From peptides to transmembrane proteins : helix versus kink formations in highly dynamical systems

This thesis describes investigations of the relationships between the sequence of small peptides and their folding propensities and the conformational changes of membrane lipids upon interactions with proteins, within the context of varying membrane potentials. In addition, a novel conformational change of a membrane protein will be presented.
The determination of structures of folded proteins has progressed remarkably, notably due to outstanding techniques like crystallography, nuclear magnetic resonance or cryo-electron microscopy. However, proteins are highly dynamic and, under physiological conditions, their behavior depends on the chemical and physical environment. On the other hand, a better understanding of the intrinsically disordered proteins requires approaches, which consider their dynamical nature. All-atom molecular dynamics simulations constitute a tool of choice to capture the conformational changes of peptides as well as larger systems involving bilayers and membrane proteins. The first part of this thesis is dedicated to the structural propensities of peptides explored at the amino acid level. The investigations have shown how subtle interactions with the solvent affect their fate towards helical conformations. These findings are further validated through a procedure aimed at reducing the differences between predicted and experimental values while maximizing the entropy of the ensemble. The short-lived conformations found along transition paths are difficult to observe experimentally. Consequently, a statistical approach to investigate at the picosecond timescale the dynamics of the folding events in relation to the surrounding molecules is introduced and successfully tested on a β–hairpin of known structure. These successful results lead to a proposal of a systematic study to elucidate the sequence-conformation(s) relationships at a larger scale.
The second project describes the interactions between spider toxins, the cell membrane and a voltage sensor domain in the context of ion channel gating modification. Spider toxins have contributed substantially to the understanding of ion channels. Most of them are gating modifiers, thus affecting the energy level required by ion channels to open or close. Because these molecules are capable of fine-tuning the function of ion channels, they represent very attractive candidates in the field of drug discovery, and some successes have been achieved in this regard. The initial objective of the study was to explore whether the toxin-induced perturbation of the membrane affect consequently the voltage-gated ion channels without any direct binding to the target. A demanding statistical approach was chosen, which takes the high specificity of spider toxins observed in vivo into account. Although the inserted toxins altered noticeably several membrane features, the results support the idea that an indirect, lipid-mediated mode of action of spider toxins on the voltage-sensor domain is not the main driver of the voltage-gated modifier mechanism. However, the investigations led to unexpected discoveries. The strategy employed to investigate an indirect mechanism of spider toxin involved more than 100 replicated simulations of independent bilayers and voltage-sensor domains exposed to a wide range of membrane potentials. The analyses showed surprisingly that the membrane perturbation, induced by the voltage sensor domain, is voltage-dependent. In addition, a novel conformational change of the voltage sensor upon polarization was observed, namely a kink in the S4 helix.
The results discussed here aim to contribute to a better understanding in three domains:
1) The interplay between water and the amino acid side chains during conformational changes, precisely the hydration fluctuations of just a few amide or carbonyl functional groups are shown to affect the helix formation propensities of a small peptide.
2) The lipid-mediated gating modifier mechanism is not supported by the simulations.
3) A novel conformational change of the voltage-sensor domain is described as a response to variation of the membrane potential. Precisely, a kink in the middle of the S4 helix occurs only upon polarization. This kink formation allows gating charges to move across the membrane without exposing any hydrophobic residues to the cytoplasm.