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Ligand exchange between proteins. Exchange of biotin and biotin derivatives between avidin and streptavidin.

Pazy Y, Kulik T, Bayer EA, Wilchek M, Livnah O
J Biol Chem 277 30892-900 (2002)
Related entries: 1lcw, 1lcz, 1ldo, 1ldq, 1lel

Cited: 34 times
EuropePMC logo PMID: 12055191

Abstract

We have studied the structural elements that affect ligand exchange between the two high affinity biotin-binding proteins, egg white avidin and its bacterial analogue, streptavidin. For this purpose, we have developed a simple assay based on the antipodal behavior of the two proteins toward hydrolysis of biotinyl p-nitrophenyl ester (BNP). The assay provided the experimental basis for these studies. It was found that biotin migrates unidirectionally from streptavidin to avidin. Conversely, the biotin derivative, BNP, is transferred in the opposite direction, from avidin to streptavidin. A previous crystallographic study (Huberman, T., Eisenberg-Domovich, Y., Gitlin, G., Kulik, T., Bayer, E. A., Wilchek, M., and Livnah, O. (2001) J. Biol. Chem. 276, 32031-32039) provided insight into a plausible explanation for these results. These data revealed that the non-hydrolyzable BNP analogue, biotinyl p-nitroanilide, was almost completely sheltered in streptavidin as opposed to avidin in which the disordered conformation of a critical loop resulted in the loss of several hydrogen bonds and concomitant exposure of the analogue to the solvent. In order to determine the minimal modification of the biotin molecule required to cause the disordered loop conformation, the structures of avidin and streptavidin were determined with norbiotin, homobiotin, and a common long-chain biotin derivative, biotinyl epsilon-aminocaproic acid. Six new crystal structures of the avidin and streptavidin complexes with the latter biotin analogues and derivatives were thus elucidated. It was found that extending the biotin side chain by a single CH(2) group (i.e. homobiotin) is sufficient to result in this remarkable conformational change in the loop of avidin. These results bear significant biotechnological importance, suggesting that complexes containing biotinylated probes with streptavidin would be more stable than those with avidin. These findings should be heeded when developing new drugs based on lead compounds because it is difficult to predict the structural and conformational consequences on the resultant protein-ligand interactions.

Articles - 1lcv mentioned but not cited (2)

  1. Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations. Cerutti DS, Le Trong I, Stenkamp RE, Lybrand TP. J Phys Chem B 113 6971-6985 (2009)
  2. Crystal diffraction prediction and partiality estimation using Gaussian basis functions. Brehm W, White T, Chapman HN. Acta Crystallogr A Found Adv 79 145-162 (2023)


Reviews citing this publication (3)

  1. Essentials of biorecognition: the (strept)avidin-biotin system as a model for protein-protein and protein-ligand interaction. Wilchek M, Bayer EA, Livnah O. Immunol Lett 103 27-32 (2006)
  2. Genetic Optimization of Metalloenzymes: Enhancing Enzymes for Non-Natural Reactions. Hyster TK, Ward TR. Angew Chem Int Ed Engl 55 7344-7357 (2016)
  3. Synthetic strategies for the biotinylation of bioactive small molecules. Trippier PC. ChemMedChem 8 190-203 (2013)

