Journal of Biomolecular Structure and Dynamics, Taylor & Francis, 2017
Deficiency of 5-taurinomethyl-2-thiouridine, τm5s2U at the 34th ‘wobble’ position in tRNALys caus... more Deficiency of 5-taurinomethyl-2-thiouridine, τm5s2U at the 34th ‘wobble’ position in tRNALys causes MERRF (Myoclonic Epilepsy with Ragged Red Fibers), a neuromuscular disease. This modified nucleoside of mt tRNALys, 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 tRNALys 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 tRNALys 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 tRNALys 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, tRNALys 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.
Hypermodified bases present at 3′-adjacent (37th) position in anticodon loop of tRNAPhe are well ... more Hypermodified bases present at 3′-adjacent (37th) position in anticodon loop of tRNAPhe 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 37th position in tRNAPhe. 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 tRNAPhe. 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 37th position along with other modified bases present in ASL of tRNAPhe. 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.
Transfer RNAs (tRNAs) contain various uniquely modified nucleosides thought to be useful for main... more Transfer RNAs (tRNAs) contain various uniquely modified nucleosides thought to be useful for maintaining the structural stability of tRNAs. However, their significance for upholding the tRNA structure has not been investigated in detail at the atomic level. In this study, molecular dynamic simulations have been performed to assess the effects of methylated nucleic acid bases, N2-methylguanosine (m2G) and N2-N2-dimethylguanosine (m22G) at position 26, i.e., the hinge region of E. coli tRNAPhe on its structure and dynamics. The results revealed that tRNAPhe having unmodified guanosine in the hinge region (G26) shows structural rearrangement in the core of the molecule, resulting in lack of base stacking interactions, U-turn feature of the anticodon loop, and TΨC loop. We show that in the presence of the unmodified guanosine, the overall fold of tRNAPhe is essentially not the same as that of m2G26 and m22G26 containing tRNAPhe. This structural rearrangement arises due to intrinsic factors associated with the weak hydrogen-bonding patterns observed in the base triples of the tRNAPhe molecule. The m2G26 and m22G26 containing tRNAPhe retain proper three-dimensional fold through tertiary interactions. Single-point energy and molecular electrostatics potential calculation studies confirmed the structural significance of tRNAs containing m2G26 and m22G26 compared to tRNA with normal G26, showing that the mono-methylated (m2G26) and dimethylated (m22G26) modifications are required to provide structural stability not only in the hinge region but also in the other parts of tRNAPhe. Thus, the present study allows us to better understand the effects of modified nucleosides and ionic environment on tRNA folding.
Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the ‘wobble’ 34t... more Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the ‘wobble’ 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD) simulations of various anticodon stem loop (ASL) models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process. The MD simulation results revealed that τm5U34 recognizes G/A ending codons by ‘wobble’ as well as a novel ‘single’ hydrogen bonding interactions. RMSD and RMSF values indicate the comparative stability of the ASL models containing τm5U34 modification over the other models, lacking τm5U34. Another MD simulation study of 55S mammalian mitochondrial rRNA with tRNALeu showed crucial interactions between the A-site residues, A918, A919, G256 and codon-anticodon bases. Thus, these results could improve our understanding about the decoding efficiency of human mt tRNALeu with τm5U34 to recognize UUG and UUA codons.
The myoclonus epilepsy associated with ragged-red fibers (MERRF) is a mitochondrial encephalomyop... more The myoclonus epilepsy associated with ragged-red fibers (MERRF) is a mitochondrial encephalomyopathic disease caused due to the lack of hypermodified nucleoside 5-taurinomethyl-2-thiouridine at ‘wobble’ 34th position in the anticodon loop of human mitochondrial tRNALys. Understanding the structural significance of τm5s2U might be helpful to get more information about the MERRF disease in detail at the atomic level. Hence, conformational preferences of hypermodified nucleoside 5-taurinomethyl-2-thiouridine 5′-monophosphate, ‘p-τm5s2U,’ have been studied using semiempirical quantum chemical RM1 method. Full geometry optimization using ab initio molecular orbital HF-SCF (6-31G**) and DFT (B3LYP/6-31G**) methods has also been used to compare the salient features. The RM1 preferred most stable conformation of ‘p-τm5s2U’ has been stabilized by hydrogen bonding interactions between O(11a)…HN(8), O1P(34)…HN(8), O1P(34)…HC(10), O4′(34)…HC(6), S(2)…HC1′(34), O5′(34)…HC(6), and O(4)…HC(7). Another conformational study of 5-taurinomethyl-2-thiouridine side chain in the presence of anticodon loop bases of human mitochondrial tRNALys showed similar conformation as found in RM1 preferred most stable conformation of ‘p-τm5s2U.’ The glycosyl torsion angle of τm5s2U retains ‘anti’ conformation. Similarly, MD simulation results are also found in accordance with RM1 preferred stable structure. The solvent-accessible surface area calculations revealed surface accessibility of τm5s2U in human mt tRNALys anticodon loop. The MEPs calculations of codon–anticodon models of τm5s2U(34):G3 and τm5s2U(34):A3 showed unique potential tunnels between the hydrogen bond donor and acceptor atoms. These results might be useful to understand the exact role of τm5s2U(34) to recognize AAG/AAA codons and to design new strategies to prevent mitochondrial disease, MERRF.
