Mechanics of Proteins and RNA

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Date/Time:Monday, 08 Mar 2010 from 4:10 pm to 5:10 pm
Location:Physics, room 5
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Robert Jernigan (Iowa State University)

Computing the functional motions from protein structures is a major challenge in computational biology. We are learning that the structures are usually designed to have a limited repertoire of feasible motions. This more deterministic, less stochastic viewpoint of biomolecular structure has many consequences for establishing mechanisms of action in biology. Elastic network models provide strong evidence that proteins substantially restrict their motions to functional motions. The elastic network models are entropic models, and their successes in describing protein functional motions point up the importance of entropy. These models represent the structures as highly cohesive rubbery materials, reflecting hydrophobicity. Such models exhibit strong control over their motions, including even the control of the motions of functional loops by domain motions and the motion of reactive atoms at enzyme active sites in coordination with their chemical reactions. There is accumulating evidence that the behavior of biological machines can be understood with these models. For the ribosome, the results clearly indicate that its motions relate strongly to multiple aspects of its function. In some ways this structure resembles a clockwork. We observe its known functional motions when we pull on the mRNA, which it processes to decode for protein synthesis. 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 freedom.

1. Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P. Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model. Biophys J. 2009;97:1178-87.

2. Yang L, Song G, Jernigan RL. Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci U S A. 2009;106:12347-52.

3. Kurkcuoglu O, Doruker P, Sen TZ, Kloczkowski A, Jernigan RL. The ribosome
structure controls and directs mRNA entry, translocation and exit dynamics. Phys Biol. 2008;5:46005.