Hammes-Schiffer, S. & Klinman, J. Emerging concepts about the role of protein motion in enzyme catalysis. Acc. Chem. Res. 48, 899–899 (2015).
Google Scholar
Lobb, R. R. & Auld, D. S. Determination of enzyme mechanisms by radiationless energy transfer kinetics. Proc. Natl Acad. Sci. USA 76, 2684–2688 (1979).
Google Scholar
Au, H.-W., Tsang, M.-W., So, P.-K., Wong, K.-Y. & Leung, Y.-C. Thermostable β-lactamase mutant with its active site conjugated with fluorescein for efficient β-lactam antibiotic detection. ACS Omega 4, 20493–20502 (2019).
Google Scholar
Vallée-Bélisle, A. & Michnick, S. W. Visualizing transient protein-folding intermediates by tryptophan-scanning mutagenesis. Nat. Struct. Mol. Biol. 19, 731–736 (2012).
Google Scholar
Gregorio, G. G. et al. Single-molecule analysis of ligand efficacy in β2AR–G-protein activation. Nature 547, 68–73 (2017).
Google Scholar
Comstock, M. J. et al. Direct observation of structure-function relationship in a nucleic acid–processing enzyme. Science 348, 352–354 (2015).
Google Scholar
Hwang, H. & Myong, S. Protein induced fluorescence enhancement (PIFE) for probing protein–nucleic acid interactions. Chem. Soc. Rev. 43, 1221–1229 (2014).
Google Scholar
Lerner, E. et al. Toward dynamic structural biology: two decades of single-molecule Förster resonance energy transfer. Science 359, eaan1133 (2018).
Google Scholar
Chen, Y., Tsao, K. & Keillor, J. W. Fluorogenic protein labelling: a review of photophysical quench mechanisms and principles of fluorogen design. Can. J. Chem. 93, 389–398 (2015).
Google Scholar
Unnikrishnan, B., Wu, R.-S., Wei, S.-C., Huang, C.-C. & Chang, H.-T. Fluorescent carbon dots for selective labeling of subcellular organelles. ACS Omega 5, 11248–11261 (2020).
Google Scholar
Eisenmesser, E. Z., Bosco, D. A., Akke, M. & Kern, D. Enzyme dynamics during catalysis. Science 295, 1520–1523 (2002).
Google Scholar
Ma, X., Hortelão, A. C., Patiño, T. & Sánchez, S. Enzyme catalysis to power micro/nanomachines. ACS Nano 10, 9111–9122 (2016).
Google Scholar
Abou-Zied, O. K. & Sulaiman, S. A. J. Site-specific recognition of fluorescein by human serum albumin: a steady-state and time-resolved spectroscopic study. Dyes Pigment. 110, 89–96 (2014).
Google Scholar
Pisoni, D. S. et al. Symmetrical and asymmetrical cyanine dyes. Synthesis, spectral properties, and BSA association study. J. Org. Chem. 79, 5511–5520 (2014).
Google Scholar
Millán, J.L. Mammalian Alkaline Phosphatases: From Biology to Applications in Medicine and Biotechnology (John Wiley & Sons, 2006).
Lallès, J.-P. Recent advances in intestinal alkaline phosphatase, inflammation, and nutrition. Nutr. Rev. 77, 710–724 (2019).
Google Scholar
Bates, J. M., Akerlund, J., Mittge, E. & Guillemin, K. Intestinal alkaline phosphatase detoxifies lipopolysaccharide and prevents inflammation in zebrafish in response to the gut microbiota. Cell Host Microbe 2, 371–382 (2007).
Google Scholar
Malo, M. S. et al. Intestinal alkaline phosphatase promotes gut bacterial growth by reducing the concentration of luminal nucleotide triphosphates. Am. J. Physiol. Gastrointest. Liver Physiol. 306, G826–G838 (2014).
Google Scholar
Mizumori, M. et al. Intestinal alkaline phosphatase regulates protective surface microclimate pH in rat duodenum. J. Physiol. 587, 3651–3663 (2009).
Google Scholar
Giatromanolaki, A., Sivridis, E., Maltezos, E. & Koukourakis, M. I. Down-regulation of intestinal-type alkaline phosphatase in the tumor vasculature and stroma provides a strong basis for explaining amifostine selectivity. Semin. Oncol. 29, 14–21 (2002).
Google Scholar
Hofer, M. et al. Two new faces of amifostine: protector from DNA damage in normal cells and inhibitor of DNA repair in cancer cells. J. Med. Chem. 59, 3003–3017 (2016).
Google Scholar
Riedel, C. et al. The heat released during catalytic turnover enhances the diffusion of an enzyme. Nature 517, 227–230 (2015).
