title: Subunit F modulates ATP binding and migration in the nucleotide-binding subunit B of the A(1)A(O) ATP synthase of Methanosarcina mazei Gö1.
abstract: The interaction of the nucleotide-binding subunit B with subunit F is essential in coupling of ion pumping and ATP synthesis in A(1)A(O) ATP synthases. Here we provide structural and thermodynamic insights on the nucleotide binding to the surface of subunits B and F of Methanosarcina mazei Gö1 A(1)A(O) ATP synthase, which initiated migration to its final binding pocket via two transitional intermediates on the surface of subunit B. NMR- and fluorescence spectroscopy as well as ITC data combined with molecular dynamics simulations of the nucleotide bound subunit B and nucleotide bound B-F complex in explicit solvent, suggests that subunit F is critical for the migration to and eventual occupancy of the final binding site by the nucleotide of subunit B. Rotation of the C-terminus and conformational changes in subunit B are initiated upon binding with subunit F causing a perturbation that leads to the migration of ATP from the transition site 1 through an intermediate transition site 2 to the final binding site 3. This mechanism is elucidated on the basis of change in binding affinity for the nucleotide at the specific sites on subunit B upon complexation with subunit F. The change in enthalpy is further explained based on the fluctuating local environment around the binding sites.
authors.affiliation: Bioinformatics Institute (A*STAR), Singapore 138671, Singapore.
authors.forename: Devanathan
authors.initials: D
authors.lastname: Raghunathan
authors.forename: Shovanlal
authors.initials: S
authors.lastname: Gayen
authors.forename: Anil
authors.initials: A
authors.lastname: Kumar
authors.forename: Cornelia
authors.initials: C
authors.lastname: Hunke
authors.forename: Gerhard
authors.initials: G
authors.lastname: Grüber
authors.forename: Chandra S
authors.initials: CS
authors.lastname: Verma
mesh_terms: D000255:Adenosine Triphosphate / Q000096:biosynthesis* / Q000378:metabolism*; D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism*; D002151:Calorimetry; D017020:Methanosarcina / Q000201:enzymology*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D009711:Nucleotides / Q000378:metabolism*; D011485:Protein Binding; D021122:Protein Subunits / Q000235:genetics / Q000378:metabolism*; D021381:Protein Transport; D006180:Proton-Translocating ATPases / Q000235:genetics / Q000378:metabolism*; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics
chemical_list: D019843:Archaeal Proteins; D009711:Nucleotides; D021122:Protein Subunits; D000255:Adenosine Triphosphate; C113203:A1A0 ATPase, Methanosarcina mazei; D006180:Proton-Translocating ATPases