Conformational Preferences of the Base Substituent in Hypermodified Nucleotide Queuosine 5′-monophosphate ‘pQ’ and Protonated Variant ‘pQH+’

Sonavane, Uddhavesh; Sonawane, Kailas D.; Tewari, Ravindra

doi:10.1080/07391102.2002.10506866

Cited by 11 publications

(39 citation statements)

References 47 publications

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“…As we know that sm 5 s 2 U was derived from sm 5 U modification, so we utilized side chain torsion angle values as per the sm 5 U (34) at 34th position within crystal structure of tRNA Leu [33] and also verified by utilizing side chain torsion angle values of most stable conformation of 'psm 5 U' [32]. The phosphate backbone torsion angles are notable by subscript 'b' similar to Que [34] and sm 5 U [32].…”

Section: Methodsmentioning

confidence: 99%

“…The phosphate backbone torsion angles are notable by subscript 'b' similar to Que [34] and sm 5 U [32].…”

Section: Methodsmentioning

confidence: 99%

“…Conformational preferences of hypermodified nucleoside 5-taurinomethyl-2-thiouridine, sm 5 s 2 U (34) , in the anticodon loop of human mt tRNA Lys (Me-p-C (32) -p-U (33) -p-sm 5 s 2 U (34) -p-U (35) -p-U (36) -p-t 6 A (37) -p-A (38) -pMe) have also been made using quantum chemical semiempirical RM1 method [36]. The RM1 preferred most stable torsion angels of 'p-sm 5 s 2 U' and reference source data were used for sm 5 s 2 U (34) and N 6 -(N-threonylcarbonyl) Adenine 't 6 A' (37) side chains within the anticodon loop, respectively [57].…”

Section: Methodsmentioning

confidence: 99%

“…Conformational energy calculations have been performed to understand the structural significance of various hypermodified nucleosides, for example lysidine, k 2 C [55], N(4)-acetylcytidine, ac 4 C [56], queuosine [34] present at 'wobble' (34th) position and modifications present at '3'-adjacent' (37th) position together with their protonation effect such as wybutine (yW) and hydroxywybutine (OHyW) [42,44], t 6 Ade, g 6 Ade [57,58], i 6 Ade and ms 2 i 6 Ade [59], cis-io 6 Ade, trans-io 6 Ade, cis-ms 2 io 6 Ade and trans-ms 2 io 6 Ade [60], gc 6 Ade [61], tc 6 Ade [62] as well as m 2 G and m 2 2 G which occur at the tRNA hinge region of tRNA [43].…”

Section: Methodsmentioning

confidence: 99%

“…The RM1 preferred most stable torsion angels of 'p-sm 5 s 2 U' and reference source data were used for sm 5 s 2 U (34) and N 6 -(N-threonylcarbonyl) Adenine 't 6 A' (37) side chains within the anticodon loop, respectively [57]. The ribose-phosphate backbone torsion angles for anticodon loop of human mt tRNA Lys were extracted from yeast phenylalanine tRNA crystal structure (PDB ID: 1EHZ) [65].…”

Section: Methodsmentioning

confidence: 99%

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Structural significance of modified nucleoside 5-taurinomethyl-2-thiouridine, τm5s2U, found at ‘wobble’ position in anticodon loop of human mitochondrial tRNALys

et al. 2015

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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 tRNA Lys . Understanding the structural significance of sm 5 s 2 U 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 0 -monophosphate, 'p-sm 5 s 2 U,' 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-sm 5 s 2 U' has been stabilized by hydrogen bonding interactions between O(11a)…HN (8), O1P (34) … HN(8), O1P (34) …HC(10), O4 0 (34) …HC(6), S(2)…HC1 0 (34), O5 0 (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 tRNA Lys showed similar conformation as found in RM1 preferred most stable conformation of 'p-sm 5 s 2 U.' The glycosyl torsion angle of sm 5 s 2 U 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 sm 5 s 2 U in human mt tRNA Lys anticodon loop. The MEPs calculations of codon-anticodon models of sm 5 s 2 U (34) :G 3 and sm 5 s 2 U (34) :A 3 showed unique potential tunnels between the hydrogen bond donor and acceptor atoms. These results might be useful to understand the exact role of sm 5 s 2 U (34) to recognize AAG/ AAA codons and to design new strategies to prevent mitochondrial disease, MERRF.

