Structural evidence and much experimental data have demonstrated the presence of non-canonical helical substructures (π and 3 10 ) 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-3 10 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.

The transient receptor potential (TRP) superfamily of cation channels is divided into several subfamilies. The TRPV (vanilloid) subfamily is composed of proteins that undergo a closed-to-open gating transition in response to various physical and chemical stimuli, including heat transfer phenomena. TRPV1, the prototypical member of these thermo-TRP channels, is activated under physiological conditions by noxious high temperatures (>42°C), and by pungent chemicals including capsaicin and resiniferatoxin . Like TRPV1, TRPV2 is also activated at >52°C as well as 2-aminoethoxydiphenyl borate and cannabidiol. On the other hand, the main stimulus for Kv channels is the potential difference across the membrane. Notwithstanding these differences in their activation temperatures, ligand- or voltage-dependence, the gating mechanisms of these channels exhibit conformational transition pathways in common. Understanding these conformational changes in terms of the sequence determinants underlying these structural transitions helps to reveal residues with great functional relevance. This work examines the side-chain flexibility in regions undergoing peculiar helical transitions. We found that α-to-π helical transitions are associated with patterns of local rigidity whereas α-to-3 transitions are mainly associated with high local flexibility profiles. We also study the relationship between flexibility and protein order, both in these dynamic regions and in the rest of the transmembrane domains of these proteins. Our analysis shows that flexibility and protein disorder are two complementary parameters that could reveal conformational heterogeneity and the dynamic behavior of specific segments.

After ligand binding, many ion channels undergo rearrangements at the voltage sensor domain (VSD) that often modulate their gating activity with important physiological repercussions. Since the VSD is dynamic, it is interesting to establish a correlation between the potential mobility of this element in terms of its intrinsic flexibility and its ability to accommodate several ligands by induced-fit mechanisms. We presume that these associations are not causal since the flexibility of the VSD could have an important impact on the ligand coupling event. Many significantly flexible ion channels show a general architecture and composition compatible with important conformational changes and capable of accommodating chemically diverse agonists. In this contribution, the structural bases of this subtle and probably unexpected relationship between the VSD flexibility and its influence during the dynamic coupling of the ligand are exposed. Thus, given its physiological relevance, the study of ion channel malfunction can be associated with ligand accommodation events to the VSD, which could depend on its local flexibility. This could contribute to a better understanding of the molecular bases of a variety of physiological disorders. In consequence, considering these effects during the protein/ligand interaction could be determinant to the rational design of novel drugs.