Effect of nucleoside modifications on the structure and thermal stability of Escherichia coli valinetRNA

Molecular Dynamics Simulations of Solvated Yeast tRNAAsp

“…In agreement with this result, NMR investigations of various tRNA molecules have shown that tertiary base pairs exhibit lifetimes in the millisecond range, even in the absence of Mg 2ϩ ions (Leroy et al, 1985). Likewise, other studies have shown that NMR resonances associated with tertiary base pairs can be detected in various tRNAs under different ionic conditions and temperatures (Kintanar et al, 1994;Choi and Redfield, 1995).…”

Molecular Dynamics Simulations of Solvated Yeast tRNAAsp

“…In agreement with this result, NMR investigations of various tRNA molecules have shown that tertiary base pairs exhibit lifetimes in the millisecond range, even in the absence of Mg 2ϩ ions (Leroy et al, 1985). Likewise, other studies have shown that NMR resonances associated with tertiary base pairs can be detected in various tRNAs under different ionic conditions and temperatures (Kintanar et al, 1994;Choi and Redfield, 1995).…”

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

“…The Mg 2+ ions have been reported to stabilize the structure of the ASL of yeast tRNA Phe . , It has been also observed from in vitro studies that the effect of the lack of modifications on the conformational flexibility and thermal stability of tRNA Phe and tRNA Asp from yeast and tRNA Val , tRNA Phe , and tRNA Gln from E. coli can be compensated by increased concentration of the Mg 2+ ions. ,− Additionally, Leroy et al showed that divalent cations promoted the formation of native-like tRNA structure. During MD simulations, issues related to the force field parametrization for the Mg 2+ ion, such us the use of highly charged ion in pairwise simulation model, ionic radii, and the compensating effect of the other ions were anticipated to be the contributing factors to the unusual behavior of simulation’s stability and folding of RNA structures. ,, In a previous study, the slightly distorted structure of the anticodon and YYG residue was reported in the presence of Mg 2+ ions during the MD simulations of the ASLs of yeast tRNA Phe bound to the UUC and/or UUA codons .…”

Dependence of RelA-Mediated (p)ppGpp Formation on tRNA Identity

“…Others have clearly demonstrated that the post-transcriptional modifications of the tRNA Val 1 isoacceptor are important for tRNA folding and stability at low magnesium concentrations. The absence of post-transcriptional modifications can be accommodated during in vitro studies by having sufficient millimolar concentrations of magnesium ions present in the sample. , tRNA Phe only exhibits a marginal 2-fold reduction in A-Site binding in the absence of post-transcriptional modifications . Unless noted otherwise, experiments were all performed with in vitro transcribed tRNAs and thus lacked all post-transcriptional modifications.…”

Molecular Dynamics Simulations of Solvated Yeast tRNAAsp

“…In agreement with this result, NMR investigations of various tRNA molecules have shown that tertiary base pairs exhibit lifetimes in the millisecond range, even in the absence of Mg 2ϩ ions (Leroy et al, 1985). Likewise, other studies have shown that NMR resonances associated with tertiary base pairs can be detected in various tRNAs under different ionic conditions and temperatures (Kintanar et al, 1994;Choi and Redfield, 1995).…”

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

“…The Mg 2+ ions have been reported to stabilize the structure of the ASL of yeast tRNA Phe . , It has been also observed from in vitro studies that the effect of the lack of modifications on the conformational flexibility and thermal stability of tRNA Phe and tRNA Asp from yeast and tRNA Val , tRNA Phe , and tRNA Gln from E. coli can be compensated by increased concentration of the Mg 2+ ions. ,− Additionally, Leroy et al showed that divalent cations promoted the formation of native-like tRNA structure. During MD simulations, issues related to the force field parametrization for the Mg 2+ ion, such us the use of highly charged ion in pairwise simulation model, ionic radii, and the compensating effect of the other ions were anticipated to be the contributing factors to the unusual behavior of simulation’s stability and folding of RNA structures. ,, In a previous study, the slightly distorted structure of the anticodon and YYG residue was reported in the presence of Mg 2+ ions during the MD simulations of the ASLs of yeast tRNA Phe bound to the UUC and/or UUA codons .…”

Dependence of RelA-Mediated (p)ppGpp Formation on tRNA Identity

“…Others have clearly demonstrated that the post-transcriptional modifications of the tRNA Val 1 isoacceptor are important for tRNA folding and stability at low magnesium concentrations. The absence of post-transcriptional modifications can be accommodated during in vitro studies by having sufficient millimolar concentrations of magnesium ions present in the sample. , tRNA Phe only exhibits a marginal 2-fold reduction in A-Site binding in the absence of post-transcriptional modifications . Unless noted otherwise, experiments were all performed with in vitro transcribed tRNAs and thus lacked all post-transcriptional modifications.…”

Molecular Dynamics Simulations of Solvated Yeast tRNAAsp

“…In agreement with this result, NMR investigations of various tRNA molecules have shown that tertiary base pairs exhibit lifetimes in the millisecond range, even in the absence of Mg 2ϩ ions (Leroy et al, 1985). Likewise, other studies have shown that NMR resonances associated with tertiary base pairs can be detected in various tRNAs under different ionic conditions and temperatures (Kintanar et al, 1994;Choi and Redfield, 1995).…”

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

“…The Mg 2+ ions have been reported to stabilize the structure of the ASL of yeast tRNA Phe . , It has been also observed from in vitro studies that the effect of the lack of modifications on the conformational flexibility and thermal stability of tRNA Phe and tRNA Asp from yeast and tRNA Val , tRNA Phe , and tRNA Gln from E. coli can be compensated by increased concentration of the Mg 2+ ions. ,− Additionally, Leroy et al showed that divalent cations promoted the formation of native-like tRNA structure. During MD simulations, issues related to the force field parametrization for the Mg 2+ ion, such us the use of highly charged ion in pairwise simulation model, ionic radii, and the compensating effect of the other ions were anticipated to be the contributing factors to the unusual behavior of simulation’s stability and folding of RNA structures. ,, In a previous study, the slightly distorted structure of the anticodon and YYG residue was reported in the presence of Mg 2+ ions during the MD simulations of the ASLs of yeast tRNA Phe bound to the UUC and/or UUA codons .…”

Dependence of RelA-Mediated (p)ppGpp Formation on tRNA Identity

“…Others have clearly demonstrated that the post-transcriptional modifications of the tRNA Val 1 isoacceptor are important for tRNA folding and stability at low magnesium concentrations. The absence of post-transcriptional modifications can be accommodated during in vitro studies by having sufficient millimolar concentrations of magnesium ions present in the sample. , tRNA Phe only exhibits a marginal 2-fold reduction in A-Site binding in the absence of post-transcriptional modifications . Unless noted otherwise, experiments were all performed with in vitro transcribed tRNAs and thus lacked all post-transcriptional modifications.…”