Mycobacterium tuberculosis is a Gram positive, acid-fast bacteria belonging to genus Mycobacteriu... more Mycobacterium tuberculosis is a Gram positive, acid-fast bacteria belonging to genus Mycobacterium, is the leading causative agent of most cases of tuberculosis. The pathogenicity of the bacteria is enhanced by its developed DNA repair mechanism which consists of machineries such as nucleotide excision repair. Nucleotide excision repair consists of excinuclease protein UvrABC endonuclease, multi-enzymatic complex which carries out repair of damaged DNA in sequential manner. UvrC protein is a part of this complex and thus helps to repair the damaged DNA of M. tuberculosis. Hence, structural bioinformatics study of UvrC protein from M. tuberculosis was carried out using homology modeling and molecular docking techniques. Assessment of the reliability of the homology model was carried out by predicting its secondary structure along with its model validation. The predicted structure was docked with the ATP and the interacting amino acid residues of UvrC protein with the ATP were found to be TRP539, PHE89, GLU536, ILE402 and ARG575. The binding of UvrC protein with the DNA showed two different domains. The residues from domain I of the protein VAL526, THR524 and LEU521 interact with the DNA whereas, amino acids interacting from the domain II of the UvrC protein included ARG597, GLU595, GLY594 and GLY592 residues. This predicted model could be useful to design new inhibitors of UvrC enzyme to prevent pathogenesis of Mycobacterium and so the tuberculosis.
Journal of Biomolecular Structure and Dynamics, Taylor & Francis, 2017
Deficiency of 5-taurinomethyl-2-thiouridine, τm5s2U at the 34th ‘wobble’ position in tRNALys caus... more Deficiency of 5-taurinomethyl-2-thiouridine, τm5s2U at the 34th ‘wobble’ position in tRNALys causes MERRF (Myoclonic Epilepsy with Ragged Red Fibers), a neuromuscular disease. This modified nucleoside of mt tRNALys, 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 tRNALys 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 tRNALys 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 tRNALys 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, tRNALys 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.
Hypermodified bases present at 3′-adjacent (37th) position in anticodon loop of tRNAPhe are well ... more Hypermodified bases present at 3′-adjacent (37th) position in anticodon loop of tRNAPhe 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 37th position in tRNAPhe. 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 tRNAPhe. 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 37th position along with other modified bases present in ASL of tRNAPhe. 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.
Transfer RNAs (tRNAs) contain various uniquely modified nucleosides thought to be useful for main... more Transfer RNAs (tRNAs) contain various uniquely modified nucleosides thought to be useful for maintaining the structural stability of tRNAs. However, their significance for upholding the tRNA structure has not been investigated in detail at the atomic level. In this study, molecular dynamic simulations have been performed to assess the effects of methylated nucleic acid bases, N2-methylguanosine (m2G) and N2-N2-dimethylguanosine (m22G) at position 26, i.e., the hinge region of E. coli tRNAPhe on its structure and dynamics. The results revealed that tRNAPhe having unmodified guanosine in the hinge region (G26) shows structural rearrangement in the core of the molecule, resulting in lack of base stacking interactions, U-turn feature of the anticodon loop, and TΨC loop. We show that in the presence of the unmodified guanosine, the overall fold of tRNAPhe is essentially not the same as that of m2G26 and m22G26 containing tRNAPhe. This structural rearrangement arises due to intrinsic factors associated with the weak hydrogen-bonding patterns observed in the base triples of the tRNAPhe molecule. The m2G26 and m22G26 containing tRNAPhe retain proper three-dimensional fold through tertiary interactions. Single-point energy and molecular electrostatics potential calculation studies confirmed the structural significance of tRNAs containing m2G26 and m22G26 compared to tRNA with normal G26, showing that the mono-methylated (m2G26) and dimethylated (m22G26) modifications are required to provide structural stability not only in the hinge region but also in the other parts of tRNAPhe. Thus, the present study allows us to better understand the effects of modified nucleosides and ionic environment on tRNA folding.
Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the ‘wobble’ 34t... more Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the ‘wobble’ 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD) simulations of various anticodon stem loop (ASL) models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process. The MD simulation results revealed that τm5U34 recognizes G/A ending codons by ‘wobble’ as well as a novel ‘single’ hydrogen bonding interactions. RMSD and RMSF values indicate the comparative stability of the ASL models containing τm5U34 modification over the other models, lacking τm5U34. Another MD simulation study of 55S mammalian mitochondrial rRNA with tRNALeu showed crucial interactions between the A-site residues, A918, A919, G256 and codon-anticodon bases. Thus, these results could improve our understanding about the decoding efficiency of human mt tRNALeu with τm5U34 to recognize UUG and UUA codons.
The myoclonus epilepsy associated with ragged-red fibers (MERRF) is a mitochondrial encephalomyop... more The myoclonus epilepsy associated with ragged-red fibers (MERRF) is a mitochondrial encephalomyopathic disease caused due to the lack of hypermodified nucleoside 5-taurinomethyl-2-thiouridine at ‘wobble’ 34th position in the anticodon loop of human mitochondrial tRNALys. Understanding the structural significance of τm5s2U might be helpful to get more information about the MERRF disease in detail at the atomic level. Hence, conformational preferences of hypermodified nucleoside 5-taurinomethyl-2-thiouridine 5′-monophosphate, ‘p-τm5s2U,’ have been studied using semiempirical quantum chemical RM1 method. Full geometry optimization using ab initio molecular orbital HF-SCF (6-31G**) and DFT (B3LYP/6-31G**) methods has also been used to compare the salient features. The RM1 preferred most stable conformation of ‘p-τm5s2U’ has been stabilized by hydrogen bonding interactions between O(11a)…HN(8), O1P(34)…HN(8), O1P(34)…HC(10), O4′(34)…HC(6), S(2)…HC1′(34), O5′(34)…HC(6), and O(4)…HC(7). Another conformational study of 5-taurinomethyl-2-thiouridine side chain in the presence of anticodon loop bases of human mitochondrial tRNALys showed similar conformation as found in RM1 preferred most stable conformation of ‘p-τm5s2U.’ The glycosyl torsion angle of τm5s2U retains ‘anti’ conformation. Similarly, MD simulation results are also found in accordance with RM1 preferred stable structure. The solvent-accessible surface area calculations revealed surface accessibility of τm5s2U in human mt tRNALys anticodon loop. The MEPs calculations of codon–anticodon models of τm5s2U(34):G3 and τm5s2U(34):A3 showed unique potential tunnels between the hydrogen bond donor and acceptor atoms. These results might be useful to understand the exact role of τm5s2U(34) to recognize AAG/AAA codons and to design new strategies to prevent mitochondrial disease, MERRF.
Mycobacterium tuberculosis is a Gram positive, acid-fast bacteria belonging to genus Mycobacteriu... more Mycobacterium tuberculosis is a Gram positive, acid-fast bacteria belonging to genus Mycobacterium, is the leading causative agent of most cases of tuberculosis. The pathogenicity of the bacteria is enhanced by its developed DNA repair mechanism which consists of machineries such as nucleotide excision repair. Nucleotide excision repair consists of excinuclease protein UvrABC endonuclease, multi-enzymatic complex which carries out repair of damaged DNA in sequential manner. UvrC protein is a part of this complex and thus helps to repair the damaged DNA of M. tuberculosis. Hence, structural bioinformatics study of UvrC protein from M. tuberculosis was carried out using homology modeling and molecular docking techniques. Assessment of the reliability of the homology model was carried out by predicting its secondary structure along with its model validation. The predicted structure was docked with the ATP and the interacting amino acid residues of UvrC protein with the ATP were found to be TRP539, PHE89, GLU536, ILE402 and ARG575. The binding of UvrC protein with the DNA showed two different domains. The residues from domain I of the protein VAL526, THR524 and LEU521 interact with the DNA whereas, amino acids interacting from the domain II of the UvrC protein included ARG597, GLU595, GLY594 and GLY592 residues. This predicted model could be useful to design new inhibitors of UvrC enzyme to prevent pathogenesis of Mycobacterium and so the tuberculosis.
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Papers by Prayagraj M Fandilolu