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Title
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Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals.
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Authors
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E.Westhof,
P.Dumas,
D.Moras.
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Ref.
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Acta Crystallogr A, 1988,
44,
112-123.
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PubMed id
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Abstract
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Four transfer RNA crystals, the monoclinic and orthorhombic forms of yeast
tRNA(Phe) as well as forms A and B of yeast tRNA(Asp), have been submitted to
the same restrained least-squares refinement program and refined to an R factor
well below 20% for about 4500 reflections between 10 and 3 A. In yeast tRNA(Asp)
crystals the molecules exist as dimers with base pairings of the anticodon (AC)
triplets and labilization of the tertiary interaction between one invariant
guanine of the dihydrouridine (D) loop and the invariant cytosine of the thymine
(T) loop (G19-C56). In yeast tRNA(Phe) crystals, the molecules exist as monomers
with only weak intermolecular packing contacts between symmetry-related
molecules. Despite this, the tertiary folds of the L-shaped tRNA structures are
identical when allowance is made for base sequence changes between tRNA(Phe) and
tRNA(Asp). However, the relative mobilities of two regions are inverse in the
two structures with the AC loop more mobile than the D loop in tRNA(Phe) and the
D loop more mobile than the AC loop in tRNA(Asp). In addition, the T loop
becomes mobile in tRNA(Asp). The present refinements were performed to exclude
packing effects or refinement bias as possible sources of such differential
dynamic behavior. It is concluded that the transfer of flexibility from the
anticodon to the D- and T-loop region in tRNA(Asp) is not a crystal-line
artefact. Further, analysis of the four structures supports a mechanism for the
flexibility transfer through base stacking in the AC loop and concomitant
variations in twist angles between base pairs of the anticodon helix which
propagate up to the D- and T-loop region.
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