Computational analyses of cryptic intermediates in the native unfolding pathways of barnase and thioredoxin

Abstract

AbstractOwing to various experimental constraints, detection and characterization of cryptic intermediates (CIs) presumably existing in the unfolding kinetics of barnase and thioredoxin were not successful by native-state hydrogen-deuterium exchange method at pH 6.4, 306 K and pH 7.0, 298 K, respectively. We have herein demonstrated possible existence of CIs under the solution conditions in native unfolding of the proteins by means of OneG-Vali. Structure and stability of each CI detected for the two proteins by the computational tool have also been delineated and the results were in good agreement with folding intermediates detected in the energetic landscapes of the proteins by variety of methods as reported in the literature. Moreover, we have also discussed unique merits of the computational tool to addressing extent of contributions of cis/trans proline isomerization and CIs on estimating overall thermodynamic stabilities (by various types of equilibrium unfolding experiments) of the proteins.