Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
RNA Three-Way Junctions Can Act as Flexible RNA Structural Elements in Large RNA Molecules: A Molecular Simulation Analysis
Ribosome is a large stochastic biomolecular machine which resembles a brick-box composed of molecular building blocks - RNA motifs having different shapes, flexibilities and capabilities to interact with ribosomal surrounding elements. For example K-turns can act as flexible elbows (1), other segments can act as isotropic elastic rods with sequence-dependent flexibility (2) and many others can be rather stiff with reduced thermal fluctuations (3). Molecular dynamics (MD) simulation is a suitable method to reveal intrinsic flexibilities of individual RNA segments.
This research is focused on dynamics of one of the important ribosomal building block - RNA three-way junction (3WJ) family C (4). These structures are composed of three helices P1, P2 and P3 diverging from one point, while P1 and P2 helices are coaxially stacked.  There are also tertiary interactions between stems P1 and P3, which are characteristic especially for the family C (4). We have analyzed three ribosomal junctions - Peptidyl Transferase Center 3WJ (helices 90-92), GTP-ase associated center 3WJ (helices 40-42) and 3WJ from the 5S rRNA. Crystallographic structures from archea Haloarcula Marismortui and bacteria Escherichia coli ribosomes were used.
Extensive MD simulations of total length more than 0.6 µs showed two dominant structural motions which are very similar for all three 3WJs. The first one consists of anisotropic hinge-like fluctuations between the coaxially stacked stems P1/P3 (forming the compact upper part of the structure) and P2 (Figure 1 B-C). The second one is internal dynamics of stems P1 and P3 called breathing-like motion (Figure 1 A). All three studied junctions are associated with extended regions of negative electrostatic potentials which are in many cases major binders of monovalent cations with 100% occupancy and very slow exchange of ions.
To sum up, 3WJs belong to RNA building blocks with specific elasticity signatures that can be relevant to function.
1Institute of Biophysics
Figure 1: Overlay of 5S 3WJ structures with maximal and minimal amplitudes of the (A) breathing- like motion and (B, C) hinge- like motion.
References and Footnotes