Effect of the nucleotide-37 on the interaction of tRNAPhe with the P site of Escherichia coli ribosomes

Posttranscriptional modifications at the 37th position in the anticodon stem–loop of tRNA: structural insights from MD simulations

“…Thus, the yW family of modifications provides additional stability to the anticodon loop through increased stacking. This finding agrees with previous suggestions in the literature based on the anticipated increased nucleobase hydrophobicity and size (Dao et al 1994) and the previously noted decreased stability when the parent yW is replaced with A (Katunin et al 1994), as well as the trends discussed for the t 6 A family in the present work. Due to their large size and range of orientations in tRNA, these modified bases also possibly stack with the incoming first codon base during translation and thereby further increase the stability of the codon-anticodon duplex.…”

Posttranscriptional modifications at the 37th position in the anticodon stem–loop of tRNA: structural insights from MD simulations

“…Thus, the yW family of modifications provides additional stability to the anticodon loop through increased stacking. This finding agrees with previous suggestions in the literature based on the anticipated increased nucleobase hydrophobicity and size (Dao et al 1994) and the previously noted decreased stability when the parent yW is replaced with A (Katunin et al 1994), as well as the trends discussed for the t 6 A family in the present work. Due to their large size and range of orientations in tRNA, these modified bases also possibly stack with the incoming first codon base during translation and thereby further increase the stability of the codon-anticodon duplex.…”

Structural Stability of the Anticodon Stem Loop Domains of the Unmodified Yeast and Escherichia coli tRNAPhe: Differing Views from Different Force Fields

“…92 Modification of G37 in the ASL of yeast tRNA Phe was also reported to facilitate base stacking at the 3′-end and formation of a functional conformation that binds to a cognate codon inside the ribosome. 93,94 Our results on the small extent of stacking for A36/G37 in the yeast tRNA Phe with both the ff99bsc0TOR YIL 67 and ff99bsc0χ OL3 69 force fields (Figure 9A, Supporting Information, Table S12) were in agreement with the experimental data which suggested that even the natural modification yW37 in yeast tRNA Phe was not always in stacked conformation. 95,96 In the case of the unmodified ASLs of the E. coli tRNA Phe , we observed large average base-stacking ratios for the residues around A37 with both the ff99bsc0TOR YIL 67 and ff99bsc0χ OL3 69 force fields which showed the formation of a continued stacked conformation of the A37 toward both the 5′-and 3′-side (Figure 9B, Supporting Information, Table S12).…”

“…It has been assumed that the loss of modification at position 37 in yeast tRNA Phe promotes flexibility in the ASL domain . Modification of G37 in the ASL of yeast tRNA Phe was also reported to facilitate base stacking at the 3′-end and formation of a functional conformation that binds to a cognate codon inside the ribosome. , Our results on the small extent of stacking for A36/G37 in the yeast tRNA Phe with both the ff99bsc0TOR YIL and ff99bsc0χ OL3 force fields (Figure A, Supporting Information, Table S12) were in agreement with the experimental data which suggested that even the natural modification yW37 in yeast tRNA Phe was not always in stacked conformation. , …”

Naturally-occurring Modification Restricts the Anticodon Domain Conformational Space of tRNA Phe

“…A study of ribosome-mediated codon binding by native and position 37-altered yeast tRNA Phe reached the same conclusion. 72 Thus, taken together, the observations we and others have made support an argument that modified bases in the anticodon domain of tRNAs achieve the necessary architecture for accurate binding of codon on the ribosome by limiting conformational space.…”

Posttranscriptional modifications at the 37th position in the anticodon stem–loop of tRNA: structural insights from MD simulations

“…Thus, the yW family of modifications provides additional stability to the anticodon loop through increased stacking. This finding agrees with previous suggestions in the literature based on the anticipated increased nucleobase hydrophobicity and size (Dao et al 1994) and the previously noted decreased stability when the parent yW is replaced with A (Katunin et al 1994), as well as the trends discussed for the t 6 A family in the present work. Due to their large size and range of orientations in tRNA, these modified bases also possibly stack with the incoming first codon base during translation and thereby further increase the stability of the codon-anticodon duplex.…”

Structural Stability of the Anticodon Stem Loop Domains of the Unmodified Yeast and Escherichia coli tRNAPhe: Differing Views from Different Force Fields

