Enabling Biophysical Characterization of Intrinsically Disordered Protein Ensembles

Abstract

Elucidating structural details of protein conformations and its relation to protein function is a forefront area in structural biology. In this project, we will investigate nuclear co- activator binding domain (NCBD), an intrinsically disordered protein (IDP) implicated in acute myeloid/lymphatic leukemia (AML/ALL), which has the propensity to adopt extended conformations in unbound form and undergoes synergistic folding with substrate specific conformations when bound. Since IDPs like NCBD are highly flexible, their full conformational range is not observable by any one structure determination technique. We have developed a novel, integrated experimental and computational technique to elicit high-resolution structural details of such IDP ensembles. Specifically, we have (1) developed methods to prepare amino-acid-type selectively deuterated NCBD and utilize SANS contrast variation techniques to refine high-resolution conformational ensembles; (2) constructed parallel ensemble simulation strategies on heterogeneous computer architectures to generate millisecond timescale atomistic simulations; and (3) designed Bayesian inference techniques for statistical characterization of IDP conformational ensembles. The integrated approach enables accurate understanding, simulation and prediction of recognition mechanisms of NCBD under physiological condition.