Supporting Text

By using an elastic network model based on the x-ray structure of Yusupov et al. (1) a normal mode analysis (NMA) was performed to explore the elastic deformations of the underlying complex architecture. The five lowest modes observed from these calculations appear to correspond well with motions either directly observed based on different structures of the ribosome from cryo-electron microscopy (cryo-EM) or x-ray studies, or inferred based on biophysical and biochemical measurements (see ref. 2). The nature of these motions is demonstrated in the animations below and may be described as:

Mode 1.

 Motion of the L1 stalk in a fashion that modulates access to the E-site. This motion appears to be similar to that seen in the analysis of cryo-EM maps by Frank and coworkers (3).

Mode 2.

 Motion involving some twisting of the L7/L12 stalk region and displacement of the 30S subunit relative to the 50S. This motion shares some features of the ratchet-like reorganization described below, but does not correspond as well with the functional displacement observed by Frank and Agrawal (4).

Mode 3.

 This mode corresponds well with the ratchet-like reorganization of the ribosome believed to be involved in the translocation steps of ribosome activity.

Mode 4.

 This mode involves a twisting of the L1 stalk and motions of the L7/L12 stalk region. The functional significance of this mode is not understood.

Mode 5.

 The motion associated with this mode involves the hinge-like rearrangement of the 30S ribosomal unit. The motion is quite similar to the rotation of the head, platform and shoulder toward the A site observed by Carter et al. in their x-ray structure of the 30S ribosomal unit with and without initiation factor IF1 bound (5). The hinge appears to be associated with motion about h28 in this mode.

Ratchet-Like Motion (Mode 3)

Supporting Movie 1

Movie 1.

 This movie depicts a ratchet-like rearrangement of the 70S ribosome. The rotation of the 30S ribosomal subunit relative to the 50S subunit shows high correspondence to motion captured in cryo-EM maps of the ribosome and postulated to be a key mechanical step in the translocation of the mRNA•tRNAs complex. The normal mode representing this motion provides near-atomic-level annotation of this functional rearrangement. Displayed in the movie are important displacements occurring during the ratchet-like rotation shown from a number of perspectives.

Motion of the L1-Stalk (Mode 1)

Supporting Movie 2

Movie 2.

 The L1 stalk is suggested to be involved in the opening/closing of the intersubunit space and facilitate the exit of tRNA from the E site. This movie shows the motion of the L1 stalk described by one of the elastic normal modes of the 70S ribosome. Denoted are the pivot point for the L1 stalk, the 30S and 50S ribosomal units, as well as the tRNA.

Hinge Motion in 30S (Mode 5)

Supporting Movie 3

Movie 3.

 Binding of the initiation factor IF1 has been demonstrated to involve a hinge-like rearrangement of the domains of the 30S ribosomal unit. This movie depicts similar motions observed as a result of displacements along mode 5 from the elastic network normal modes. Only the 30S subunit is shown, and the hinge region is highlighted in red. It is noteworthy that the motions observed here represent relatively localized (to 30S) deformations from the NMA of the entire 70S ribosome.

For further information, see Fig. 5.

 

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  2. Ramakrishnan, V. (2002) Cell 108, 557–572.
  1. Valle, M, Zavialov, J., Sengupta, J., Rawat, U., Ehrenberg, M. & Frank, J. (2003) Cell, in press.
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