Molecular dynamics simulations of oligomeric ion channels within lipid bilayers

University Of The Sciences Philadelphia, Philadelphia PA

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Abstract

DESCRIPTION (provided by applicant): Membranes and their embedded ion channels play a crucial role in numerous cell processes such as: signaling, energy conversion, and ion conductance. The long term goal of the proposed studies is to provide a detailed understanding of the biophysical properties of these biological membranes through molecular modeling. For this proposal, we aim to obtain a detailed description of oligomeric ion channel structure and dynamics embedded within a membrane. Completion of this aim will promote public health by providing essential information needed for the rational design of novel antimicrobial, antiviral, and pharmaceutical agents which target ion channels. The knowledge gained has the potential to further enable humans to combat many diseases and to alleviate some of the shortcomings currently encountered with today's therapeutics. We propose to elucidate the spatial (about 1 micrometer) and temporal (about 1 millisecond) mesoscale salient features of membrane associated ion channels using coarse grain molecular modeling, such as the mechanism of formation from monomeric peptides. Currently, these spatial and temporal regions are difficult to determine either experimentally or with conventional simulation methodologies. These novel coarse grain methods allow us to elucidate fundamental membrane mechanisms such as oligomerization. The specific aims are a carefully planned series of simulations to examine the interactions of ion channels embedded within membranes. The goal is to quantify the structural and dynamical properties of ion channels and their interactions with membranes. Calculations will begin with the structural and dynamical characterization of single transmembrane amphipathic peptides, and we will simultaneously analyze the perturbations caused by the peptide on the lipid membrane. Additionally, we will measure the structural and dynamical characteristics of homo-oligomeric ion channels composed of several transmembrane amphipathic peptides. Ultimately, we aim to calculate the binding free energy of ion channel formation, and elucidate the mechanism of formation of homo-oligomeric ion channels from monomeric peptides.