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Conformational changes in transfer RNA. I. Equilibrium theory
Author(s) -
De Lisi Charles
Publication year - 1973
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.1973.360120802
Subject(s) - transfer rna , chemistry , protein secondary structure , thermodynamics , helix (gastropod) , melting temperature , rna , protein tertiary structure , crystallography , chemical physics , physics , biochemistry , materials science , ecology , biology , snail , composite material , gene
Abstract We report the results of semi‐empirical calculations describing thermodynamic properties of transfer RNA conformations. The most important new features of the procedure are: ( 1 ) the use of parameters obtained from model oligoribonucleotides to evaluate the free energy of helical regions and small hairpin loops, and ( 2 ) the use of a model which is somewhat more realistic than the freely jointed chain for evaluating internal loops and intermediate size hairpin loops. The new parameters lead to important quantitative and qualitative differences from predictions which would have been made in the past and lead to a priori predictions of tRNA melting temperatures which are within about 6°C of the experimental values. The results suggest the following conclusions: ( 1 ) The early melting transition observed in several tRNA's is partly the result of tertiary unfolding, and partly the result of the loss of some secondary structure. ( 2 ) The part of the secondary structure which melts during the early transition is different for different tRNA's. For fMet and Tyr from E. coli , the calculations predict that the dihydrouradiene arm melts out early. For yeast Phe the acceptor stem and anticodon helix melt first. ( 3 ) The results also suggest the possibility that tertiary unfolding and early secondary structural melting do not occur independently but are coupled, so that the two types of structure are probably mutually stabilizing.