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Title: Engineering a disulfide-gated switch in streptavidin enables reversible binding without sacrificing binding affinity

Abstract

Although high affinity binding between streptavidin and biotin is widely exploited, the accompanying low rate of dissociation prevents its use in many applications where rapid ligand release is also required. To combine extremely tight and reversible binding, we have introduced disulfide bonds into opposite sides of a flexible loop critical for biotin binding, creating streptavidin muteins (M88 and M112) with novel disulfide-switchable binding properties. Crystal structures reveal how each disulfide exerts opposing effects on structure and function. Whereas the disulfide in M112 disrupts the closed conformation to increase koff, the disulfide in M88 stabilizes the closed conformation, decreasing koff 260-fold relative to streptavidin. The simple and efficient reduction of this disulfide increases koff 19,000-fold, thus creating a reversible redox-dependent switch with 70-fold faster dissociation kinetics than streptavidin. The facile control of disulfide formation in M88 will enable the development of many new applications requiring high affinity and reversible binding.

Authors:
 [1];  [1];  [2];  [1];  [1]
  1. Univ. of Calgary, AB (Canada). Dept. of Biological Scienes
  2. Univ. of Calgary, AB (Canada). Dept. of Biological Scienes; Univ. of Hawaii, Honolulu, HI (United States). Dept. of Molecular Biosciences and Bioengineering
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division; Natural Sciences and Engineering Research Council of Canada (NSERC); National Institutes of Health (NIH); National Center for Research Resources
OSTI Identifier:
1816245
Grant/Contract Number:  
AC02-76SF00515; 690573; 05728; P41GM103393; P41RR001209
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; biochemistry; biological techniques; molecular engineering; protein design; proteins

Citation Formats

Marangoni, Jesse M., Wu, Sau-Ching, Fogen, Dawson, Wong, Sui-Lam, and Ng, Kenneth K. S. Engineering a disulfide-gated switch in streptavidin enables reversible binding without sacrificing binding affinity. United States: N. p., 2020. Web. doi:10.1038/s41598-020-69357-5.
Marangoni, Jesse M., Wu, Sau-Ching, Fogen, Dawson, Wong, Sui-Lam, & Ng, Kenneth K. S. Engineering a disulfide-gated switch in streptavidin enables reversible binding without sacrificing binding affinity. United States. https://doi.org/10.1038/s41598-020-69357-5
Marangoni, Jesse M., Wu, Sau-Ching, Fogen, Dawson, Wong, Sui-Lam, and Ng, Kenneth K. S. Mon . "Engineering a disulfide-gated switch in streptavidin enables reversible binding without sacrificing binding affinity". United States. https://doi.org/10.1038/s41598-020-69357-5. https://www.osti.gov/servlets/purl/1816245.
@article{osti_1816245,
title = {Engineering a disulfide-gated switch in streptavidin enables reversible binding without sacrificing binding affinity},
author = {Marangoni, Jesse M. and Wu, Sau-Ching and Fogen, Dawson and Wong, Sui-Lam and Ng, Kenneth K. S.},
abstractNote = {Although high affinity binding between streptavidin and biotin is widely exploited, the accompanying low rate of dissociation prevents its use in many applications where rapid ligand release is also required. To combine extremely tight and reversible binding, we have introduced disulfide bonds into opposite sides of a flexible loop critical for biotin binding, creating streptavidin muteins (M88 and M112) with novel disulfide-switchable binding properties. Crystal structures reveal how each disulfide exerts opposing effects on structure and function. Whereas the disulfide in M112 disrupts the closed conformation to increase koff, the disulfide in M88 stabilizes the closed conformation, decreasing koff 260-fold relative to streptavidin. The simple and efficient reduction of this disulfide increases koff 19,000-fold, thus creating a reversible redox-dependent switch with 70-fold faster dissociation kinetics than streptavidin. The facile control of disulfide formation in M88 will enable the development of many new applications requiring high affinity and reversible binding.},
doi = {10.1038/s41598-020-69357-5},
journal = {Scientific Reports},
number = 1,
volume = 10,
place = {United States},
year = {Mon Jul 27 00:00:00 EDT 2020},
month = {Mon Jul 27 00:00:00 EDT 2020}
}

Works referenced in this record:

The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins: Bradavidin II: Highly Dynamic Oligomeric State
journal, June 2013

  • Leppiniemi, Jenni; Meir, Amit; Kähkönen, Niklas
  • Protein Science, Vol. 22, Issue 7
  • DOI: 10.1002/pro.2281

Energetic Roles of Hydrogen Bonds at the Ureido Oxygen Binding Pocket in the Streptavidin−Biotin Complex
journal, May 1998

  • Klumb, Lisa A.; Chu, Vano; Stayton, Patrick S.
  • Biochemistry, Vol. 37, Issue 21
  • DOI: 10.1021/bi9803123

Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997

  • Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3
  • DOI: 10.1107/S0907444996012255

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

Streptavidin–biotin technology: improvements and innovations in chemical and biological applications
journal, September 2013

  • Dundas, Christopher M.; Demonte, Daniel; Park, Sheldon
  • Applied Microbiology and Biotechnology, Vol. 97, Issue 21
  • DOI: 10.1007/s00253-013-5232-z

