Calculating the Na+ translocating V-ATPase catalytic site affinity for substrate binding by homology modeled NtpA monomer using molecular dynamics/free energy calculation

Vacuolar ATPase (V-ATPase) of Enterococcus hirae is composed of a soluble catalytic domain (V1; NtpA3-B3-D-G) and an integral membrane domain (Vo; NtpI-K10) connected by a central and two peripheral stalks (NtpC, NtpD-G and NtpE-F). Recently nucleotide binding of catalytic NtpA monomer has been reported (Arai et al. [19]). In the present study, we calculated the nucleotide binding affinity of NtpA by molecular dynamics (MD) simulation/free energy calculation using MM-GBSA approach based on homology modeled structure of NtpA monomer docked with ATP analogue, adenosine 5′-[β, γ-imido] triphosphate (AMP-PNP). The calculated binding free energies showed qualitatively good agreement with experimental data. The calculation was cross-validated further by the rigorous method, thermodynamic integration (TI) simulation. Finally, the interaction between NtpA and nucleotides at the atomic level was investigated by the analyses of components of free energy and the optimized model structures obtained from MD simulations, suggesting that electrostatic contribution is responsible for the difference in nucleotide binding to NtpA monomer. This is the first observation and suggestion to explain the difference of nucleotide binding properties in V-ATPase NtpA subunit, and our method can be a valuable primary step to predict nucleotide binding affinity to other subunits (NtpAB, NtpA3B3) and to explore subunit interactions and eventually may help to understand energy transduction mechanism of E. hirae V-ATPase.

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► We report the difference of the nucleotide binding properties of V-ATPase.
► We employed molecular dynamics (MD)/free energy calculation.
► Calculated data was in good agreement with experimental values.
► This is the first findings to explain reason behind difference in nucleotide binding.
► Our method can be a valuable primary step to predict nucleotide binding affinity.