title: Calculating the Na⁺ translocating V-ATPase catalytic site affinity for substrate binding by homology modeled NtpA monomer using molecular dynamics/free energy calculation.
abstract: Vacuolar ATPase (V-ATPase) of Enterococcus hirae is composed of a soluble catalytic domain (V₁; NtpA₃-B₃-D-G) and an integral membrane domain (V₀; 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.). 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.
authors.affiliation: Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan.
authors.forename: Zahed
authors.initials: Z
authors.lastname: Muhammed
authors.forename: Satoshi
authors.initials: S
authors.lastname: Arai
authors.forename: Shinya
authors.initials: S
authors.lastname: Saijo
authors.forename: Ichiro
authors.initials: I
authors.lastname: Yamato
authors.forename: Takeshi
authors.initials: T
authors.lastname: Murata
authors.forename: Atsushi
authors.initials: A
authors.lastname: Suenaga
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry* / Q000378:metabolism*; D000266:Adenylyl Imidodiphosphate / Q000737:chemistry / Q000378:metabolism; D000595:Amino Acid Sequence; D020134:Catalytic Domain; D027682:Cation Transport Proteins / Q000737:chemistry* / Q000378:metabolism*; D016983:Enterococcus / Q000201:enzymology; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D020539:Sequence Analysis, Protein; D013816:Thermodynamics
chemical_list: D027682:Cation Transport Proteins; D000266:Adenylyl Imidodiphosphate; D000251:Adenosine Triphosphatases; C021838:sodium-translocating ATPase