Mechanism Of Conduction In Urea Transporter DvUT Revealed By Molecular Dynamics Simulations

Urea is a small and highly polar molecule, and its unassisted permeation through lipid bilayers is significantly low. Fortunately, an integral membrane protein named urea transporter (UT) has evolved to conduct urea across the membrane. Recently, the X-ray structure of urea transporter from Desulfovibrio vulagaris, dvUT, was successfully resolved, which provide the opportunity for investigating the mechanism of conduction in dvUT through molecular dynamics simulations. Urea spontaneous diffusion in the pore of dvUT was simulated to acquire knowledge of the intrinsic conduction mechanism. The characteristics of water conduction were also probed. Here I elucidate for the first time the dynamic mechanism of substrate (urea and water) permeating through dvUT in atomatic details, which may be applied to other UT members since the high conservation of residues lining in the SF.First, during the sliding movements of urea through dvUT, there must be binding sites along the channel axis to stabilize urea molecule. In the SF, oxygen ladders provide a continuous line of binding sites for hydrogen bonding with urea molecule, and the threonine hydroxyl arms could adjust flexibly and largely to stabilize urea molecules in the SF.Second, the displacements of urea are mainly due to the disruption of old hydrogen bonds and the formation of new ones. However, there are some distances between the neighboring binding sites of the oxygen ladders, and the zigzag line of the six oxygen atoms makes urea to change its orientation for better binding during the sliding movements. Therefore, it is difficult for urea to climb the oxygen ladders only depending on the protein without external forces. Additionally, the breakup of old hydrogen bonds between urea and protein also needs the perturbation by external forces, and the formation of new ones needs the transient stabilization by external forces. In the equilibrium MD simulations, I observed that water molecules act as the role of external forces to stabilize urea or compete with urea for the same binding site. Nevertheless, water rarely occurs in the SF. and its random movements couldn't pull urea permeate through the whole channel.Third, two slot formed by flexible aromatic rings in either side of the SF present barriers for the urea diffusion. Radom forces from water molecules could not induce urea permeating through these two regions. Therefore, urea molecule needs directional and steady forces in order to permeate through the whole channel. In the physiological conditions, urea molecules diffused across the dvUT from the high concentration to the low concentration; the concentration gradient of urea across the membrane serves as the directional and steady external forces which induce urea conduction through urea transporter. The concentration gradient switches the effective conduction of urea through dvUT.In addition, water can permeate through dvUT with a slow rate,0.8 H2O/ns/channel. Water molecules in the SF are usually disrupted, and occasionally they show a single file configuration with bipolar orientation, either of which could effectively obstructs proton transport through the channel, thereby preserving the electrochemical gradient across the membrane.