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Section: Methodsmentioning

confidence: 99%

“…The phosphate backbone torsion angles are notable by subscript 'b' similar to Que [34] and sm 5 U [32].…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Structural significance of modified nucleoside 5-taurinomethyl-2-thiouridine, τm5s2U, found at ‘wobble’ position in anticodon loop of human mitochondrial tRNALys

et al. 2015

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Hydrogen bonding of modified bases involving Watson-Crick sites: Crystal structure and conformation of Benzyl 6-aminopurine-7-carboxylate

Ohrt

Dutta

Srikrishnan³

2006

Cryst. Res. Technol.

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Crystals of benzyl 6-aminopurine-7-carboxylate (C 13 H 11 N 5 O 2 ) are monoclinic, space group C2/c, Z=8, with a= 25.448 (9), b= 6.052 (1), c= 16.975 (6)Å, β= 112.05 (5) . The structure was determined from three-dimensional diffractometric data by the multisolution technique and refined to a final reliability factor of 0.068. The molecule is planar with an intramolecular hydrogen bond from one of the amino hydrogens, H a (N6) to the keto oxygen O(10) of the acyl group. The molecules are hydrogen bonded across the center of inversion by a pair of intermolecular hydrogen bonds using the WatsonCrick sites.

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Conformational Preferences of Modified Nucleoside N2-methylguanosine (m2G) and Its Derivative N2, N2-dimethylguanosine (m 2 2 G) Occur at 26th Position (Hinge Region) in tRNA

Bavi

Kamble

Kumbhar

et al. 2011

Cell Biochem Biophys

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Conformational preferences of the modified nucleosides N(2)-methylguanosine (m(2)G) and N(2), N(2)-dimethylguanosine (m(2)(2)G) have been studied theoretically by using quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. Automated complete geometry optimization using semiempirical quantum chemical RM1, along with ab initio molecular orbital Hartree-Fock (HF-SCF), and density functional theory (DFT) calculations has also been made to compare the salient features. Single-point energy calculation studies have been made on various models of m(2)G26:C/A/U44 and m(2)(2)G26:C/A/U44. The glycosyl torsion angle prefers "syn" (χ = 286°) conformation for m(2)G and m(2)(2)G molecules. These conformations are stabilized by N(3)-HC2' and N(3)-HC3' by replacing weak interaction between O5'-HC(8). The N(2)-methyl substituent of (m(2)G26) prefers "proximal" or s-trans conformation. It may also prefer "distal" or s-cis conformation that allows base pairing with A/U44 instead of C at the hinge region. Thus, N(2)-methyl group of m(2)G may have energetically two stable s-trans m(2)G:C/A/U or s-cis m(2)G:A/U rotamers. This could be because of free rotations around C-N bond. Similarly, N(2), N(2)-dimethyl substituent of (m(2)(2)G) prefers "distal" conformation that may allow base pairing with A/U instead of C at 44th position. Such orientations of m(2)G and m(2)(2)G could play an important role in base-stacking interactions at the hinge region of tRNA during protein biosynthesis process.

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Conformational Preferences of the Base Substituent in Hypermodified Nucleotide Queuosine 5′-monophosphate ‘pQ’ and Protonated Variant ‘pQH+’

Cited by 11 publications

References 47 publications

Structural significance of modified nucleoside 5-taurinomethyl-2-thiouridine, τm5s2U, found at ‘wobble’ position in anticodon loop of human mitochondrial tRNALys

Structural significance of modified nucleoside 5-taurinomethyl-2-thiouridine, τm5s2U, found at ‘wobble’ position in anticodon loop of human mitochondrial tRNALys

Hydrogen bonding of modified bases involving Watson-Crick sites: Crystal structure and conformation of Benzyl 6-aminopurine-7-carboxylate

Conformational Preferences of Modified Nucleoside N2-methylguanosine (m2G) and Its Derivative N2, N2-dimethylguanosine (m 2 2 G) Occur at 26th Position (Hinge Region) in tRNA

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