A Single-Molecule Interaction Spectrum for Non-Covalent Interaction Inside Membrane Protein Channel

Abstract

Dynamic non-covalent interactions of biomolecules are ubiquitous in almost all biological process. In particular, it underlies the successive transport of ions or target carriers by membrane protein, controlling many key cellular functions. However, few experimental approaches can directly define the multiple non-covalent interactions within the channel. Since all the dynamic non-covalent dynamic interaction inside membrane protein have been all recorded but hide in the traditional single-channel recording of ionic current, here, we present a rational strategy in the combination of experiments, MD simulations and frequency-energy spectra of ionic flow to quantify and quality a role of non-covalent interaction for membrane protein channel in transporting the carriers. We employed wild-type aerolysin transporting of methylcytosine and cytosine as a model to detailed explore the dynamic ionic signatures with the non-stationary and non-linear frequency analysis. The results demonstrate that The main frequency peak position in frequency-energy spectrum represents the main ion mobility inside membrane protein while its energy suggests the vibration amplitude of the related ions. The sudden spikes in the frequency-energy considered as the fingerprint spectra for potential characterization of non-covalent interaction. The frequency-energy spectrum of ions flowing inside membrane channels constituting a Single-Molecule Interaction Spectrum, which bridges the gap in-between traditional ionic current recording and the MD simulations, facilitating the qualitative and quantify describe the non-covalent interactions inside membrane channels.