Computational framework to investigate the inorganic ion transporters

Abstract Transmembrane transporters play a critical gatekeeper role in determining and controlling the intracellular concentration of ions, nutrients, toxins, or drugs in all cells. Our current knowledge of transmembrane transporters is mainly gained by extensive studies on proton, alkali, and alkaline earth metal cation transporters,

while the transport of anions and transition metals is overlooked despite their significantly different properties. The (dys)function of anions and transition metal transporters is now linked directly to resistance against antibiotics, chemotherapeutic agents, and metal-based drugs and is associated with many human diseases such

as cystic fibrosis, myotonia, Menkes, and Wilson’s diseases. Despite their biological importance, the underlying biochemical and biophysical basis at the atomic and molecular level for the selectivity, transport mechanism, stoichiometry, and conformational dynamics of anion and transition metal transporters remain largely elusive.

The long-term research goal of my laboratory is to fill this gap in the field of transmembrane transporters by combining different advanced computational approaches. To this end, this MIRA application aims to investigate two phylogenetically unrelated families of bacterial fluoride export protein: CLCF F-/H+ antiporters and fluoride ion channels, and P1B-type ATPases which transport Cu+,

Cu2+, and Zn2+ across cellular membranes. My laboratory has established a computational platform by integrating different advanced computational approaches to study various complex biological systems including transmembrane proteins. In the proposed research, we will combine quantum, molecular, and statistical

mechanics, and advanced polarizable force field development and will integrate our advanced computational techniques with experimental and co-evolutionary investigation to 1) monitor the dynamics and local conformational changes of the transmembrane transporters, 2) characterize the selectivity filter and coordination

chemistry of the transported ions, 3) identify contributing residues in ion transport, 4) introduce mutations that potentially alter the ion selectivity, 5) find promising inhibitors, 6) determine transport stoichiometry and counter- transport ions, and 7) map out the transport mechanism. Built upon our experience, we will focus on the inclusion

of explicit polarization in modeling transmembrane transporters because ions in particular anions and transition metals have high polarizability. We will provide a comprehensive comparison between the models developed with polarizable and non-polarizable force fields. The developed polarizable force field for lipid molecules will

have a novel feature to make it transferable to other studies of biological systems. The proposed project will target a neglected aspect in studying transmembrane transporters, will establish an innovative computational framework to study these complex systems, and will train a new generation of biomedical scientists. The outcomes of the proposed project will address the emerging global challenge of

antibiotic and metal-based drug resistance and aid bioengineers in designing novel effective therapeutic agents.