PHYS 137 |
| Computing the functional motions from protein structures is an important challenge in computational biology. Elastic network models are providing strong evidence that proteins control all their functional motions through their slow, domain motions. A major strength of these models appears to be their ability to represent the structures as highly cohesive rubbery materials. Such models exhibit strong control over their motions, including control of the motions of surface loops by domain motions and even the motion of reactive atoms at enzyme active sites in coordination with domain motions. These can be used to suggest enzyme mechanisms. Is this a proper representation of structure or are the proteins actually less cohesive? Nonetheless there is accumulating evidence that the behavior of protein machines can be understood with these models, and the important large domain motions can be obtained readily. For the ribosome, the results clearly indicate that its motions relate strongly to many aspects of its function. Already we have seen that the large ribosomal ratchet motion simultaneously causes the t-RNAs and mRNA to translate in the processing direction. The control of the mRNA at the codon/anti-codon binding site is extremely strong, to ensure fidelity of copying, with the mRNA being moved translationally as a fully rigid body, with no internal motions. |
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Multiscale Modeling in Biophysics
8:20 AM-12:20 PM, Monday, April 7, 2008 Morial Convention Center -- Rm. R03, Oral
Division of Physical Chemistry |