Molecular Dynamics Simulations of the Ribosome - Biophysical Approaches to Translational Control of Gene Expression - page 59

tend to be more synchronized. Because the L1 stalk interacts with the P/E position
and E/E position tRNA, it is thought to be involved with E-site tRNA dissociation.
Single molecule studies also show the L7/L12 stalk to fluctuate rapidly.
The L7/L12 protein complex itself is thought to be the most dynamic region of
the ribosome. This consists of a long alpha helix (L10) bolstered by several L7/L12
NTD dimers (Diaconu et al. 2005 ; Bocharov et al. 2004 ). Each L7/L12 NTD domain
is connected to its CTD by a long disordered flexible linker. These allow the CTD
to undergo tremendous large fluctuations which may aid in capturing translation
factors in a fly-casting mechanism (Shoemaker et al. 2000 ) .

3.4 Molecular Dynamics Simulations and Other

Computational Studies of the Ribosome

3.4.1 Background

Rapid kinetics, single molecule FRET, X-ray crystallography, and cryo-EM have
provided an excellent glimpse into the dynamics of the ribosome. To obtain the free
energy landscape of the ribosome and a more complete understanding of elonga-
tion, this large body of experiments must be integrated into a coherent picture.
Molecular dynamics simulation is an excellent tool to provide a theoretical frame-
work to ground interpretation of experimental results.
By labeling strategic regions of the ribosome, rapid kinetics experiments have
been able to isolate the various substeps of elongation, giving us the framework for
how translation proceeds (Wintermeyer et al. 2004 ). Single molecule FRET experi-
ments use donor-acceptor label pairs to obtain time-dependent distance constraints
on specific conformational changes (Blanchard 2009 ) . X-ray crystallography struc-
tures produce high-resolution atomic models of the ribosome in its resting states
(classical, EF-G bound, and EF-Tu bound) (Yusupova et al. 2006 ; Selmer et al.
2006 ; Schuwirth et al. 2000, 2005 ; Korostelev et al. 2006 ; Ban et al. 2000 ) . Three-
dimensional cryo-EM reconstructions call us to construct atomic models of the
ribosome in a wide variety of functional states (Zhang et al. 2008 ; Fischer et al.
2010 ; Ratje et al. 2010 ). Molecular dynamics simulations integrate the above data
into a single coherent mechanistic framework (Whitford et al. 2010b ) .
Modeling efforts (Malhotra et al. 1990, 1994 ) and advances in high-performance
computing have produced an era in which molecular modeling and simulations can
clarify the relationship between static ribosome structures (Ratje et al. 2010 ; Villa
et al. 2009 ), structural fluctuations about these local energetic minima (Tama et al.
2003 ; Wang et al. 2004 ), transitions between minima, and ribosome function
(Whitford et al. 2010a ; Sanbonmatsu and Joseph 2003 a; Sanbonmatsu et al. 2005 ) .
Molecular dynamics simulations and modeling studies have explored the decoding
center (Sanbonmatsu and Joseph 2003 b; Lim and Curran 2001 ; VanLoock et al.