Urea channel dvUT transparent mechanism of molecular dynamics simulation
|Course||Biochemistry and Molecular Biology|
|Keywords||Urea channel Molecular Dynamics Oxygen ladder Threonine hydroxyl Concentration gradient|
Urea is a smaller but with a very high polar molecule, which in the free diffusion of lipid molecules at very low speed. However, a transmembrane protein (urea channel) can be mediated by a high rate of urea molecules transmembrane transport. Recently, Desulfovibrio urea channel protein structure (dvUT) was successfully parsed, which is studied by means of molecular dynamics simulations of urea channel transparent mechanism provided the conditions. In order to study the mechanism dvUT intrinsic permeability, this simulates the free urea molecule dvUT movement, while also studied the water molecules present in the channel characteristics. This article first details of the atomic interactions clarified urea and water molecules through dvUT kinetic mechanism, based on SF (selectivity filter) region highly conserved amino acids, these mechanisms can prompt urea urea molecules in some other channel protein family members of the microscopic processes transparent. Urea molecule along the channel axis during movement, dvUT hydrogen to provide a plurality of binding sites to stabilize the urea molecules. In the SF area, urea molecular oxygen ladder provides a continuous chain of hydrogen bonding sites, the channel center threonine hydroxyl groups of the two flexible arm can be converted in a wide range of conformations and thus to support the urea molecules in the central region of SF movement. Urea molecules in the SF area mainly due to the movement of proteins some of the urea molecules and hydrogen bonding sites of the fracture, as well as other sites of hydrogen bond formation. Urea molecules along the channel axis movement mainly in the ladder constantly changing oxygen binding sites. However, the ladder of oxygen between two adjacent oxygen atoms at a distance, and six oxygen atoms of oxygen on the ladder line formed such that the urea molecules must be constantly changing its orientation to the ladder with oxygen to form a stable hydrogen bonds. Therefore, only by difficult for the role of protein structure in urea ladder molecular oxygen along the up or down, then the need for outside help. In addition, the breaking of hydrogen bonds old also require external interference can occur, the new hydrogen bond formation force is sometimes necessary to temporarily in a specific direction to stabilize the urea molecules. In the MD (molecular dynamics) simulations, the water molecules act as a force Role: urea molecules along the channel axis transition, the vast majority are due to the instantaneous water molecules of urea or urea molecules stabilizing hydrogen bonding bit old points out competition, thus promoting the urea molecules to move forward. However, SF relatively small area of ??the water molecules and the water molecules to produce a force unstable and very random, it is difficult to promote the dvUT urea pore molecular permeability. In the SF area clamped at both ends of the benzene ring formed by the two slits for the urea molecule transport set up obstacles. Random force water molecules can not induce urea molecules through these two regions, indicating that these two regions are dvUT most selective two obstacles. Therefore, urea and stable molecular orientation of force required to pass these two regions, and thus the protein pore permeability. In physiological conditions, the urea molecule is the side from the high concentration of urea channel proteins by low concentrations of one side to the transmembrane. The urea concentration gradient across the membrane of the driving force and stability can be a force directed to the urea molecules mediated by channel proteins. Transmembrane concentration gradient of urea is equivalent to a switch, when the concentration gradient is high, the urea molecules through protein channels at a rate significantly increased; while when the concentration gradient is eliminated, is not easy to pass the urea molecule. In addition, dvUT water permeability also been confirmed through the MD simulation. Water molecules can lower rate (0.8H2O/ns/channel) by dvUT. Water molecules are often present in the form discontinuous SF area, but occasionally showed a continuous chain of water arranged in sexual bipolar, two water molecules are effectively stop configurations transmembrane proton transport, thereby maintaining electrochemical gradient across the membrane.