ArticleEuropean biophysics journal : EBJ2004
The conformational states of Mg.ATP in water.
Article in European biophysics journal : EBJ, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 52 citations in OpenAlex.
- How Does MgJournal of the American Chemical Society · 2024Article
- Common Mechanism of Activated Catalysis in P-loop Fold Nucleoside Triphosphatases-United in Diversity.Biomolecules · 2022Article
- Gas-Phase Internal Ribose Residue Loss from Mg-ATP and Mg-ADP Complexes: Experimental and Theoretical Evidence for Phosphate-Mg-Adenine Interaction.Journal of the American Society for Mass Spectrometry · 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
- ATP-Magnesium Coordination: Protein Structure-Based Force Field Evaluation and Corrections.Journal of chemical theory and computation · 2021Article
- Article
- Triple resonance EPR spectroscopy determines the MnJournal of magnetic resonance (San Diego, Calif. : 1997) · 2018Article
- High-Dimensional Mutant and Modular Thermodynamic Cycles, Molecular Switching, and Free Energy Transduction.Annual review of biophysics · 2017Review
- Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis.Structural dynamics (Melville, N.Y.) · 2017Article
- Modeling Membrane Protein-Ligand Binding Interactions: The Human Purinergic Platelet Receptor.The journal of physical chemistry. B · 2016Article
- Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications.The journal of physical chemistry. B · 2015Article
- Dual mechanism of ion permeation through VDAC revealed with inorganic phosphate ions and phosphate metabolites.PloS one · 2015Article
- Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1.Nature structural & molecular biology · 2014Article
- Capture and quality control mechanisms for adenosine-5'-triphosphate binding.Journal of the American Chemical Society · 2013Article
- Free energy simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2.The journal of physical chemistry. B · 2011Article
- A computational study of a recreated G protein-GEF reaction intermediate competent for nucleotide exchange: fate of the Mg ion.PloS one · 2010Article
- A computational analysis of ATP binding of SV40 large tumor antigen helicase motor.PLoS computational biology · 2009Article
- Mg2+-assisted catalysis by B. stearothermophilus TrpRS is promoted by allosteric effects.Structure (London, England : 1993) · 2009Article
- Crystal structure of human phosphoribosylpyrophosphate synthetase 1 reveals a novel allosteric site.The Biochemical journal · 2007Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The conformational equilibria of Mg.ATP in solution is studied using molecular dynamics (MD) augmented with umbrella sampling methods. Free energy comparisons show that the Mg(2+) ion is equally likely to coordinate the oxygens of the two end phosphates, or of all three phosphates. The MD trajectories reveal two major degrees of freedom of the Mg.ATP molecule in solution, and we compute the free energy as a function of these variables, and determine its elastic properties. Comparing the free energy function with several crystallographic structures of ATP analogs, we find that the crystal structures correspond to states where ATP would be elastically strained. The average water density around Mg.ATP is investigated to show the average number of hydrogen bonds and the hydrophobicity.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.