Structural Control of Motions?

Tuesday, January 15, 2008 - 3:40pm - 4:10pm
EE/CS 3-180
Robert Jernigan (Iowa State University)
Are protein motions limited because of a higher level of cooperativity than indicated by usual potentials?

Recently derived four-body coarse-grained potentials show improved performance in threading over pairwise potentials. Their apparently increased extent of cooperativity is consistent with the high level of control of motions manifested in the elastic network model computations. The elastic network models are providing strong evidence that proteins control their functional motions through their most important slowest domain motions. A major strength of these models appears to be their ability to represent the structures as highly cohesive rubbery materials, and much evidence supporting them has now accumulated. Such models exhibit strong control over their motions, arising principally from the shape, sometimes even including control of the motions of surface loops by domain motions and the motion of reactive atoms at enzyme active sites. These highly coordinated atom motions may be relevant to enzyme mechanisms. 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 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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