FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2912879542> ?p ?o ?g. }

• W2912879542 endingPage "3044" @default.
• W2912879542 startingPage "3029" @default.
• W2912879542 abstract "Unmodified tRNAs provide essential insights into the structural and functional role of the extensive and diverse post-transcriptional modifications that naturally occur in tRNAs. The X-ray crystal structure of the completely unmodified Escherichia coli tRNAPhe showed preserved anticodon stem loop (ASL) conformation compared with that of the natively modified mature yeast tRNAPhe. On the other hand, NMR studies reveal that both unmodified E. coli and incompletely modified yeast tRNAPhe ASL structures differ from the canonical conformation by adopting altered conformations resembling extended stems and shorter loops. In the present work, we performed molecular dynamics simulation of the ASL domains of the unmodified counterparts of the yeast and E. coli tRNAPhe in explicit water with two recently revised AMBER force fields for RNA, ff99bsc0TORYIL and ff99bsc0χOL3, starting from the X-ray derived structures in the canonical conformation. For a single ASL system, five independent simulations of 200 ns each were performed yielding 4000 ns (or 4 μs) of simulation time in total. The ff99bsc0χOL3 force field was found to retain the X-ray-like conformational features during the entire course of simulations of both the ASLs in the absence of natural modifications. In the case of the ff99bsc0TORYIL force field, the observed deviations from the initial structures, conformational flexibility, and destabilization in the canonical U-turn structure and in the A-RNA-like conformational preferences for the backbone torsion angles were noticeably larger compared with those obtained with the ff99bsc0χOL3 force field. The observed destabilization in the canonical anticodon stair-stepped conformation was larger for the unmodified ASLs of yeast tRNAPhe compared with that of E. coli. However, none of the force fields could reproduce the conformational characteristics reported in the solution NMR studies of unmodified E. coli and incompletely modified yeast tRNAPhe ASL structures." @default.
• W2912879542 created "2019-02-21" @default.
• W2912879542 creator A5033021345 @default.
• W2912879542 creator A5044367461 @default.
• W2912879542 creator A5052850159 @default.
• W2912879542 creator A5066310992 @default.
• W2912879542 date "2019-02-12" @default.
• W2912879542 modified "2023-10-17" @default.
• W2912879542 title "Structural Stability of the Anticodon Stem Loop Domains of the Unmodified Yeast and <i>Escherichia coli</i> tRNA^Phe: Differing Views from Different Force Fields" @default.
• W2912879542 cites W1484204974 @default.
• W2912879542 cites W1897551952 @default.
• W2912879542 cites W1908437703 @default.
• W2912879542 cites W1963766165 @default.
• W2912879542 cites W1964176219 @default.
• W2912879542 cites W1967737979 @default.
• W2912879542 cites W1968529304 @default.
• W2912879542 cites W1969758655 @default.
• W2912879542 cites W1975372074 @default.
• W2912879542 cites W1975586269 @default.
• W2912879542 cites W1976464319 @default.
• W2912879542 cites W1976499671 @default.
• W2912879542 cites W1977095694 @default.
• W2912879542 cites W1979911160 @default.
• W2912879542 cites W1981629946 @default.
• W2912879542 cites W1982117955 @default.
• W2912879542 cites W1986988560 @default.
• W2912879542 cites W1989683090 @default.
• W2912879542 cites W1991058622 @default.
• W2912879542 cites W1991151329 @default.
• W2912879542 cites W1991667171 @default.
• W2912879542 cites W1992043883 @default.
• W2912879542 cites W1994207191 @default.
• W2912879542 cites W1995314607 @default.
• W2912879542 cites W1996075279 @default.
• W2912879542 cites W2005420540 @default.
• W2912879542 cites W2007648224 @default.
• W2912879542 cites W2008296375 @default.
• W2912879542 cites W2009591144 @default.
• W2912879542 cites W2012253277 @default.
• W2912879542 cites W2019437199 @default.
• W2912879542 cites W2022430866 @default.
• W2912879542 cites W2022754910 @default.
• W2912879542 cites W2026004038 @default.
• W2912879542 cites W2026172209 @default.
• W2912879542 cites W2027042879 @default.
• W2912879542 cites W2029559360 @default.
• W2912879542 cites W2030813091 @default.
• W2912879542 cites W2031406076 @default.
• W2912879542 cites W2035266068 @default.
• W2912879542 cites W2036683766 @default.
• W2912879542 cites W2037003688 @default.
• W2912879542 cites W2037577397 @default.
• W2912879542 cites W2038354555 @default.
• W2912879542 cites W2040485185 @default.
• W2912879542 cites W2040860361 @default.
• W2912879542 cites W2043848348 @default.
• W2912879542 cites W2045979907 @default.
• W2912879542 cites W2048113400 @default.
• W2912879542 cites W2050839209 @default.
• W2912879542 cites W2051158366 @default.
• W2912879542 cites W2054882130 @default.
• W2912879542 cites W2055092040 @default.
• W2912879542 cites W2061029954 @default.
• W2912879542 cites W2061822610 @default.
• W2912879542 cites W2065847836 @default.
• W2912879542 cites W2067174909 @default.
• W2912879542 cites W2067249172 @default.
• W2912879542 cites W2069169076 @default.
• W2912879542 cites W2071462258 @default.
• W2912879542 cites W2071930821 @default.
• W2912879542 cites W2081046982 @default.
• W2912879542 cites W2085928743 @default.
• W2912879542 cites W2086019465 @default.
• W2912879542 cites W2089204784 @default.
• W2912879542 cites W2091218156 @default.
• W2912879542 cites W2092221199 @default.
• W2912879542 cites W2094366412 @default.
• W2912879542 cites W2096184392 @default.
• W2912879542 cites W2104249079 @default.
• W2912879542 cites W2104930084 @default.
• W2912879542 cites W2106140689 @default.
• W2912879542 cites W2108332331 @default.
• W2912879542 cites W2108563895 @default.
• W2912879542 cites W2111098742 @default.
• W2912879542 cites W2112597896 @default.
• W2912879542 cites W2113404023 @default.
• W2912879542 cites W2114478647 @default.
• W2912879542 cites W2115495500 @default.
• W2912879542 cites W2116413427 @default.
• W2912879542 cites W2120349627 @default.
• W2912879542 cites W2122199548 @default.
• W2912879542 cites W2122260546 @default.
• W2912879542 cites W2127749120 @default.
• W2912879542 cites W2129342854 @default.
• W2912879542 cites W2130880846 @default.
• W2912879542 cites W2131288855 @default.
• W2912879542 cites W2136729627 @default.
• W2912879542 cites W2139273948 @default.

• next