How to distinguish ligand-binding mechanisms: an example of conformational selection disguised as an induced fit

References

• Abe, K., K. Tani, T. Friedrich, and Y. Fujiyoshi. 2012. “Cryo-EM Structure of Gastric H+,K+-ATPase with a Single Occupied Cation-binding Site.” Proceedings of the National Academy of Sciences of the United States of America 109 (45): 18401–18406. November 06. doi:10.1073/pnas.1212294109. PubMed PMID: 23091039; PubMed Central PMCID: PMCPMC3494912.
   PubMed Web of Science ®Google Scholar
• Abe, K., K. Tani, and Y. Fujiyoshi. 2010. “Structural and Functional Characterization of H+, K+-ATPase with Bound Fluorinated Phosphate Analogs.” Journal of Structural Biology 170 (1): 60–68. April. doi:10.1016/j.jsb.2009.12.008. PubMed PMID: 20005959.
   PubMed Web of Science ®Google Scholar
• Arneson, J. B., and E. G. Offerdahl. 2018. “Visual Literacy in Bloom: Using Bloom’s Taxonomy to Support Visual Learning Skills.” CBE Life Sciences Education 17 (1). Spring. doi:10.1187/cbe.17-08-0178. PubMed PMID: 29351910.
   PubMed Web of Science ®Google Scholar
• Bagshaw, C. R. 2017a. “Kinetic Theory; 2.6 Two-step Reversible Reaction; 2.7 Two-step Reversible Binding Reaction: Induced Fit; 2.8 Two-step Reversible Binding Reaction: Conformational Selection.” Chap. 2 in Biomolecular Kinetics: A Step-by-Step Guide. Foundations of Biochemistry and Biophysics. Boca Raton: Taylor & Francis/CRC Press.
   Google Scholar
• Bagshaw, C. R. 2017b. “Instrumentation; 7.2.2 Stopped-flow Methods.” Chap. 7 in Biomolecular Kinetics: A Step-by-Step Guide. Foundations of Biochemistry and Biophysics. Boca Raton: Taylor & Francis/CRC Press.
   Google Scholar
• Bloom, B. S. (editor). 1956. Taxonomy of educational objectives: The classification of educational goals. Harlow, Essex, England: Longman Group.
   Google Scholar
• Bonwell, Charles C., and James A. Eison. 1991. Active learning: creating excitement in the classroom. Washington, D.C.: School of Education and Human Development, George Washington University.
   Google Scholar
• Bublitz, M. 2015. P-Type ATPases: Methods and Protocols. New York: Springer.
   Google Scholar
• Clausen, J. D., D. B. McIntosh, D. G. Woolley, and J. P. Andersen. 2011. “Modulatory ATP Binding Affinity in Intermediate States of E2P Dephosphorylation of Sarcoplasmic Reticulum Ca2+-ATPase.” The Journal of Biological Chemistry 286 (13): 11792–11802. April 1. doi:10.1074/jbc.M110.206094. PubMed PMID: 21288896; PubMed Central PMCID: PMCPMC3064230.
   PubMed Web of Science ®Google Scholar
• Cornelius, F., Y. A. Mahmmoud, and C. Toyoshima. 2011. “Metal Fluoride Complexes of Na,K-ATPase: Characterization of Fluoride-stabilized Phosphoenzyme Analogues and Their Interaction with Cardiotonic Steroids.” The Journal of Biological Chemistry 286 (34): 29882–29892. August 26. doi:10.1074/jbc.M111.259663. PubMed PMID: 21708939; PubMed Central PMCID: PMCPMC3191029.
   PubMed Web of Science ®Google Scholar
• Danko, S., K. Yamasaki, T. Daiho, and H. Suzuki. 2004. “Distinct Natures of Beryllium Fluoride-bound, Aluminum Fluoride-bound, and Magnesium Fluoride-bound Stable Analogues of an ADP-insensitive Phosphoenzyme Intermediate of Sarcoplasmic Reticulum Ca2+-ATPase: Changes in Catalytic and Transport Sites during Phosphoenzyme Hydrolysis.” The Journal of Biological Chemistry 279 (15): 14991–14998. April 9. doi:10.1074/jbc.M313363200. PubMed PMID: 14754887.
