Ian T. Suydam, Christopher D. Snow, Vijay S. Pande, Steven G. Boxer.
SUMMARY: The ability to quantitatively predict electric fields in proteins has remained a great challenge. In this paper, we combine new experimental methods with new theoretical methods made possible by Folding@home distributed computing to greatly push the boundary of what one could previously predict. In particular, we see that a single structure is insufficient to make accurate predictions, suggesting that the ensemble approaches inherent to Folding@home may be important in predicting electrostatics in proteins.
ABSTRACT: The electric fields produced in folded proteins influence nearly every aspect of protein function. We present a vibrational spectroscopy technique that measures changes in electric field at a specific site of a protein as shifts in frequency (Stark shifts) of a calibrated nitrile vibration. A nitrile-containing inhibitor is used to deliver a unique probe vibration to the active site of human aldose reductase, and the response of the nitrile stretch frequency is measured for a series of mutations in the enzyme active site. These shifts yield quantitative information on electric fields that can be directly compared with electrostatics calculations. We show that extensive molecular dynamics simulations and ensemble averaging are required to reproduce the observed changes in field.