On Evolution, Structure and Dynamics in Potassium Channels

Ion channels play fundamental roles in living organisms ranging from propagation of action potentials to chemotaxis. While the sequences of ion channels can differ greatly, their function and their structure share great similarities. Structurally, the here investigated channels follow a basic, structural composition with inner and outer helices entrenching a pore helix and an selectivity filter. These homotetrameric structures form water filled pores through which ions can pass upon opening of the channel. To investigate structure-function correlates within this broad group of proteins we derive in this thesis novel approaches to capture evolutionary substitution behaviors, investigate co-evolutionary complexity and analyze structural relations. The first chapter captures an overview of stand-alone scientific contributions with a brief introduction to their methodological aspects as well as their results. Within the following chapters of this thesis we will integrate and expand parts of these publications to further the understanding in interdependencies within ion channels. The second chapter revolves around a novel type of substitution matrices derived from Pfam alignments of channel proteins. Using the novel PFASUM algorithm (Keul et al., 2017) we generate family-specific substitution matrices and show their improved performance in comparison to BLOSUM matrices for channel protein sequences. We find that these novel PFASUM matrices cluster amino acids with diverse physico-chemical properties stronger than their BLOSUM counterparts which in turn leads to improved alignments. In the third chapter of this work we aim at capturing amino acid sequence inherent information from two major channel protein families through information theoretical methods. Here, we devise the measure of co-evolutionary complexity DeltaCMI which measures the deviation of observed evolutionary mechanics from a reference model. When applied to potassium channel sequences we find large differences in complexity of the evolutionary mechanism within the outer helix between channels with two transmembrane domains and six. We attribute the substantially different evolutionary behavior of six transmembrane domain channels to the interaction between the so called voltage sensing domain and outer transmembrane helix. In the last chapter we use coarse-grained elastic network models to compare protein dynamics between open and closed channel structures through analyzing changes in the free energy of the fold. Furthermore, we investigate relationships between the regions within channel pore of differently sized channels from numerous organisms by examining the influence of perturbations between the regions. Hereby, we focus on changes in free energy in a subspace of the molecular Hamiltonian when subjected to perturbation while still considering the entirety of all interactions within the Hamiltonian. This allows us the comparison of perturbation thought experiments on differently sized, but similarly organized structures. Through this we are able show that the selectivity filter of ion channels is decoupled from the all other pore forming segments. Furthermore, we find that – in the context of elastic network models – fold dynamics within the analyzed subspace of the Hamiltonian are independent of sequence information