Transport of nucleosides in the vcCNT facilitated by sodium gradients from molecular dynamics simulations

Nucleosides are required for DNA and RNA synthesis, and the nucleoside adenosine has a function in a variety of signaling processes. Nucleosides require a specialized class of integral membrane proteins, known as nucleoside transporters (NTs), for specific transport across cell membranes. NTs are also important determinants for the transport of nucleoside-derived drugs across cell membranes. Recently, the crystal structure of the vcCNT (Vibrio cholerae Concentrative Nucleoside Transporter) was reported. Here we perform molecular dynamics (MD) simulations for the vcCNT structure in the presence of various sodium gradients, since CNTs are sodium-coupled transporters. The results highlight the important role of sodium bound to the vcCNT in the transport of uridine. Our MD simulations show that, without NaCl, uridine remains stable in the binding pocket of the vcCNT. In the presence of 20 mM NaCl, uridine moves from the binding pocket and approaches the entrance of the intracellular side. In the presence of 100 mM NaCl, uridine passes through most part of the entrance and approaches the intracellular side. The polar/charged amino acids in the binding pocket are important in the transport process. They first "fix" the ribose and allow the uracil base of uridine to approach the entrance of the intracellular side, and then "release" the ribose to allow uridine to move freely into the intracellular side coupled with the movement of sodium ions and HP1b. Finally, we propose a detailed mechanism of the nucleoside transport from the binding pocket to the intracellular side of the vcCNT.