Differences in conformational dynamics of ribonucleases A and S as observed by infrared spectroscopy and hydrogen-deuterium exchange

Abstract

Differences in conformational dynamics of bovine pancreatic RNase A and RNase S have been investigated using hydrogen-deuterium (H-D) exchange in conjunction with Fourier transform infrared spectroscopy. Deuteration-induced spectral changes in the amide I and II regions were monitored as a function of time. Second-derivative analysis revealed similar amide I spectral patterns for both proteins in H2O as well as fully deuterated in D2O. However, the rate of amide proton exchange of RNase S is much faster than that of RNase A at 25 degrees C as determined by changes in the intensity ratio of amide II/amide I bands and frequency red-shifts of amide I components. The frequency red-shifts of the amide I components ascribed to beta-sheet, alpha-helix, and beta-turns are continuous as a function of time, indicating that both proteins are too small to contain isolated secondary structural groups containing only exchanged or unexchanged amide protons in the partially deuterated intermediate states. Despite the dramatic difference in H-D exchange rate, the patterns of spectral changes in the conformation-sensitive amide I regions of RNase A and RNase S are very similar throughout the course of deuteration, indicating a similar pathway of amide proton exchange in both proteins.