“…92 Modification of G37 in the ASL of yeast tRNA Phe was also reported to facilitate base stacking at the 3′-end and formation of a functional conformation that binds to a cognate codon inside the ribosome. 93,94 Our results on the small extent of stacking for A36/G37 in the yeast tRNA Phe with both the ff99bsc0TOR YIL 67 and ff99bsc0χ OL3 69 force fields (Figure 9A, Supporting Information, Table S12) were in agreement with the experimental data which suggested that even the natural modification yW37 in yeast tRNA Phe was not always in stacked conformation. 95,96 In the case of the unmodified ASLs of the E. coli tRNA Phe , we observed large average base-stacking ratios for the residues around A37 with both the ff99bsc0TOR YIL 67 and ff99bsc0χ OL3 69 force fields which showed the formation of a continued stacked conformation of the A37 toward both the 5′-and 3′-side (Figure 9B, Supporting Information, Table S12).…”

“…It has been assumed that the loss of modification at position 37 in yeast tRNA Phe promotes flexibility in the ASL domain . Modification of G37 in the ASL of yeast tRNA Phe was also reported to facilitate base stacking at the 3′-end and formation of a functional conformation that binds to a cognate codon inside the ribosome. , Our results on the small extent of stacking for A36/G37 in the yeast tRNA Phe with both the ff99bsc0TOR YIL and ff99bsc0χ OL3 force fields (Figure A, Supporting Information, Table S12) were in agreement with the experimental data which suggested that even the natural modification yW37 in yeast tRNA Phe was not always in stacked conformation. , …”

Naturally-occurring Modification Restricts the Anticodon Domain Conformational Space of tRNA Phe

“…A study of ribosome-mediated codon binding by native and position 37-altered yeast tRNA Phe reached the same conclusion. 72 Thus, taken together, the observations we and others have made support an argument that modified bases in the anticodon domain of tRNAs achieve the necessary architecture for accurate binding of codon on the ribosome by limiting conformational space.…”

Posttranscriptional modifications at the 37th position in the anticodon stem–loop of tRNA: structural insights from MD simulations

“…Thus, the yW family of modifications provides additional stability to the anticodon loop through increased stacking. This finding agrees with previous suggestions in the literature based on the anticipated increased nucleobase hydrophobicity and size (Dao et al 1994) and the previously noted decreased stability when the parent yW is replaced with A (Katunin et al 1994), as well as the trends discussed for the t 6 A family in the present work. Due to their large size and range of orientations in tRNA, these modified bases also possibly stack with the incoming first codon base during translation and thereby further increase the stability of the codon-anticodon duplex.…”

Structural Stability of the Anticodon Stem Loop Domains of the Unmodified Yeast and Escherichia coli tRNAPhe: Differing Views from Different Force Fields

“…92 Modification of G37 in the ASL of yeast tRNA Phe was also reported to facilitate base stacking at the 3′-end and formation of a functional conformation that binds to a cognate codon inside the ribosome. 93,94 Our results on the small extent of stacking for A36/G37 in the yeast tRNA Phe with both the ff99bsc0TOR YIL 67 and ff99bsc0χ OL3 69 force fields (Figure 9A, Supporting Information, Table S12) were in agreement with the experimental data which suggested that even the natural modification yW37 in yeast tRNA Phe was not always in stacked conformation. 95,96 In the case of the unmodified ASLs of the E. coli tRNA Phe , we observed large average base-stacking ratios for the residues around A37 with both the ff99bsc0TOR YIL 67 and ff99bsc0χ OL3 69 force fields which showed the formation of a continued stacked conformation of the A37 toward both the 5′-and 3′-side (Figure 9B, Supporting Information, Table S12).…”

“…It has been assumed that the loss of modification at position 37 in yeast tRNA Phe promotes flexibility in the ASL domain . Modification of G37 in the ASL of yeast tRNA Phe was also reported to facilitate base stacking at the 3′-end and formation of a functional conformation that binds to a cognate codon inside the ribosome. , Our results on the small extent of stacking for A36/G37 in the yeast tRNA Phe with both the ff99bsc0TOR YIL and ff99bsc0χ OL3 force fields (Figure A, Supporting Information, Table S12) were in agreement with the experimental data which suggested that even the natural modification yW37 in yeast tRNA Phe was not always in stacked conformation. , …”

Naturally-occurring Modification Restricts the Anticodon Domain Conformational Space of tRNA Phe

“…A study of ribosome-mediated codon binding by native and position 37-altered yeast tRNA Phe reached the same conclusion. 72 Thus, taken together, the observations we and others have made support an argument that modified bases in the anticodon domain of tRNAs achieve the necessary architecture for accurate binding of codon on the ribosome by limiting conformational space.…”