   PubMed Web of Science ®Google Scholar
• Faraj, S. E., M. Centeno, R. C. Rossi, and M. R. Montes. 2019. “A Kinetic Comparison between E2P and the E2P-like State Induced by A Beryllium Fluoride Complex in the Na,K-ATPase. Interactions with Rb().” Biochimica Et Biophysica Acta - Biomembranes 1861 (2): 355–365. February 1. doi:10.1016/j.bbamem.2018.10.020. PubMed PMID: 30412697.
   PubMed Web of Science ®Google Scholar
• Fedosova, N. U., F. Cornelius, and I. Klodos. 1998. “E2P Phosphoforms of Na,K-ATPase. I. Comparison of Phosphointermediates Formed from ATP and Pi by Their Reactivity toward Hydroxylamine and Vanadate.” Biochemistry 37 (39): 13634–13642. September 29. doi:10.1021/bi980703h. PubMed PMID: 9753450; eng.
   PubMed Web of Science ®Google Scholar
• Fersht, A. 1998. “Analysis of Pre-steady State and Relaxation Kinetics in Chapter 4: Measurement and Magnitude of Individual Rate Constants.” In Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. 1st ed., 139–158. New York: W. H. Freeman.
   Google Scholar
• Gianni, S., J. Dogan, and P. Jemth. 2014. “Distinguishing Induced Fit from Conformational Selection.” Biophysical Chemistry 189 (May 01): 33–39. doi:10.1016/j.bpc.2014.03.003.
   PubMed Web of Science ®Google Scholar
• Gibson, Q. H. 1969. Chapter 6. Rapid mixing: Stopped flow. In Kustin, K. (ed.) Methods in Enzymology: Fast Reactions. Academic Press. New York. Vol. 16: 187-228.
   Google Scholar
• Hammes, G. G., Y. C. Chang, and T. G. Oas. 2009. “Conformational Selection or Induced Fit: A Flux Description of Reaction Mechanism.” Proceedings of the National Academy of Sciences of the United States of America 106 (33): 13737–13741. August 18. doi:10.1073/pnas.0907195106. PubMed PMID: 19666553; PubMed Central PMCID: PMCPMC2728963.
   PubMed Web of Science ®Google Scholar
• Heredia, V. V., J. Thomson, D. Nettleton, and S. Sun. 2006. “Glucose-induced Conformational Changes in Glucokinase Mediate Allosteric Regulation: Transient Kinetic Analysis.” Biochemistry 45 (24): 7553–7562. June 20. doi:10.1021/bi060253q. PubMed PMID: 16768451.
   PubMed Web of Science ®Google Scholar
• Holyoak, T. 2013. “Molecular Recognition: Lock-And-Key, Induced Fit, and Conformational Selection.” In Encyclopedia of Biophysics, edited by G. C. K. Roberts, 1584–1588. Berlin, Heidelberg: Springer Berlin Heidelberg.
   Google Scholar
• Lai, M.-T., E. Di Cera, and J. A. Shafer. 1997. “Kinetic Pathway for the Slow to Fast Transition OF Thrombin: Evidence of Linked Ligand Binding at Structurally Distinct Domains.” Journal of Biological Chemistry 272 (48): 30275–30282. doi:10.1074/jbc.272.48.30275. November 28.
   PubMed Web of Science ®Google Scholar
• Leone, F. A., R. P. M. Furriel, J. C. McNamara, J. D. Horisberger, and I. A. Borin. 2010. “Cation Transport Coupled to ATP Hydrolysis by the (na, K)-ATPase.” Biochemistry and Molecular Biology Education 38 (4): 276–279. doi:10.1002/bmb.20404.
   PubMed Web of Science ®Google Scholar
• Lowry, O. H., N. J. Rosebrough, A. L. Farr, and R. J.Randall. 1951. “Protein Measurement with the Folin Phenol Reagent.” The Journal of Biological Chemistry 193 (1): 265–275. November. PubMed PMID: 14907713.