Google Scholar
Tsai, L.-C. et al. Expression and regulation of alkaline phosphatases in human breast cancer MCF-7 cells. Eur. J. Biochem. 267, 1330–1339 (2000).
Google Scholar
Rao, S. R. et al. Tumour-derived alkaline phosphatase regulates tumour growth, epithelial plasticity and disease-free survival in metastatic prostate cancer. Br. J. Cancer 116, 227–236 (2017).
Google Scholar
Hung, H.-Y. et al. Preoperative alkaline phosphatase elevation was associated with poor survival in colorectal cancer patients. Int. J. Colorectal Dis. 32, 1775–1778 (2017).
Google Scholar
Namikawa, T. et al. Prognostic significance of serum alkaline phosphatase and lactate dehydrogenase levels in patients with unresectable advanced gastric cancer. Gastric Cancer 22, 684–691 (2019).
Google Scholar
Kaliannan, K. et al. Intestinal alkaline phosphatase prevents metabolic syndrome in mice. Proc. Natl Acad. Sci. USA 110, 7003–7008 (2013).
Google Scholar
José, L. M. & Michael, P. W. Alkaline Phosphatase and Hypophosphatasia. Calcif. Tissue Int. 98, 398–416 (2016).
Waymire, K. G. et al. Mice lacking tissue non-specific alkaline phosphatase die from seizures due to defective metabolism of vitamin B-6. Nat. Genet. 11, 45–51 (1995).
Google Scholar
Park, J.-B. et al. Serum alkaline phosphatase is a predictor of mortality, myocardial infarction, or stent thrombosis after implantation of coronary drug-eluting stent. Eur. Heart J. 34, 920–931 (2012).
Google Scholar
Yang, W. H. et al. Recurrent infection progressively disables host protection against intestinal inflammation. Science 358, eaao5610 (2017).
Google Scholar
To, K. K.-W. et al. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study. Lancet Infect. Dis. 20, 565–574 (2020).
Google Scholar
Stec, B., Holtz, K. M. & Kantrowitz, E. R. A revised mechanism for the alkaline phosphatase reaction involving three metal ions. J. Mol. Biol. 299, 1303–1311 (2000).
Google Scholar
Holtz, K. M., Stec, B. & Kantrowitz, E. R. A model of the transition state in the alkaline phosphatase reaction. J. Biol. Chem. 274, 8351–8354 (1999).
Google Scholar
Peck, A., Sunden, F., Andrews, L. D., Pande, V. S. & Herschlag, D. Tungstate as a transition state analog for catalysis by alkaline phosphatase. J. Mol. Biol. 428, 2758–2768 (2016).
Google Scholar
Roston, D., Demapan, D. & Cui, Q. Leaving group ability observably affects transition state structure in a single enzyme active site. J. Am. Chem. Soc. 138, 7386–7394 (2016).
Google Scholar
Bortolato, M., Besson, F. & Roux, B. Role of metal ions on the secondary and quaternary structure of alkaline phosphatase from bovine intestinal mucosa. Proteins 37, 310–318 (1999).
Google Scholar
Ásgeirsson, B., Markússon, S., Hlynsdóttir, S. S., Helland, R. & Hjörleifsson, J. G. X-ray crystal structure of Vibrio alkaline phosphatase with the non-competitive inhibitor cyclohexylamine. Biochem. Biophys. Rep. 24, 100830 (2020).
Google Scholar
Aziz, H. et al. Synthesis, characterization, in vitro tissue-nonspecific alkaline phosphatase (TNAP) and intestinal alkaline phosphatase (IAP) inhibition studies and computational evaluation of novel thiazole derivatives. Bioorg. Chem. 102, 104088 (2020).
Google Scholar
Kiffer-Moreira, T. et al. Catalytic signature of a heat-stable, chimeric human alkaline phosphatase with therapeutic potential. PLoS ONE 9, e89374 (2014).
Google Scholar
Jiang, Y., Li, X. & Walt, D. R. Single-molecule analysis determines isozymes of human alkaline phosphatase in serum. Angew. Chem. Int. Ed. Engl. 59, 18010–18015 (2020).
Google Scholar
Bessey, O. A., Lowry, O. H. & Brock, M. J. A method for the rapid determination of alkaline phosphatase with five cubic millimeters of serum. J. Biol. Chem. 164, 321–329 (1946).
Google Scholar
Fernley, H. & Walker, P. Kinetic behaviour of calf-intestinal alkaline phosphatase with 4-methylumbelliferyl phosphate. Biochem. J. 97, 95–103 (1965).
Google Scholar
Deng, J., Yu, P., Wang, Y. & Mao, L. Real-time ratiometric fluorescent assay for alkaline phosphatase activity with stimulus responsive infinite coordination polymer nanoparticles. Anal. Chem. 87, 3080–3086 (2015).
