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Large‐amplitude bending motions in phenylalanine transfer RNA
Author(s) -
Tung ChangShung,
Harvey Stephen C.,
McCammon J. Andrew
Publication year - 1984
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360231106
Subject(s) - chemistry , intramolecular force , bent molecular geometry , transfer rna , steric effects , molecule , solvation , bending , crystallography , acceptor , stereochemistry , computational chemistry , thermodynamics , rna , physics , biochemistry , organic chemistry , gene , condensed matter physics
Conformational energy calculations on yeast tRNA Phe reveal several likely modes of intramolecular bending, including both hingelike motions (rotations about a discrete point) and distributed flexibility (deformations that bend a double‐helical segment along a smooth curve). By combining these modes of motion, the molecule can be bent from the L‐shaped crystallographic structure to two extremes. It can be straightened into a nearly linear conformation at an energy cost of about 50 kcal/mol, and it can be doubled over to a conformation where the anticodon and the amino acid acceptor terminus are separated by about 40 Å at an energy cost of less than 100 kcal/mol. A bending range of over 100° can be covered for 50 kcal/mol, and we estimate that this value could be cut in half with a minimization algorithm that produced optimum stereochemistry. These energies are comparable to those that would be associated with changes in solvation due to changes in surface area as the molecule bends, indicating that there are no major steric barriers to tRNA flexibility and that variations in solvent conditions and interactions with other molecules may produce large changes in the overall conformation of tRNA.