ArticleBiophysics (Nagoya-shi, Japan)2013
Distinct Conformation of ATP Molecule in Solution and on Protein.
Article in Biophysics (Nagoya-shi, Japan), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 24 citations in OpenAlex.
- Direct energy consumption by inhibitory GABAFrontiers in neuroscience · 2026Article
- OTMol: Robust Molecular Structure Comparison via Optimal Transport.Journal of chemical information and modeling · 2025Article
- Purinergic system in cancer stem cells.Purinergic signalling · 2025Review
- Solid-state NMR chemical shift analysis for determining the conformation of ATP bound to Na,K-ATPase in its native membrane.RSC advances · 2023Article
- Impact of the Cellular Environment on Adenosine Triphosphate Conformations.The journal of physical chemistry letters · 2022Article
- A Leucyl-tRNA Synthetase Urzyme: Authenticity of tRNA Synthetase Catalytic Activities and Promiscuous Phosphorylation of Leucyl-5'AMP.International journal of molecular sciences · 2022Article
- Molecular dynamics free energy simulations of ATP:MgMolecular simulation · 2021Article
- Structural Analysis of (p)ppGpp Reveals Its Versatile Binding Pattern for Diverse Types of Target Proteins.Frontiers in microbiology · 2020Article
- Genome Segregation by the Venus Flytrap Mechanism: Probing the Interaction Between the ParF ATPase and the ParG Centromere Binding Protein.Frontiers in molecular biosciences · 2020Article
- Multiple conformations facilitate PilT function in the type IV pilus.Nature communications · 2019Article
- Relationship between conformation shift and disease related variation sites in ATP-binding cassette transporter proteins.Biophysics and physicobiology · 2019Article
- Conformational shift in the closed state of GroEL induced by ATP-binding triggers a transition to the open state.Biophysics and physicobiology · 2016Article
- Case study on the evolution of hetero-oligomer interfaces based on the differences in paralogous proteins.Biophysics and physicobiology · 2015Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Adenosine triphosphate (ATP) is a versatile molecule used mainly for energy and a phosphate source. The hydrolysis of γ phosphate initiates the reactions and these reactions almost always start when ATP binds to protein. Therefore, there should be a mechanism to prevent spontaneous hydrolysis reaction and a mechanism to lead ATP to a pure energy source or to a phosphate source. To address these questions, we extensively analyzed the effect of protein to ATP conformation based on the sampling of the ATP solution conformations obtained from molecular dynamics simulation and the sampling of ATP structures bound to protein found in a protein structure database. The comparison revealed mainly the following three points; 1) The ribose ring in ATP molecule, which puckers in many ways in solution, tends to assume either C2' exo or C2' endo when it binds to protein. 2) The adenine ring in ATP molecule, which takes open-book motion with the two ring structures, has two distinct structures when ATP binds to protein. 3) The glycosyl-bond and the bond between phosphate and the ribose have unique torsion angles, when ATP binds to protein. The combination of torsion angles found in protein-bound forms is under-represented in ATP molecule in water. These findings suggest that ATP-binding protein exerts forces on ATP molecule to assume a conformation that is rarely found in solution, and that this conformation change should be a trigger for the reactions on ATP molecule.
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