   PubMed Web of Science ®Google Scholar
• Mesmer, R. E., and C. F. Baes. 1969. “Fluoride Complexes of beryllium(II) in Aqueous Media.” Inorganic Chemistry 8 (3): 618–626. doi:10.1021/ic50073a042. March 01.
   Web of Science ®Google Scholar
• Montes, M. R., R. M. Gonzalez-Lebrero, P. J. Garrahan, and R. C. Rossi. 2006. “Eosin Fluorescence Changes during Rb+ Occlusion in the Na+/K(+)-ATPase [article].” Biochemistry 45 (43): 13093–13100. October 31. doi:10.1021/bi060778i. PubMed PMID: 17059226; English.
   PubMed Web of Science ®Google Scholar
• Purich, D. L. 2010a. “Initial-Rate Kinetics of One-Substrate Enzyme-Catalyzed Reactions; 5.12.3. Induced-fit Behavior and Enzyme Specificity.” Chap. 5 in Enzyme Kinetics: Catalysis & Control. A Reference of Theory and Best-practice Methods. San Diego: Elsevier Academic.
   Google Scholar
• Purich, D. L. 2010b. “Probing Fast Enzyme Processes; 10.2. Flow Techniques.” Chap. 10 in Enzyme Kinetics: Catalysis & Control. A Reference of Theory and Best-practice Methods. San Diego: Elsevier Academic.
   Google Scholar
• Skou, J. C., and M. Esmann. 1981. “Eosin, a Fluorescent Probe of ATP Binding to the Na,K-ATPase [article].” Biochimica Et Biophysica Acta 647 (2): 232–240. October 2. doi:10.1016/0005-2736(81)90251-0. PubMed PMID: 6170332; English.
   PubMed Web of Science ®Google Scholar
• Teague, S. J. 2003. “Implications of Protein Flexibility for Drug Discovery [review Article].” Nature Reviews Drug Discovery 2: 527. July 01 online. doi:10.1038/nrd1129.
   PubMed Web of Science ®Google Scholar
• Toyoshima, C. 2008. “Structural Aspects of Ion Pumping by Ca2+-ATPase of Sarcoplasmic Reticulum.” Archives of Biochemistry and Biophysics 476 (1): 3–11. August 1. doi:10.1016/j.abb.2008.04.017. PubMed PMID: 18455499; eng.
   PubMed Web of Science ®Google Scholar
• Toyoshima, C., H. Nomura, and T. Tsuda. 2004. “Lumenal Gating Mechanism Revealed in Calcium Pump Crystal Structures with Phosphate Analogues [article].” Nature 432 (7015): 361–368. November 18. doi:10.1038/nature02981. PubMed PMID: 15448704.
   PubMed Web of Science ®Google Scholar
• Tummino, P. J., and R. A. Copeland. 2008. “Residence Time of Receptor-ligand Complexes and Its Effect on Biological Function.” Biochemistry 47 (20): 5481–5492. May 20. doi:10.1021/bi8002023. PubMed PMID: 18412369; eng.
   PubMed Web of Science ®Google Scholar
• Vogt, A. D., and E. Di Cera. 2012. “Conformational Selection or Induced Fit? A Critical Appraisal of the Kinetic Mechanism.” Biochemistry 51 (30): 5894–5902. July 31. doi:10.1021/bi3006913. PubMed PMID: 22775458; PubMed Central PMCID: PMCPMC3550001.
   PubMed Web of Science ®Google Scholar
• Weikl, T. R., and C. von Deuster. 2009. “Selected-fit versus Induced-fit Protein Binding: Kinetic Differences and Mutational Analysis.” Proteins 75 (1): 104–110. April. doi:10.1002/prot.22223. PubMed PMID: 18798570.
   PubMed Web of Science ®Google Scholar
• Yechun, X., C. J. Ph, J. Hualiang, I. Silman, J. L. Sussman, and M. Weik. 2008. “Induced-fit or Preexisting Equilibrium Dynamics? Lessons from Protein Crystallography and MD Simulations on Acetylcholinesterase and Implications for Structure-based Drug Design.” Protein Science 17 (4): 601–605. doi:10.1110/ps.083453808.
   PubMed Web of Science ®Google Scholar