Google Scholar
Sanzhaeva, U. et al. Imaging of enzyme activity by electron paramagnetic resonance: concept and experiment using a paramagnetic substrate of alkaline phosphatase. Angew. Chem. Int. Ed. Engl. 57, 11701–11705 (2018).
Google Scholar
Gyurcsányi, R. E., Bereczki, A., Nagy, G., Neuman, M. R. & Lindner, E. Amperometric microcells for alkaline phosphatase assay. Analyst 127, 235–240 (2002).
Google Scholar
Baykov, A. A., Evtushenko, O. A. & Avaeva, S. M. A malachite green procedure for orthophosphate determination and its use in alkaline phosphatase-based enzyme immunoassay. Anal. Biochem. 171, 266–270 (1988).
Google Scholar
Liu, Y. & Schanze, K. S. Conjugated polyelectrolyte-based real-time fluorescence assay for alkaline phosphatase with pyrophosphate as substrate. Anal. Chem. 80, 8605–8612 (2008).
Google Scholar
Liu, Y. et al. Selective sensing of phosphorylated peptides and monitoring kinase and phosphatase activity with a supramolecular tandem assay. J. Am. Chem. Soc. 140, 13869–13877 (2018).
Google Scholar
Wang, Y., Wang, G., Moitessier, N. & Mittermaier, A. K. Enzyme kinetics by isothermal titration calorimetry: allostery, inhibition, and dynamics. Front. Mol. Biosci. 7, 583826 (2020).
Google Scholar
Di Trani, J. M., Moitessier, N. & Mittermaier, A. K. Complete kinetic characterization of enzyme inhibition in a single isothermal titration calorimetric experiment. Anal. Chem. 90, 8430–8435 (2018).
Google Scholar
Honarmand Ebrahimi, K., Hagedoorn, P.-L., Jacobs, D. & Hagen, W. R. Accurate label-free reaction kinetics determination using initial rate heat measurements. Sci. Rep. 5, 16380 (2015).
Google Scholar
Zhang, L., Buchet, R. & Azzar, G. Phosphate binding in the active site of alkaline phosphatase and the interactions of 2-nitrosoacetophenone with alkaline phosphatase-induced small structural changes. Biophys. J. 86, 3873–3881 (2004).
Google Scholar
Akerström, B., Brodin, T., Reis, K. & Björck, L. Protein G: a powerful tool for binding and detection of monoclonal and polyclonal antibodies. J. Immunol. 135, 2589–2592 (1985).
Google Scholar
Kada, G., Falk, H. & Gruber, H. J. Accurate measurement of avidin and streptavidin in crude biofluids with a new, optimized biotin–fluorescein conjugate. Biochim. Biophys. Acta 1427, 33–43 (1999).
Google Scholar
Buranda, T. et al. Ligand receptor dynamics at streptavidin-coated particle surfaces: a flow cytometric and spectrofluorimetric study. J. Phys. Chem. B 103, 3399–3410 (1999).
Google Scholar
Iyer, A., Chandra, A. & Swaminathan, R. Hydrolytic enzymes conjugated to quantum dots mostly retain whole catalytic activity. Biochim. Biophys. Acta Gen. Subj. 1840, 2935–2943 (2014).
Google Scholar
Fairhead, M., Krndija, D., Lowe, E. D. & Howarth, M. Plug-and-play pairing via defined divalent streptavidins. J. Mol. Biol. 426, 199–214 (2014).
Google Scholar
Neish, C. S., Martin, I. L., Henderson, R. M. & Edwardson, J. M. Direct visualization of ligand-protein interactions using atomic force microscopy. Br. J. Pharmacol. 135, 1943–1950 (2002).
Google Scholar
Deetanya, P. et al. Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identification. Comput. Struct. Biotechnol. J. 19, 3364–3371 (2021).
Google Scholar
Chen, H., Ahsan, S. S., Santiago-Berrios, M. E. B., Abruña, H. D. & Webb, W. W. Mechanisms of quenching of Alexa fluorophores by natural amino acids. J. Am. Chem. Soc. 132, 7244–7245 (2010).
Google Scholar
Togashi, D. M., Szczupak, B., Ryder, A. G., Calvet, A. & O’Loughlin, M. Investigating tryptophan quenching of fluorescein fluorescence under protolytic equilibrium. J. Phys. Chem. A 113, 2757–2767 (2009).
Google Scholar
Nguyen, B., Ciuba, M. A., Kozlov, A. G., Levitus, M. & Lohman, T. M. Protein environment and DNA orientation affect protein-induced Cy3 fluorescence enhancement. Biophys. J. 117, 66–73 (2019).
