Book of Abstracts: Albany 2003
June 17-21 2003
The Mg2+ Binding Sites of the 5S rRNA Loop E Motif Investigated by Molecular Dynamics Simulations
Molecular dynamics (MD) simulations (for a total of more than 50 ns) have been used to investigate the binding features of each of the five Mg2+ that were detected by crystallography in the deep groove of the eubacterial 5S rRNA loop E (1). The motif, phylogenetically conserved (2), is constituted by a unique stack of seven non-canonical base pairs. At a broad level, it is observed that the binding of Mg2+ ions stabilizes the stack of non-canonical base pairs indicating that, inline with numerous experimental data, Mg2+ ions have to be considered as an integral part of this motif. More precisely, it is found that the ions interact with the RNA through a rigid hydration sphere (on the present time scale the first shell water molecules do not exchange with those of the bulk and retain their positions with respect to each other). Thus, the behavior of an ion and its bound water molecules has to be described as collective tumbling motions. At a local level, the simulations allowed to characterize the dynamical features of two recurrent binding modes: (i) hexahydrated ions bound to the deep groove of GpG steps and (ii) pentahydrated ions bound to oxygen atoms. It is found that by optimizing the number of water/RNA hydrogen bonds, Mg2+ ions bind more specifically to the deep groove of a non-canonical rather than to a Watson-Crick GpG step. For pentahydrated ions, the immobilization of the apical water molecule (opposite to the direct O?Mg2+ contact) allows the ion to strengthen further its interactions with the RNA. It is found that, although electrostatic interactions are an important determinant of divalent binding events, their specificity depends on the number and strength of the contacts established between the hydrated ion and the biomolecule. These observations have important implications related to the stabilizing mechanism of divalent species.
Besides the binding of single Mg2+ ions, a very unique feature of the crystal structure of the 5S loop E motif is related to the detection of an unusual bimetallic Mg2+ cluster in its deep groove (ion to ion distance of 2.7 Å). Several MD attempts in which constraints or bridging hydroxyl ions were used, failed to maintain the geometry of this cluster. Yet, a model that combines two simulations in which the ions have each a 50% occupancy was able to reproduce the principal structural characteristics of the bimetallic cluster. This model provides an alternative interpretation of the crystallographic data.