We use a bioinformatic description of amino acid dynamic properties, based on residue-specific average B factors, to construct a dynamics-based, large-scale description of a space of protein sequences. We examine the relationship between that space and an independently constructed, structure-based space comprising the same sequences. It is demonstrated that structure and dynamics are only moderately correlated. It is further shown that helical proteins fall into two classes with very different structure–dynamics relationships. We suggest that dynamics in the two helical classes are dominated by distinctly different modes––pseudo–one-dimensional, localized helical modes in one case, and pseudo–three-dimensional (3D) global modes in the other. Sheet/barrel and mixed-α/β proteins exhibit more conventional structure–dynamics relationships. It is found that the strongest correlation between structure and dynamic properties arises when the latter are represented by the sequence average of the dynamic index, which corresponds physically to the overall mobility of the protein. None of these results are accessible to bioinformatic methods hitherto available.

我们使用基于残基特异性平均B因子的氨基酸动态特性的生物信息学描述，来构建基于动态的蛋白质序列空间的大规模描述。我们检查了该空间与一个独立构建的，包含相同序列的基于结构的空间之间的关系。结果表明，结构和动力学仅适度相关。进一步表明，螺旋蛋白分为两类，具有非常不同的结构-动力学关系。我们建议，两种螺旋类中的动力学主要由明显不同的模式所主导，一种是伪一维局部螺旋模式，另一种是伪三维三维模式。板/桶和混合的α/β蛋白表现出更常规的结构-动力学关系。发现当动态特性的序列平均值代表结构和动态特性时，结构和动态特性之间最强的相关性出现，动态平均值的序列平均值物理上对应于蛋白质的整体迁移率。迄今为止，这些结果都无法通过生物信息学方法获得。