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Preface; Fluorescence Sensing of Inorganic Phosphate and Pyrophosphate Using Small Molecular Sensors and Their Applications; Abstract; 1 Introduction; 2 Molecular Sensors Based on Conventional Host
Guest Chemistry and Their Applications; 2.1 Hydrogen Bonding; 2.1.1 Pi Sensing; 2.1.2 PPi Sensing; 2.2 Coordination Chemistry; 2.2.1 Pi Sensing; 2.2.2 PPi Sensing; 3 Molecular Sensors Based on New Sensing Mechanisms and Their Applications; 3.1 Displacement Assay; 3.1.1 Pi Sensing; 3.1.2 PPi Sensing; 3.2 Aggregation Induced Emission and Quenching; 3.3 Chemical Reactions; 3.3.1 Pi Sensing
3.3.2 PPi Sensing4 Conclusion; Acknowledgements; References; Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes; Abstract; 1 Background; 1.1 Basics of Phosphoryl Transfer; 1.2 Historic Development of Mechanisms; 2 Development of Metal Fluorides as Phosphate Analogs; 2.1 The 'Burst Phase' of Analog Discovery; 3 MFx Ground State Analogs; 3.1 BeF3- as a Ground State Phosphate Mimic; 3.1.1 Aspartyl Trifluoroberyllates; 3.1.2 BeF3- Nucleotide Structures; 3.1.3 Histidine Trifluoroberyllates; 3.1.4 Structural Conclusions
4 MFx in Transition State Analog Complexes4.1 Tetrafluoroaluminate TS Complexes-AlF4-; 4.1.1 Aspartyl Tetrafluoroaluminates; 4.1.2 Nucleotide Guanosine Diphosphate (GDP) Tetrafluoroaluminates; 4.1.3 Nucleotide Adenosine Diphosphate (ADP) Tetrafluoroaluminates; 4.2 Octahedral Aluminum Trifluoride Phosphate TS Mimics; 5 MF3 Improved Geometry Transition State Mimics; 5.1 MgF3-, Trifluoromagnesate; 5.2 AlF30, Aluminum Trifluoride; 5.3 A Combined MgF3-
and AlF30 Structural Analysis; 5.4 MgF4=, Tetrafluoromagnesate; 6 19F NMR Studies of MFx Complexes; 7 Computational Analyses of MFx Complexes
7.1 Balancing Accuracy of Energy/Structure and Conformational Sampling7.2 Tradeoff in Accuracy of Energy/Structure: Parameterization Simplification vs. Mathematical Complexity; 7.3 Tradeoffs in Conformational Sampling: Dynamics vs. Statics; 7.4 KS-DFT as a QM Region Description; 7.5 EVB as a QM Region Description; 7.6 The Use of MFx in Computational Studies of Enzyme Mechanisms; 7.6.1 Validation of MFx as a TSA for Phosphoryl Transfer; 7.6.2 Studies Linking Reaction Mechanisms from Model Systems to MFx Enzyme Complexes; 7.7 Computations Transposing GDPmiddotMFx into GTP Enzyme Complexes
7.7.1 Ras Family and GTP Hydrolysis7.7.2 Other GTPases and GTP Hydrolysis; 7.8 Computations Transposing ADPmiddotMFx into ATP Enzyme Complexes; 7.8.1 ATP Hydrolysis by Myosin; 7.8.2 ATP Hydrolysis by F1 ATPase; 7.8.3 Phosphoryl Transfer in Kinases; 7.9 Thoughts from Computations; 8 Conclusions; Acknowledgments; References; Importance of Radioactive Labelling to Elucidate Inositol Polyphosphate Signalling; Abstract; 1 Introduction; 2 Phosphoinositides and Inositol Phosphates; 3 Radioactive Labels for Inositol; 4 Inositol Polyphosphate in Vivo Studies Using Radioactive Metabolic Labelling
Guest Chemistry and Their Applications; 2.1 Hydrogen Bonding; 2.1.1 Pi Sensing; 2.1.2 PPi Sensing; 2.2 Coordination Chemistry; 2.2.1 Pi Sensing; 2.2.2 PPi Sensing; 3 Molecular Sensors Based on New Sensing Mechanisms and Their Applications; 3.1 Displacement Assay; 3.1.1 Pi Sensing; 3.1.2 PPi Sensing; 3.2 Aggregation Induced Emission and Quenching; 3.3 Chemical Reactions; 3.3.1 Pi Sensing
3.3.2 PPi Sensing4 Conclusion; Acknowledgements; References; Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes; Abstract; 1 Background; 1.1 Basics of Phosphoryl Transfer; 1.2 Historic Development of Mechanisms; 2 Development of Metal Fluorides as Phosphate Analogs; 2.1 The 'Burst Phase' of Analog Discovery; 3 MFx Ground State Analogs; 3.1 BeF3- as a Ground State Phosphate Mimic; 3.1.1 Aspartyl Trifluoroberyllates; 3.1.2 BeF3- Nucleotide Structures; 3.1.3 Histidine Trifluoroberyllates; 3.1.4 Structural Conclusions
4 MFx in Transition State Analog Complexes4.1 Tetrafluoroaluminate TS Complexes-AlF4-; 4.1.1 Aspartyl Tetrafluoroaluminates; 4.1.2 Nucleotide Guanosine Diphosphate (GDP) Tetrafluoroaluminates; 4.1.3 Nucleotide Adenosine Diphosphate (ADP) Tetrafluoroaluminates; 4.2 Octahedral Aluminum Trifluoride Phosphate TS Mimics; 5 MF3 Improved Geometry Transition State Mimics; 5.1 MgF3-, Trifluoromagnesate; 5.2 AlF30, Aluminum Trifluoride; 5.3 A Combined MgF3-
and AlF30 Structural Analysis; 5.4 MgF4=, Tetrafluoromagnesate; 6 19F NMR Studies of MFx Complexes; 7 Computational Analyses of MFx Complexes
7.1 Balancing Accuracy of Energy/Structure and Conformational Sampling7.2 Tradeoff in Accuracy of Energy/Structure: Parameterization Simplification vs. Mathematical Complexity; 7.3 Tradeoffs in Conformational Sampling: Dynamics vs. Statics; 7.4 KS-DFT as a QM Region Description; 7.5 EVB as a QM Region Description; 7.6 The Use of MFx in Computational Studies of Enzyme Mechanisms; 7.6.1 Validation of MFx as a TSA for Phosphoryl Transfer; 7.6.2 Studies Linking Reaction Mechanisms from Model Systems to MFx Enzyme Complexes; 7.7 Computations Transposing GDPmiddotMFx into GTP Enzyme Complexes
7.7.1 Ras Family and GTP Hydrolysis7.7.2 Other GTPases and GTP Hydrolysis; 7.8 Computations Transposing ADPmiddotMFx into ATP Enzyme Complexes; 7.8.1 ATP Hydrolysis by Myosin; 7.8.2 ATP Hydrolysis by F1 ATPase; 7.8.3 Phosphoryl Transfer in Kinases; 7.9 Thoughts from Computations; 8 Conclusions; Acknowledgments; References; Importance of Radioactive Labelling to Elucidate Inositol Polyphosphate Signalling; Abstract; 1 Introduction; 2 Phosphoinositides and Inositol Phosphates; 3 Radioactive Labels for Inositol; 4 Inositol Polyphosphate in Vivo Studies Using Radioactive Metabolic Labelling