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- Distance constraints were divided into the following four reions: (i)1.8–3.0 Å (strong volumes), (ii) 1.8–4.0 Å (medium), (iii) 1.8–5.0 Å (weak) and (iv) 1.8–7.0 Å (very weak volumes). The volume for the H5-H6 crosspeak of C9 at each mixing time was used as reference volume with a corresponding distance of 2.46 Å
- Additional distance constraints: 20 hydrogen bond constraints for the seven basepairs in the stem, 12 distance constraints involving the H1-H1′ crosspeaks (see Fig. 1) in the stem, six planarity constraints to ensure planarity of the basepairs, and 122 dihedral constraints (α, β, γ, ε, ζ, χ and V0-V4) to keep the stem nucleotides in an A-RNA conformation
- Borgias , B. A. , Thomas , P. D. , Liu , H. , Kumar , A. , Tonelli , M. and James , T. L. 1995 . MARDIGRAS 5.1 , San Fransisco , CA : University of California .
- Cornell , W. D. , Cieplak , P. , Bayly , C. I. , Gould , I. R. , Men , K. M. Jr. , Ferguson , D. M. , Spellmeyer , D. C. , Fox , T. , Caldwell , J. W. and Kollman , P. A. 1995 . J. Am. Chem. Soc. , 117 : 5179 – 5197 .
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- All AMBER calculations were performed in vacuo with a constant dielectric of 4.0 (ε=4.0) and infinite non–bonded cutoffs. Shake17 was used for bonds involving hydrogen atoms and the time step was 1 fs for all MDs. The Berendsen algorithm18 was used to control the temperature with τ=0.2 ps
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- Extra five distance constraints: hydrogen bonds in C7-G15 basepair and H1 of G15 to H1′ of C8 and to H1′ of C166, and 20 additional torsional constraints on backbone and sugar torsions of C7 and G15 (α, β, γ, ε, ζ, χ and v0-v4)
- Force constants: 40 kcal.mol−1.Å−2 for distances derived from NOESY spectra, 80 kcal.mol−1.Å−2 for hydrogen bond distances, 160 kcal.mol−1.Å−2 for the two H1-H1′ distances, and 400 kcal.mol−1.rad−2 for torsions
- Force constants: 5 kcal.mol−1.Å−2 for distances derived from NOESY spectra, 10 kcal.mol−1.Å−2 for hydrogen bond distances, 2.5 kcal.mol−1.Å−2 for the twelve H1-H1′ distances, and 50 kcal.mol−1.rad−2 for torsions
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- Schmitz , U. , Ulyanov , N. B. , Kumar , A. and James , T. L. 1993 . J. Mol. Biol. , 234 : 373 – 389 .
- González , C. , Stec , W. , Reynolds , M. A. and James , T. L. 1995 . Biochemistry , 34 : 4969 – 4982 .