Conformational dynamics of ATP/Mg:ATP in motor proteins via data mining and molecular simulation

Modeling of minimal systems based on ATP-Zn coordination for chemically fueled self-assembly

Following nature's example, there is currently strong interest in using adenosine 5'-triphosphate (ATP) as a fuel for the self-assembly of functional materials with transient/non-equilibrium behaviours. These hold great promise for applications, e.g. in catalysis and drug delivery. In a recent seminal work [Maiti et al., Nat. Chem., 2016, 8, 725], binding of ATP to the metallosurfactant zinc hexadecyl-1,4,7-triazacyclononane ([ZnC₁₆ TACN]²⁺) was exploited to produce ATP-fueled transient vesicles. Crucial to the complex formation is the ability of ATP to bind to the metal ion. As a first step to unveil the key elements underlying this process, we investigate the interaction of ATP with Zn²⁺ and with methyl-1,4,7-triazacyclononane ([ZnCH₃ TACN]²⁺), using all-atom molecular dynamics simulations. The free energy landscape of the complex formation is sampled using well-tempered metadynamics with three collective variables, corresponding to the coordination numbers of Zn²⁺ with the oxygen atoms of the three phosphate groups. We find that the structure of the ternary complex is controlled by direct triphosphate coordination to zinc, with a minor role played by the interactions between ATP and CH₃ TACN which, however, may be important for the build-up of supramolecular assemblies.

Mechanistic Insight on General Protein-Binding Ability of ATP and the Impacts of Arginine Residues

Recent experiments suggested that adenosine triphosphate (ATP) can regulate liquid-liquid phase separation (LLPS) of various proteins and inhibit protein aggregations at its physiological concentration, which is highly correlated with the nonspecific interactions of ATP to a wide variety of proteins. However, the mechanism underlying the general binding capability of ATP largely remains unclear. In this work, we used molecular dynamics simulation to study the binding of ATPs to three proteins with distinct net charges: TDP-43 NTD (-7 e), TAF15-RRM (0 e), HWEL (+8 e). Negatively charged ATP exhibits a strong trend to accumulate around all of these proteins. While only a fraction of the accumulated ATPs directly binds to the limited regions of the protein surface, additional ATPs indirectly bind to proteins by aggregating into ATP clusters. Hence, the proportion of the directly bound ATPs in the clusters as well as their binding regions can be adjusted in response to different proteins, which makes ATP well adapted to a variety of proteins. Moreover, our results suggest that ATP tightly binds to Arg with high affinity, and Arg dominates the direct binding of ATP. Meanwhile, Arg also affects the self-association of accumulated ATPs. The size of the ATP cluster is effectively regulated by the distribution of Arg. Considering the ubiquity of Arg in proteins, our findings are helpful to understand the general binding capability of ATP.

How Diverse Are the Protein-Bound Conformations of Small-Molecule Drugs and Cofactors?

Knowledge of the bioactive conformations of small molecules or the ability to predict them with theoretical methods is of key importance to the design of bioactive compounds such as drugs, agrochemicals, and cosmetics. Using an elaborate cheminformatics pipeline, which also evaluates the support of individual atom coordinates by the measured electron density, we compiled a complete set ("Sperrylite Dataset") of high-quality structures of protein-bound ligand conformations from the PDB. The Sperrylite Dataset consists of a total of 10,936 high-quality structures of 4,548 unique ligands. Based on this dataset, we assessed the variability of the bioactive conformations of 91 small molecules-each represented by a minimum of ten structures-and found it to be largely independent of the number of rotatable bonds. Sixty-nine molecules had at least two distinct conformations (defined by an RMSD greater than 1 Å). For a representative subset of 17 approved drugs and cofactors we observed a clear trend for the formation of few clusters of highly similar conformers. Even for proteins that share a very low sequence identity, ligands were regularly found to adopt similar conformations. For cofactors, a clear trend for extended conformations was measured, although in few cases also coiled conformers were observed. The Sperrylite Dataset is available for download from http://www.zbh.uni-hamburg.de/sperrylite_dataset.

Catalytic Mechanism of the Maltose Transporter Hydrolyzing ATP

We use quantum mechanical and molecular mechanical (QM/MM) simulations to study ATP hydrolysis catalyzed by the maltose transporter. This protein is a prototypical member of a large family that consists of ATP-binding cassette (ABC) transporters. The ABC proteins catalyze ATP hydrolysis to perform a variety of biological functions. Despite extensive research efforts, the precise molecular mechanism of ATP hydrolysis catalyzed by the ABC enzymes remains elusive. In this work, the reaction pathway for ATP hydrolysis in the maltose transporter is evaluated using a QM/MM implementation of the nudged elastic band method without presuming reaction coordinates. The potential of mean force along the reaction pathway is obtained with an activation free energy of 19.2 kcal/mol in agreement with experiments. The results demonstrate that the reaction proceeds via a dissociative-like pathway with a trigonal bipyramidal transition state in which the cleavage of the γ-phosphate P-O bond occurs and the O-H bond of the lytic water molecule is not yet broken. Our calculations clearly show that the Walker B glutamate as well as the switch histidine stabilizes the transition state via electrostatic interactions rather than serving as a catalytic base. The results are consistent with biochemical and structural experiments, providing novel insight into the molecular mechanism of ATP hydrolysis in the ABC proteins.

Mg²⁺ coordinating dynamics in Mg:ATP fueled motor proteins

The coordination of Mg(2+) with the triphosphate group of adenosine triphosphate (ATP) in motor proteins is investigated using data mining and molecular dynamics. The possible coordination structures available from crystal data for actin, myosin, RNA polymerase, DNA polymerase, DNA helicase, and F1-ATPase are verified and investigated further by molecular dynamics. Coordination states are evaluated using structural analysis and quantified by radial distribution functions, coordination numbers, and pair interaction energy calculations. The results reveal a diverse range of both transitory and stable coordination arrangements between Mg(2+) and ATP. The two most stable coordinating states occur when Mg(2+) coordinates two or three oxygens from the triphosphate group of ATP. Evidence for five-site coordination is also reported involving water in addition to the triphosphate group. The stable states correspond to a pair interaction energy of either ∼-2750 kJ/mol or -3500 kJ/mol. The role of water molecules in the hydration shell surrounding Mg(2+) is also reported.