结构域交换蛋白质二聚体中的连接
Linking in domain-swapped protein dimers
摘要：
结的存在已被观察到在一小部分的单结构域蛋白质和相关的热力学和动力学性质。结构域交换蛋白质的典型特征是相同结构元件的交换，这使得这种二聚体成为合适的候选物，以验证链之间的相互缠结可能对蛋白质复合物起类似作用的可能性。我们认为这种纠缠是由链接数捕获的。对于两条闭合曲线，这表示每条曲线围绕另一条曲线缠绕的次数。我们发现，关闭曲线是没有必要的，作为一个新的参数$G'$，称为高斯纠缠，是强烈相关的链接数。基于$110$非冗余结构域交换的二聚体，我们的分析证明了高比例的链具有显著的缠绕，即与$|G'| > 1$。我们报告说，自然促进负相互纠缠的配置，令人惊讶的是，它似乎抑制长蛋白质二聚体的缠绕。支持二聚体解离的数值模拟，我们的研究结果提供了一种新的基于拓扑结构的蛋白质交换二聚体的分类与一些初步的证据，其对它们的物理和生物学特性的影响。
英文摘要：
The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, make such dimers suitable candidates to validate the possibility that mutual entanglement between chains may play a similar role for protein complexes. We suggest that such entanglement is captured by the linking number. This represents, for two closed curves, the number of times that each curve winds around the other. We show that closing the curves is not necessary, as a novel parameter $G'$, termed Gaussian entanglement, is strongly correlated with the linking number. Based on $110$ non redundant domain-swapped dimers, our analysis evidences a high fraction of chains with a significant intertwining, that is with $|G'| > 1$. We report that Nature promotes configurations with negative mutual entanglement and surprisingly, it seems to suppress intertwining in long protein dimers. Supported by numerical simulations of dimer dissociation, our results provide a novel topology-based classification of protein-swapped dimers together with some preliminary evidence of its impact on their physical and biological properties.
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