Correlated Inter-Domain Motions in Adenylate Kinase

Correlated inter-domain motions in proteins can mediate fundamental biochemical processes such as signal transduction and allostery. Here we characterize at structural level the inter-domain coupling in a multidomain enzyme, Adenylate Kinase (AK), using computational methods that exploit the shape information encoded in residual dipolar couplings (RDCs) measured under steric alignment by nuclear magnetic resonance (NMR). We find experimental evidence for a multi-state equilibrium distribution along the opening/closing pathway of Adenylate Kinase, previously proposed from computational work, in which inter-domain interactions disfavour states where only the AMP binding domain is closed. In summary, we provide a robust experimental technique for study of allosteric regulation in AK and other enzymes.Author Summary: Most proteins contain several domains, and inter-domain motions play important roles in their biological functions. Describing the various inter-domain orientations that multi-domain proteins adopt at equilibrium is challenging, but key for understanding the relationship between protein structure and function. When more than two domains are present in a protein, correlated domain motions can be of fundamental importance for biological function. This type of behaviour is typical of molecular machines but is extremely challenging to characterize both from experimental and theoretical viewpoints. In this paper, we present a hybrid experimental/computational approach to address this problem by exploiting the information on molecular shape contained in nuclear magnetic resonance experiments to determine accurate conformation ensembles for the multi-domain enzyme adenylate kinase with help of advanced simulation methods.