Mona Minkara - Effect of 10.5 M Aqueous Urea on Helicobacter pylori Urease: A Molecular Dynamics Study.

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        Minkara, M. S.;   Weaver, M. N.; Merz, K. M. Jr. Effect of 10.5 M Aqueous Urea on   Helicobacter pylori Urease: A Molecular Dynamics   Study. Biochemistr 201554 (26),pp.4121-30


      The effects of a 10.5 M solution of aqueous urea on Helicobacter   pylori urease were investigated over the course of a 500 ns   molecular dynamics (MD) simulation. The enzyme was solvated by   25321 water molecules, and additionally, 4788 urea molecules were   added to the solution. Although concentrated urea solutions are   known laboratory denaturants, the protein secondary structure is   retained throughout the simulation largely because of the short   simulation time (urea denaturation occurs on the millisecond time   scale). The relatively constant solvent accessible surface area   over the last 400 ns of the simulation further confirms the   overall lack of denaturation. The wide-open flap state observed   previously in Klebsiella areogenes urease [Roberts, B. P., et al.   (2012) J. Am. Chem. Soc. 134, 9934] and H. pylori [Minkara, M.   S., et al. (2014) J. Chem. Theory Comput. 10, 1852−1862] was also   identified in this aqueous urea simulation. Over the course of   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 initial   coordination step of the hydrolysis mechanism. We also observed a   specific and unique pattern in the regions of the protein with a   high root-mean-square fluctuation (rmsf). The high-rmsf regions   in the β-chain form a horseshoelike arrangement surrounding the   active site-covering flap on the surface of the protein. We   hypothesize that the function of these regions is to both attract   and shuttle urea toward the loop of the active site-covering flap   before entry into the cavity. Indeed, urea is observed to   interact with these regions for extended periods of simulation   time before active site ingress.

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