Date of Award
Bachelor of Science
exchange, environment, molecular dynamics, ion, protein
Although it has been shown that the hydrogen exchange rates between the most slowly exchanging amide protons of a protein and the solvent can be used to predict the global thermodynamic stability of a protein, the great majority of amide hydrogens along the backbone of a protein exchange from either partially or fully folded conformations, and their rate of exchange strongly depends upon the environment in that folded state. We are examining the electrostatic and conformational dependence of the hydrogen exchange kinetics of Pseudomonas aeruginosa azurin, which can bind either the diamagnetic Cu(I) or Zn(II) in its active site and Pyrococcus furiosus (Pf) rubredoxin which can be substituted with Zn(II) or Ga(III). Molecular dynamics and electrostatic calculations were used to determine the theoretical hydrogen exchange rates for these metal-substituted proteins in order to assess the relationship between metal ion charge and exchange rate.
Scoglio, Stephen, "Prediction of Metal Charge-Dependent Amide Hydrogen Exchange Rates for the Proteins Rubredoxin and Azurin" (2012). Honors Theses. 897.