Google Scholar
Rashid, F. et al. Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation. Nat. Commun. 10, 2104 (2019).
Google Scholar
Marras, S. A. E., Kramer, F. R. & Tyagi, S. Efficiencies of fluorescence resonance energy transfer and contact‐mediated quenching in oligonucleotide probes. Nucleic Acids Res. 30, e122 (2002).
Google Scholar
Zimmerle, C. T. & Frieden, C. Analysis of progress curves by simulations generated by numerical integration. Biochem. J. 258, 381–387 (1989).
Google Scholar
Palmier, M. O. & Van Doren, S. R. Rapid determination of enzyme kinetics from fluorescence: overcoming the inner filter effect. Anal. Biochem. 371, 43–51 (2007).
Google Scholar
Komazin, G. et al. Substrate structure-activity relationship reveals a limited lipopolysaccharide chemotype range for intestinal alkaline phosphatase. J. Biol. Chem. 294, 19405–19423 (2019).
Google Scholar
Ziegler, A. J., Florian, J., Ballicora, M. A. & Herlinger, A. W. Alkaline phosphatase inhibition by vanadyl-β-diketone complexes: electron density effects. J. Enzym. Inhib. Med. Chem. 24, 22–28 (2009).
Google Scholar
Chen, S. et al. Detection of dihydrofolate reductase conformational change by FRET using two fluorescent amino acids. J. Am. Chem. Soc. 135, 12924–12927 (2013).
Google Scholar
Schwaminger, S. P. et al. Immobilization of PETase enzymes on magnetic iron oxide nanoparticles for the decomposition of microplastic PET. Nanoscale Adv. 3, 4395–4399 (2021).
Google Scholar
Ritchie, R. J. & Prvan, T. A simulation study on designing experiments to measure the Km of Michaelis–Menten kinetics curves. J. Theor. Biol. 178, 239–254 (1996).
Google Scholar
Mao, H., Yang, T. & Cremer, P. S. Design and characterization of immobilized enzymes in microfluidic systems. Anal. Chem. 74, 379–385 (2002).
Google Scholar
Gordon, S. E., Munari, M. & Zagotta, W. N. Visualizing conformational dynamics of proteins in solution and at the cell membrane. eLife 7, e37248 (2018).
Pantazis, A., Westerberg, K., Althoff, T., Abramson, J. & Olcese, R. Harnessing photoinduced electron transfer to optically determine protein sub-nanoscale atomic distances. Nat. Commun. 9, 4738 (2018).
Google Scholar
Jarecki, BrianW. et al. Tethered spectroscopic probes estimate dynamic distances with subnanometer resolution in voltage-dependent potassium channels. Biophys. J. 105, 2724–2732 (2013).
Google Scholar
Mansoor, S. E., DeWitt, M. A. & Farrens, D. L. Distance mapping in proteins using fluorescence spectroscopy: the tryptophan-induced quenching (TrIQ) method. Biochemistry 49, 9722–9731 (2010).
Google Scholar
Perri, M. J. & Weber, S. H. Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program. J. Chem. Educ. 91, 2206–2208 (2014).
Google Scholar
Grosdidier, A., Zoete, V. & Michielin, O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 39, W270–W277 (2011).
Google Scholar
Grosdidier, A., Zoete, V. & Michielin, O. Fast docking using the CHARMM force field with EADock DSS. J. Comput. Chem. 32, 2149–2159 (2011).
Google Scholar
Basu, S., Finke, A., Vera, L., Wang, M. & Olieric, V. Making routine native SAD a reality: lessons from beamline X06DA at the Swiss Light Source. Acta Crystallogr. D Struct. Biol. 75, 262–271 (2019).
Google Scholar
Weissig, H., Schildge, A., Hoylaerts, M. F., Iqbal, M. & Millán, J. L. Cloning and expression of the bovine intestinal alkaline phosphatase gene: biochemical characterization of the recombinant enzyme. Biochem. J. 290, 503–508 (1993).
Google Scholar
Llinas, P. et al. Structural studies of human placental alkaline phosphatase in complex with functional ligands. J. Mol. Biol. 350, 441–451 (2005).
Google Scholar
Harada, T. et al. Characterization of structural and catalytic differences in rat intestinal alkaline phosphatase isozymes. FEBS J. 272, 2477–2486 (2005).
Google Scholar
Hanwell, M. D. et al. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J. Cheminformatics 4, 17 (2012).
Google Scholar
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Google Scholar
Molecular Operating Environment (MOE) v.2019.01 (Chemical Computing Group, 2019).
Case, D. A. et al. Amber 2020 (University of California, San Francisco, 2020).

