Non-canonical helical transitions and conformational switching are associated with characteristic flexibility and disorder indices in TRP and Kv channels

Structural evidence and much experimental data have demonstrated the presence of non-canonical helical substructures (π and 310) in regions of great functional relevance both in TRP as in Kv channels. Through an exhaustive compositional analysis of the sequences underlying these substructures, we find that each of them is associated with characteristic local flexibility profiles, which in turn are implicated in significant conformational rearrangements and interactions with specific ligands. We found that α-to-π helical transitions are associated with patterns of local rigidity whereas α-to-310 transitions are mainly leagued with high local flexibility profiles. We also study the relationship between flexibility and protein disorder in the transmembrane domain of these proteins. By contrasting these two parameters, we located regions showing a sort of structural discrepancy between these similar but not identical protein attributes. Notably, these regions are presumably implicated in important conformational rearrangements during the gating in those channels. In that sense, finding these regions where flexibility and disorder are not proportional allows us to detect regions with potential functional dynamism. From this point of view, we highlighted some conformational rearrangements that occur during ligand binding events, the compaction, and refolding of the outer pore loops in several TRP channels, as well as the well-known S4 motion in Kv channels.

结构证据与大量实验数据均已证实，在TRP通道与Kv通道的诸多功能高度相关区域中，存在非经典螺旋亚结构——π螺旋与3₁₀螺旋。通过对这些亚结构对应的序列开展详尽的组成分析，我们发现每种非经典螺旋亚结构均与特征性局部柔性特征相关联，而这类柔性特征又与显著的构象重排以及特异性配体的相互作用密切相关。我们发现，α螺旋向π螺旋的转变与局部刚性模式相关联，而α螺旋向3₁₀螺旋的转变则主要与高局部柔性特征相关。本研究还分析了上述蛋白质跨膜结构域中柔性与蛋白质无序性之间的关联。通过对比这两项参数，我们定位到了一类存在结构差异的区域：这类区域的两种属性相似却并不完全等同。值得注意的是，这类区域据推测参与了上述离子通道门控过程中的关键构象重排事件。据此，通过识别柔性与无序性不成比例的这类区域，我们能够发掘具有潜在功能动态性的位点。基于此视角，我们重点阐释了配体结合过程中发生的若干构象重排现象，包括多种TRP通道的孔外环紧缩与重折叠过程，以及Kv通道中广为人知的S4螺旋运动。