The effects of a 10.5 M solution of aqueous urea on Helicobacter pylori urease were investigated over the course of a 500 nanosecond molecular dynamics (MD) simulation. The enzyme was solvated by 25,321 water molecules and 4,788 urea molecules were added to the solution. Although concentrated urea solutions are known laboratory denaturants, the protein secondary structure is retained throughout the simulation due to the low temperature (300K) and short simulation time (urea denaturing is on the millisecond timescale). The relatively constant solvent accessible surface area over the last 400 nanoseconds of the simulation further confirms this lack of denaturing. The wide-open flap state observed previously in K. areogenes urease (Roberts, et al. J. Am. Chem. Soc. 2012  , 134, 9934) and H. pylori (Minkara et al. J. Chem. Theory Comput. 2014  , submitted) was also identified in this aqueous urea simulation. Over the course the trajectory we were able to observe urea molecules entering the active site in proportions related to the extent of opening of the active site covering flap. Furthermore, urea molecules were observed to approach the pentacoordinate Ni2+ ion in position to bind in a manner consistent with the proposed coordination step of the hydrolysis mechanism. We also observed a specific and unique pattern in the high RMSF region. These high RMSF regions form a pseudo ring that may function to channel urea toward the active site and indeed urea is observed to interact with these regions for extended periods of simulation time.

Effect of 10.5 <u>M</u> aqueous urea on <i>Helicobacter pylori</i> urease: A molecular dynamics study

248th National Meeting (2014)

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Effect of 10.5 M aqueous urea on Helicobacter pylori urease: A molecular dynamics study