From Protein Structure to Function with Bioinformatics.pdf

236 M.B. Kubitzki et al.challenge due to the long timescales involved. In this respect, E. coli adenylatekinase (ADK) is a prime example. ADK is a monomeric enzyme that plays a keyrole in energy maintenance within the cell, controlling cellular ATP levels by catalyzingthe reaction Mg 2+ :ATP + AMP«Mg 2+ :ADP + ADP. Structurally, the enzymeconsists of three domains (Fig. 9.10): the large central “CORE” domain (lightgrey), an AMP binding domain referred to as “AMPbd” (black), and a lid-shapedATP-binding domain termed “LID” (dark grey), which covers the phosphate groupsat the active centre (Müller et al. 1996). In an unligated structure of ADK the LIDand AMPbd adopt an open conformation, whereas they assume a closed conformationin a structure crystallized with the transition state inhibitor Ap 5A (Müller andSchulz 1992). Here, the ligands are contained in a highly specific environmentrequired for catalysis. Recent 15 N nuclear magnetic resonance spin relaxation studies(Shapiro and Meirovitch 2006) have shown the existence of catalytic domainmotions in the flexible AMPbd and LID domains on the nanosecond time scale,while the relaxation in the CORE domain is on the picosecond time scale (Tugarinovet al. 2002; Shapiro et al. 2002). For ADK, several computational studies haveaddressed its conformational flexibility (Temiz et al. 2004; Maragakis andKarplus 2005; Lou and Cukier 2006; Whitford et al. 2007; Snow et al. 2007).However, due to the magnitude and timescales involved, spontaneous transitionsbetween the open and closed conformations have not been achieved until now byall-atom MD simulations. Using TEE-REX, spontaneous transitions between theopen and closed structures of ADK are facilitated, and a fully atomistic descriptionof the transition pathway and its underlying mechanics could be achieved (Kubitzkiand de Groot 2008). To this end, different essential subspaces {es} were constructedfrom short MD simulations of either conformation as well as from a combinedensemble holding structures from both the open and closed conformation. Inthe latter case, {es} modes were excited containing the difference X-ray mode connectingthe open and closed experimental structures.The observed transition pathway can be characterized by two phases. Startingfrom the closed conformation (Fig. 9.10 left), the LID remains essentially closedLIDAMPbdCORECLOSED phase 1 phase 2 OPENFig. 9.10 Closed (left) and open (right) crystal structures of E. coli adenylate kinase (ADK)together with intermediate structures characterizing the two phases of the closed-open transition.ADK has domains CORE (light grey), AMPbd (black) and LID (dark grey). The transition stateinhibitor Ap 5A is removed in the closed crystal structure (left)