Maguid Sandra, Fernández-Alberti Sebastián, Parisi Gustavo, Echave Julián
Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes, Saenz Peña 180, 1876, Bernal, Buenos Aires, Argentina.
J Mol Evol. 2006 Oct;63(4):448-57. doi: 10.1007/s00239-005-0209-x. Epub 2006 Oct 4.
Internal protein dynamics is essential for biological function. During evolution, protein divergence is functionally constrained: properties more relevant for function vary more slowly than less important properties. Thus, if protein dynamics is relevant for function, it should be evolutionary conserved. In contrast with the well-studied evolution of protein structure, the evolutionary divergence of protein dynamics has not been addressed systematically before, apart from a few case studies. X-Ray diffraction analysis gives information not only on protein structure but also on B-factors, which characterize the flexibility that results from protein dynamics. Here we study the evolutionary divergence of protein backbone dynamics by comparing the C(alpha) flexibility (B-factor) profiles for a large dataset of homologous proteins classified into families and superfamilies. We show that C(alpha) flexibility profiles diverge slowly, so that they are conserved at family and superfamily levels, even for pairs of proteins with nonsignificant sequence similarity. We also analyze and discuss the correlations among the divergences of flexibility, sequence, and structure.
蛋白质内部动力学对于生物学功能至关重要。在进化过程中，蛋白质的分化受到功能限制：与功能更相关的特性变化比不太重要的特性更缓慢。因此，如果蛋白质动力学与功能相关，那么它应该在进化上是保守的。与对蛋白质结构的深入研究的进化不同，除了少数案例研究外，蛋白质动力学的进化分化以前尚未得到系统的探讨。X射线衍射分析不仅能提供蛋白质结构的信息，还能提供B因子的信息，B因子表征了由蛋白质动力学产生的灵活性。在这里，我们通过比较分类为家族和超家族的大量同源蛋白质数据集的Cα灵活性（B因子）谱，研究蛋白质主链动力学的进化分化。我们表明，Cα灵活性谱分化缓慢，因此即使对于序列相似性不显著的蛋白质对，它们在家族和超家族水平上也是保守的。我们还分析并讨论了灵活性、序列和结构分化之间的相关性。
