COMP 196 |
| The behavior of the GAA (1186-1188) hairpin triloops with their closing c-g base pairs in the large ribonucleoligand complexes (PDB IDs: 1njn, 1nwy, 1jzx) is investigated using molecular dynamics simulations. The trends of the relative energies of the motifs in the complexes with respect to that in the reference structure (unbound form of rRNA; PDB ID: 1njp) are in agreement with those of the conformational parameters previously reported. Therefore, molecular dynamics simulations associated with some small motifs of rRNA structure in large ribonucleoligand complexes speak in favor of the potential of a pseudotorsional (eta,theta) approach to be a valuable means of studying the sugar-phosphate backbone in the 2.5-3 Å resolution range. The thermodynamical parameters, based on the two-state conformational model of RNA sequences containing 15, 21 and 27 nucleotides in the immediate vicinity of the maximum entropy binding site of the ligand, are evaluated. The strain of a triloop is established as a structural feature that conforms to the trend of values of the thermodynamical variables. The considerations are well-correlated with the understanding that conformational changes, induced within localized regions of an rRNA structure, are associated with the overall response of the rRNA structure to the binding of a ligand at sites that are fairly far (in the range of 20 Å) away from the localized regions. |
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Molecular Mechanics
8:30 AM-12:05 PM, Tuesday, August 21, 2007 BCEC -- 161, Oral
Division of Computers in Chemistry |