Paper Citing NAMD - Abstract
Dynowski, M.; Ludewig, U.
TrpAQP: Computer simulations to determine the selectivity of aquaporins
High Performance Computing in Science and Engineering '06, 187-197, 2007
Membrane channels of the Major Intrinsic Protein (MIP) family are pores for water and solutes. Such channels are found in almost all organisms and are especially abundant in plants. Experimental evidence suggests that some MIPs are aquaporins and are therefore relatively selective for water. Others; in contrast, conduct small solutes such as glycerol, urea or boric acid, and are therefore called aquaglyceroporins. Some MIPs conduct solutes that in isolation would be gases, such as NH3. The structure of many aquaporins, including one from plants, has been resolved on the molecular level and all have a similar fold. To identify the molecular determinants of the selectivity of MIPs from plants and to identify the physiologically relevant transported solutes; a strategy based on computer modeling, combined with experimental verification has been set up. MIP homologs from plants were homology modeled and various simulations have been applied to measure their conductance for specific solutes, such as ammonia and/or urea. Urea is quantitatively the most important nitrogen fertilizer used worldwide; and its transport in plants is therefore of high interest. The molecular dynamics simulations suggest that specific MIPs have preferences for urea and specific solutes such as urea and/or ammonia are transported. Although the size of the solute and the pore diameter are important for transport, these do not exclusively determine if a solute is transported.
