Paper Citing NAMD - Abstract
Riley, Julie M.; Kim, Hyunjin; Averch, Timothy D.; Kim, Hyung J.
Effect of Magnesium on Calcium and Oxalate Ion Binding
JOURNAL OF ENDOUROLOGY, 27:1487-1492, DEC 1 2013
Background and Purpose: Magnesium (Mg2+) has been shown to be a kidney stone inhibitor; however, the exact mechanism of its effect is unknown. Using theoretical models, the interactions of calcium and oxalate were examined in the presence of Mg2+. Methods: Molecular dynamics simulations were performed with NAMD and CHARMM27 force field. The interaction between calcium (Ca2+) and oxalate (Ox(2-)) ions was examined with and without magnesium. Concentrations of calcium and oxalate were 0.1M and 0.03M, respectively, and placed in a cubic box of length approximate to 115 Angstrom. Na+ and Cl- ions were inserted to meet system electroneutrality. Mg2+ was then placed into the box at physiologic concentrations and the interaction between calcium and oxalate was observed. In addition, the effect of citrate and pH were examined in regard to the effect of Mg2+ inhibition. Each system was allowed to run until a stable crystalline structure was formed. Results: The presence of Mg2+ reduces the average size of the calcium oxalate and calcium phosphate aggregates. This effect is found to be Mg2+ concentration-dependent. It is also found that Mg2+ inhibition is synergistic with citrate and continues to be effective at acidic pH levels. Conclusion: The presence of magnesium ions tends to destabilize calcium oxalate ion pairs and reduce the size of their aggregates. Mg2+ inhibitory effect is synergistic with citrate and remains effective in acidic environments. Further studies are needed to see if this can be applied to in vivo models as well as extending this to other stone inhibitors and promoters.