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  2. Can we beat the biotin-avidin pair?: cucurbit[7]uril-based ultrahigh affinity host-guest complexes and their applications. Shetty D, Khedkar JK, Park KM, Kim K. Chem Soc Rev 44 8747-8761 (2015)
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  4. Rhizavidin from Rhizobium etli: the first natural dimer in the avidin protein family. Helppolainen SH, Nurminen KP, Määttä JA, Halling KK, Slotte JP, Huhtala T, Liimatainen T, Ylä-Herttuala S, Airenne KJ, Närvänen A, Jänis J, Vainiotalo P, Valjakka J, Kulomaa MS, Nordlund HR. Biochem J 405 397-405 (2007)
  5. Novel avidin-like protein from a root nodule symbiotic bacterium, Bradyrhizobium japonicum. Nordlund HR, Hytönen VP, Laitinen OH, Kulomaa MS. J Biol Chem 280 13250-13255 (2005)
  6. Activation of membrane receptors by a neurotransmitter conjugate designed for surface attachment. Vu TQ, Chowdhury S, Muni NJ, Qian H, Standaert RF, Pepperberg DR. Biomaterials 26 1895-1903 (2005)
  7. Binding properties of HABA-type azo derivatives to avidin and avidin-related protein 4. Repo S, Paldanius TA, Hytönen VP, Nyholm TK, Halling KK, Huuskonen J, Pentikäinen OT, Rissanen K, Slotte JP, Airenne TT, Salminen TA, Kulomaa MS, Johnson MS. Chem Biol 13 1029-1039 (2006)
  8. (Strept)avidin-displaying lentiviruses as versatile tools for targeting and dual imaging of gene delivery. Kaikkonen MU, Lesch HP, Pikkarainen J, Räty JK, Vuorio T, Huhtala T, Taavitsainen M, Laitinen T, Tuunanen P, Gröhn O, Närvänen A, Airenne KJ, Ylä-Herttuala S. Gene Ther 16 894-904 (2009)
  9. Synthesis of a biotin-derived alkyne for pd-catalyzed coupling reactions. Corona C, Bryant BK, Arterburn JB. Org Lett 8 1883-1886 (2006)
  10. Structural Analysis of the Glycoprotein Complex Avidin by Tandem-Trapped Ion Mobility Spectrometry-Mass Spectrometry (Tandem-TIMS/MS). Liu FC, Cropley TC, Ridgeway ME, Park MA, Bleiholder C. Anal Chem 92 4459-4467 (2020)
  11. Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis. Määttä JA, Helppolainen SH, Hytönen VP, Johnson MS, Kulomaa MS, Airenne TT, Nordlund HR. BMC Struct Biol 9 63 (2009)
  12. Dual-affinity avidin molecules. Hytönen VP, Nordlund HR, Hörhä J, Nyholm TK, Hyre DE, Kulomaa T, Porkka EJ, Marttila AT, Stayton PS, Laitinen OH, Kulomaa MS. Proteins 61 597-607 (2005)
  13. Rational modification of ligand-binding preference of avidin by circular permutation and mutagenesis. Määttä JA, Airenne TT, Nordlund HR, Jänis J, Paldanius TA, Vainiotalo P, Johnson MS, Kulomaa MS, Hytönen VP. Chembiochem 9 1124-1135 (2008)
  14. Dimer-tetramer transition between solution and crystalline states of streptavidin and avidin mutants. Pazy Y, Eisenberg-Domovich Y, Laitinen OH, Kulomaa MS, Bayer EA, Wilchek M, Livnah O. J Bacteriol 185 4050-4056 (2003)
  15. Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail. Avraham O, Meir A, Fish A, Bayer EA, Livnah O. J Struct Biol 191 139-148 (2015)
  16. Imaging the static dielectric constant in vitro and in living cells by a bioconjugable GFP chromophore analog. Signore G, Abbandonato G, Storti B, Stöckl M, Subramaniam V, Bizzarri R. Chem Commun (Camb) 49 1723-1725 (2013)
  17. Engineering monomeric streptavidin and its ligands with infinite affinity in binding but reversibility in interaction. Wu SC, Ng KK, Wong SL. Proteins 77 404-412 (2009)
  18. Site-dependent excited-state dynamics of a fluorescent probe bound to avidin and streptavidin. Fürstenberg A, Kel O, Gradinaru J, Ward TR, Emery D, Bollot G, Mareda J, Vauthey E. Chemphyschem 10 1517-1532 (2009)
  19. Neurotransmitter analog tethered to a silicon platform for neuro-BioMEMS applications. Nehilla BJ, Popat KC, Vu TQ, Chowdhury S, Standaert RF, Pepperberg DR, Desai TA. Biotechnol Bioeng 87 669-674 (2004)
  20. Structural elements responsible for conversion of streptavidin to a pseudoenzyme. Eisenberg-Domovich Y, Pazy Y, Nir O, Raboy B, Bayer EA, Wilchek M, Livnah O. Proc Natl Acad Sci U S A 101 5916-5921 (2004)
  21. Mild conditions for releasing mono and bis-biotinylated macromolecules from immobilized streptavidin. Nguyen GH, Milea JS, Rai A, Smith CL. Biomol Eng 22 147-150 (2005)
  22. Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature. Ayan E, Yuksel B, Destan E, Ertem FB, Yildirim G, Eren M, Yefanov OM, Barty A, Tolstikova A, Ketawala GK, Botha S, Dao EH, Hayes B, Liang M, Seaberg MH, Hunter MS, Batyuk A, Mariani V, Su Z, Poitevin F, Yoon CH, Kupitz C, Cohen A, Doukov T, Sierra RG, Dağ Ç, DeMirci H. Commun Biol 5 73 (2022)
  23. Love-Hate ligands for high resolution analysis of strain in ultra-stable protein/small molecule interaction. Fairhead M, Shen D, Chan LK, Lowe ED, Donohoe TJ, Howarth M. Bioorg Med Chem 22 5476-5486 (2014)
  24. Protein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family. Barison N, Cendron L, Loconte V, Proctor EA, Dokholyan NV, Zanotti G. Acta Crystallogr D Biol Crystallogr 69 1387-1394 (2013)
  25. Avidin and streptavidin ligands based on the glycoluril bicyclic system. Hidalgo-Fernández P, Ayet E, Canal I, Farrera JA. Org Biomol Chem 4 3147-3154 (2006)
  26. Bisection of biotinylated soft spherical structures. Joshi KB, Verma S. Biophys Chem 140 129-132 (2009)
  27. Specific labeling of streptavidin for better understanding of ligand modification in modular method for affinity labeling (MoAL). Kunishima M, Kato D, Nakanishi S, Kitamura M, Yamada K, Terao K, Asano T. Chem Pharm Bull (Tokyo) 62 1146-1150 (2014)
  28. Expression of various biotin-binding proteins in transgenic tobacco confers resistance to potato tuber moth, Phthorimaea operculella (Zeller) (fam. Gelechiidae). Murray C, Markwick NP, Kaji R, Poulton J, Martin H, Christeller JT. Transgenic Res 19 1041-1051 (2010)
  29. [Interaction of triiodothyronine-biotin conjugate with binding proteins in immunoassay systems]. Navakouskiĭ MJ, Vashkevich II, Sviridov OV. Bioorg Khim 38 449-457 (2012)


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