Global ribosome motions revealed with elastic network model

@article{citeulike:277925, abstract = {The motions of large systems such as the ribosome are not fully accessible with conventional molecular simulations. A coarse-grained, less-than-atomic-detail model such as the anisotropic network model (ANM) is a convenient informative tool to study the cooperative motions of the ribosome. The motions of the small 30S subunit, the larger 50S subunit, and the entire 70S assembly of the two subunits have been analyzed using ANM. The lowest frequency collective modes predicted by ANM show that the 50S subunit and 30S subunit are strongly anti-correlated in the motion of the 70S assembly. A ratchet-like motion is observed that corresponds well to the experimentally reported ratchet motion. Other slow modes are also examined because of their potential links to the translocation steps in the ribosome. We identify several modes that may facilitate the E-tRNA exiting from the assembly. The A-site t-RNA and P-site t-RNA are found to be strongly coupled and positively correlated in these slow modes, suggesting that the translocations of these two t-RNAs occur simultaneously, while the motions of the E-site t-RNA are less correlated, and thus less likely to occur simultaneously. Overall the t-RNAs exhibit relatively large deformations. Animations of these slow modes of motion can be viewed at http://ribosome.bb.iastate.edu/70SnKmode.}, author = {Wang, Yongmei and Rader, A. J. and Bahar, Ivet and Jernigan, Robert L. }, citeulike-article-id = {277925}, doi = {http://dx.doi.org/10.1016/j.jsb.2004.01.005}, journal = {Journal of Structural Biology}, keywords = {coarse-grained, gnm}, month = {September}, number = {3}, pages = {302--314}, posted-at = {2008-02-18 18:10:07}, priority = {0}, title = {Global ribosome motions revealed with elastic network model}, url = {http://dx.doi.org/10.1016/j.jsb.2004.01.005}, volume = {147}, year = {2004} }

TY - JOUR ID - citeulike:277925 L3 - citeulike-article-id:277925 TI - Global ribosome motions revealed with elastic network model JF - Journal of Structural Biology VL - 147 IS - 3 SP - 302 EP - 314 N2 - The motions of large systems such as the ribosome are not fully accessible with conventional molecular simulations. A coarse-grained, less-than-atomic-detail model such as the anisotropic network model (ANM) is a convenient informative tool to study the cooperative motions of the ribosome. The motions of the small 30S subunit, the larger 50S subunit, and the entire 70S assembly of the two subunits have been analyzed using ANM. The lowest frequency collective modes predicted by ANM show that the 50S subunit and 30S subunit are strongly anti-correlated in the motion of the 70S assembly. A ratchet-like motion is observed that corresponds well to the experimentally reported ratchet motion. Other slow modes are also examined because of their potential links to the translocation steps in the ribosome. We identify several modes that may facilitate the E-tRNA exiting from the assembly. The A-site t-RNA and P-site t-RNA are found to be strongly coupled and positively correlated in these slow modes, suggesting that the translocations of these two t-RNAs occur simultaneously, while the motions of the E-site t-RNA are less correlated, and thus less likely to occur simultaneously. Overall the t-RNAs exhibit relatively large deformations. Animations of these slow modes of motion can be viewed at http://ribosome.bb.iastate.edu/70SnKmode. KW - coarse-grained KW - gnm AU - Wang, Yongmei AU - Rader, AJ AU - Bahar, Ivet AU - Jernigan, Robert PY - 2004/09// UR - http://dx.doi.org/10.1016/j.jsb.2004.01.005 ER -