Nickels Jonathan D, Curtis Joseph E, O'Neill Hugh, Sokolov Alexei P
Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ; Department of Chemistry, The University of Tennessee, Knoxville, TN 37996-1600 USA.
J Biol Phys. 2012 Jun;38(3):497-505. doi: 10.1007/s10867-012-9268-6. Epub 2012 Apr 14.
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.Electronic supplementary material The online version of this article (doi:10.1007/s10867-012-9268-6) contains supplementary material, which is available to authorized users.
最近的研究发现，核酸（RNA和DNA）与蛋白质的动力学之间存在显著差异，尤其是在低水合度和低温条件下。这种差异主要是由蛋白质中丰富的甲基动力学引起的，而在RNA和DNA中则不存在或非常罕见。在本文中，我们提出了一个关于甲基作为蛋白质内在增塑剂的作用及其促进蛋白质动力学和活性的进化选择的假设。我们证明了甲基相对于核酸动力学对蛋白质动力学的深远影响，并指出了蛋白质类别中甲基含量与其对分子灵活性需求之间的明显相关性。此外，我们注意到一些酶的最快甲基出现在诸如铰链或活性位点等动力学中心周围。从疏水性/折叠/熵的角度来看，甲基也非常重要。然而，这些重要作用补充了我们的假设，而不是排除在生物分子动力学和进化中对甲基的认识。电子补充材料 本文的在线版本（doi:10.1007/s10867-012-9268-6）包含补充材料，授权用户可以获取。
