Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

54-POS Board 14 Structural and Mechanistic Insights into the Ε Subunit from Bacterial ATP Synthases Alexander Krah , Changbong Hyeon. Korea Institute for Advanced Study (KIAS), Seoul, South Korea. The central energy conversion machinery in all living cells, the ATP synthase, uses an electrochemical ion gradient to synthesize ATP, the main energy source in all living cells, by a catalytic rotational motion. Vice versa it can pump protons, by hydrolyzing ATP, rotating in the opposite direction. The ε subunit from bacterial ATP synthases undergoes a large conformational change from the ATPase inhibitory up- to the non-inhibitory down state upon ATP binding. However, the ATP binding affinity of ε subunits from different organisms is dramatically different, from 4 μM (thermophilic Bacillus PS3) to 20 mM ( Escherichia coli ), while others may not bind ATP at all (e.g. Mycobacterium tuberculosis ). We use MD simulations to clarify reasons for the different ligand binding affinities of the ε subunit from different organisms. In this work, we obtain the ATP binding site structure of the ε subunit from Escherichia coli , deriving molecular reasons for the dramatically decreased binding affinity compared to the ε subunit from thermophilic Bacillus PS3. Furthermore, we observe that the protonation state of one carboxylate group is essential to allow ATP binding, inducing a conformational change and ATP binding of one of the key binding residues - thus the mechanistic modes of the ε subunit from distinct bacterial organisms are controlled differently.

89