p-ms²ct⁶A periodically prefers both the C2'-endo and C3'-endo sugar with 'anti' and 'syn' conformations. This property of p-ms²ct⁶A could be useful to recognize the starting ANN codons. All atom explicit MD simulation of anticodon loop (ACL) of tRNA^Lys of Bacillus subtilis containing ms²ct⁶A at 37th position showed the U-turn feature, base stacking ability with other adjacent bases and hydrogen bonding interactions similar to the isolated base p-ms²ct⁶A. The ribose sugar puckering contributes to the orientation of the side chain conformation of p-ms²ct⁶A. Thus, the present study could be helpful to understand the structure-function relationship of the hypermodified nucleoside, ms²ct⁶A in recognition of the proper codons AAA/AAG during protein biosynthesis.

Role of Wybutosine and Mg2+ Ions in Modulating the Structure and Function of tRNAPhe: A Molecular Dynamics Study

Transfer RNA remains to be a mysterious molecule of the cell repertoire. With its modified bases and selectivity of codon recognition, it remains to be flexible inside the ribosomal machinery for smooth and hassle-free protein biosynthesis. Structural changes occurring in tRNA due to the presence or absence of wybutosine, with and without Mg²⁺ ions, have remained a point of interest for structural biologists. Very few studies have come to a conclusion correlating the changes either with the structure and flexibility or with the codon recognition. Considering the above facts, we have implemented molecular modeling methods to address these problems using multiple molecular dynamics (MD) simulations of tRNA^Phe along with codons. Our results highlight some of the earlier findings and also shed light on some novel structural and functional aspects. Changes in the stability of tRNA^Phe in native or codon-bound states result from the conformations of constituent nucleotides with respect to each other. A smaller change in their conformations leads to structural distortions in the base-pairing geometry and eventually in the ribose-phosphate backbone. MD simulation studies highlight the preference of UUC codons over UUU by tRNA^Phe in the presence of wybutosine and Mg²⁺ ions. This study also suggests that magnesium ions are required by tRNA^Phe for proper recognition of UUC/UUU codons during ribosomal interactions with tRNA.

A molecular mechanics study on GA codon box translation

The GA codon box incorporates the two-fold degeneracy of aspartic acid and of glutamic acid. Using the molecular mechanics approach of the AMBER suite, the four codons of the GA box are paired via H-bonding with two aspartic acid anticodons and two glutamic acid anticodons to yield 8 cognate and 11 non-cognate codon-anticodon duplexes. In addition four select non-cognate duplexes between the GA box codons and three alanine anticodons are also studied. These 23 duplexes display a variety of base-pairing possibilities at the wobble position. Cognate duplexes are differentiated from non-cognate duplexes on the grounds of structure and stability (chiefly the former). The results are in line with Crick's wobble hypothesis, and corroborate the observed reading properties of the aspartic acid anticodons GUC and QUC and of the glutamic acid anticodons CUC and S^mnUC.

Preferences of AAA/AAG codon recognition by modified nucleosides, τm5s2U34 and t6A37 present in tRNALys

Deficiency of 5-taurinomethyl-2-thiouridine, τm⁵s²U at the 34th 'wobble' position in tRNA^Lys causes MERRF (Myoclonic Epilepsy with Ragged Red Fibers), a neuromuscular disease. This modified nucleoside of mt tRNA^Lys, recognizes AAA/AAG codons during protein biosynthesis process. Its preference to identify cognate codons has not been studied at the atomic level. Hence, multiple MD simulations of various molecular models of anticodon stem loop (ASL) of mt tRNA^Lys in presence and absence of τm⁵s²U₃₄ and N⁶-threonylcarbamoyl adenosine (t⁶A₃₇) along with AAA and AAG codons have been accomplished. Additional four MD simulations of multiple ASL mt tRNA^Lys models in the context of ribosomal A-site residues have also been performed to investigate the role of A-site in recognition of AAA/AAG codons. MD simulation results show that, ASL models in presence of τm⁵s²U₃₄ and t⁶A₃₇ with codons AAA/AAG are more stable than the ASL lacking these modified bases. MD trajectories suggest that τm⁵s²U recognizes the codons initially by 'wobble' hydrogen bonding interactions, and then tRNA^Lys might leave the explicit codon by a novel 'single' hydrogen bonding interaction in order to run the protein biosynthesis process smoothly. We propose this model as the 'Foot-Step Model' for codon recognition, in which the single hydrogen bond plays a crucial role. MD simulation results suggest that, tRNA^Lys with τm⁵s²U and t⁶A recognizes AAA codon more preferably than AAG. Thus, these results reveal the consequences of τm⁵s²U and t⁶A in recognition of AAA/AAG codons in mitochondrial disease, MERRF.

Conformational preferences and structural analysis of hypermodified nucleoside, peroxywybutosine (o2yW) found at 37th position in anticodon loop of tRNAPhe and its role in modulating UUC codon-anticodon interactions

Hypermodified bases present at 3'-adjacent (37^th) position in anticodon loop of tRNA^Phe are well known for their contribution in modulating codon-anticodon interactions. Peroxywybutosine (o2yW), a wyosine family member, is one of such tricyclic modified bases observed at the 37^th position in tRNA^Phe. Conformational preferences and three-dimensional structural analysis of peroxywybutosine have not been investigated in detail at atomic level. Hence, in the present study quantum chemical semi-empirical RM1 and multiple molecular dynamics (MD) simulations have been used to study structural significance of peroxywybutosine in tRNA^Phe. Full geometry optimizations over the peroxywybutosine base have also been performed using ab-initio HF-SCF (6-31G**), DFT (B3LYP/6-31G**) and semi-empirical PM6 method to compare the salient properties. RM1 predicted most stable structure shows that the amino-carboxy-propyl side chain of o2yW remains 'distal' to the five membered imidazole ring of tricyclic guanosine. MD simulation trajectory of the isolated peroxy base showed restricted periodical fluctuations of peroxywybutosine side chain which might be helpful to maintain proper anticodon loop structure and mRNA reading frame during protein biosynthesis process. Another comparative MD simulation study of the anticodon stem loop with codon UUC showed various properties, which justify the functional implications of peroxywybutosine at 37^th position along with other modified bases present in ASL of tRNA^Phe. Thus, this study presents an atomic view into the structural properties of peroxywybutosine, which can be useful to determine its role in the anticodon stem loop in context of codon-anticodon interactions and frame shift mutations.