Role of methyl groups in dynamics and evolution of biomolecules |
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Authors: | Jonathan D. Nickels Joseph E. Curtis Hugh O’Neill Alexei P. Sokolov |
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Affiliation: | 1.Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ;2.Department of Chemistry, The University of Tennessee, Knoxville, TN 37996–1600 USA ;3.NIST Center for Neutron Research, 100 Bureau Drive, Gaithersburg, MD 20899 USA ;4.Energy and the Environment Group, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA |
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Abstract: | Recent studies have discovered strong differences between the dynamics of nucleic acids (RNA and DNA) and proteins, especially at low hydration and low temperatures. This difference is caused primarily by dynamics of methyl groups that are abundant in proteins, but are absent or very rare in RNA and DNA. In this paper, we present a hypothesis regarding the role of methyl groups as intrinsic plasticizers in proteins and their evolutionary selection to facilitate protein dynamics and activity. We demonstrate the profound effect methyl groups have on protein dynamics relative to nucleic acid dynamics, and note the apparent correlation of methyl group content in protein classes and their need for molecular flexibility. Moreover, we note the fastest methyl groups of some enzymes appear around dynamical centers such as hinges or active sites. Methyl groups are also of tremendous importance from a hydrophobicity/folding/entropy perspective. These significant roles, however, complement our hypothesis rather than preclude the recognition of methyl groups in the dynamics and evolution of biomolecules. |
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Keywords: | Protein dynamics RNA world RNA dynamics Nucleic acid dynamics |
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