Genetically engineered avidins and streptavidins
journal, November 2006

  • Laitinen, O. H.; Hytönen, V. P.; Nordlund, H. R.
  • Cellular and Molecular Life Sciences, Vol. 63, Issue 24
  • DOI: 10.1007/s00018-006-6288-z

MolDock:  A New Technique for High-Accuracy Molecular Docking
journal, June 2006

  • Thomsen, René; Christensen, Mikael H.
  • Journal of Medicinal Chemistry, Vol. 49, Issue 11
  • DOI: 10.1021/jm051197e

Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin
journal, May 2013

  • Le Trong, Isolde; Chu, Vano; Xing, Yi
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 6
  • DOI: 10.1107/S0907444913003855

Heterogeneous and rate-dependent streptavidin–biotin unbinding revealed by high-speed force spectroscopy and atomistic simulations
journal, March 2019

  • Rico, Felix; Russek, Andreas; González, Laura
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 14
  • DOI: 10.1073/pnas.1816909116

Secretory Production and Purification of Functional Full-Length Streptavidin from Bacillus subtilis
journal, April 2002

  • Wu, Sau-Ching; Hassan Qureshi, Mohammad; Wong, Sui-Lam
  • Protein Expression and Purification, Vol. 24, Issue 3
  • DOI: 10.1006/prep.2001.1582

Extremely high thermal stability of streptavidin and avidin upon biotin binding
journal, December 1999

  • González, Martı́n; Argaraña, Carlos E.; Fidelio, Gerardo D.
  • Biomolecular Engineering, Vol. 16, Issue 1-4
  • DOI: 10.1016/S1050-3862(99)00041-8

Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins
journal, December 2013


Site-Directed Incorporation of Fluorescent Nonnatural Amino Acids into Streptavidin for Highly Sensitive Detection of Biotin
journal, March 2000

  • Murakami, Hiroshi; Hohsaka, Takahiro; Ashizuka, Yuki
  • Biomacromolecules, Vol. 1, Issue 1
  • DOI: 10.1021/bm990012g

Iminobiotin affinity columns and their application to retrieval of streptavidin.
journal, August 1980

  • Hofmann, K.; Wood, S. W.; Brinton, C. C.
  • Proceedings of the National Academy of Sciences, Vol. 77, Issue 8
  • DOI: 10.1073/pnas.77.8.4666

Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation.
journal, April 1989

  • Hendrickson, W. A.; Pahler, A.; Smith, J. L.
  • Proceedings of the National Academy of Sciences, Vol. 86, Issue 7
  • DOI: 10.1073/pnas.86.7.2190

Binding of Biotinylated DNA to Streptavidin-Coated Polystyrene Latex: Effects of Chain Length and Particle Size
journal, May 1996

  • Huang, Shao-Chie; Stump, Mark D.; Weiss, Robert
  • Analytical Biochemistry, Vol. 237, Issue 1
  • DOI: 10.1006/abio.1996.0208

How the biotin–streptavidin interaction was made even stronger: investigation via crystallography and a chimaeric tetramer
journal, March 2011

  • Chivers, Claire E.; Koner, Apurba L.; Lowe, Edward D.
  • Biochemical Journal, Vol. 435, Issue 1
  • DOI: 10.1042/BJ20101593

Tricine–SDS-PAGE
journal, May 2006


The properties of streptavidin, a biotin-binding protein produced by Streptomycetes
journal, January 1964


Imaging proteins in live mammalian cells with biotin ligase and monovalent streptavidin
journal, March 2008


Engineering monomeric streptavidin and its ligands with infinite affinity in binding but reversibility in interaction
journal, November 2009

  • Wu, Sau-Ching; Ng, Kenneth K. -S.; Wong, Sui-Lam
  • Proteins: Structure, Function, and Bioinformatics, Vol. 77, Issue 2
  • DOI: 10.1002/prot.22446

Position-specific incorporation of dansylated non-natural amino acids into streptavidin by using a four-base codon
journal, February 2004


Evolved streptavidin mutants reveal key role of loop residue in high-affinity binding: Analysis of Streptavidin Variants
journal, May 2011

  • Magalhães, Maria L. B.; Czekster, Clarissa Melo; Guan, Rong
  • Protein Science, Vol. 20, Issue 7
  • DOI: 10.1002/pro.642

Accurate measurement of avidin and streptavidin in crude biofluids with a new, optimized biotin–fluorescein conjugate
journal, March 1999

  • Kada, Gerald; Falk, Heinz; Gruber, Hermann J.
  • Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1427, Issue 1
  • DOI: 10.1016/S0304-4165(98)00178-0

Novel Avidin-like Protein from a Root Nodule Symbiotic Bacterium, Bradyrhizobium japonicum
journal, April 2005

  • Nordlund, Henri R.; Hytönen, Vesa P.; Laitinen, Olli H.
  • Journal of Biological Chemistry, Vol. 280, Issue 14
  • DOI: 10.1074/jbc.M414336200

Structural origins of high-affinity biotin binding to streptavidin
journal, January 1989


MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

A structural snapshot of an intermediate on the streptavidin-biotin dissociation pathway
journal, July 1999

  • Freitag, S.; Chu, V.; Penzotti, J. E.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 15
  • DOI: 10.1073/pnas.96.15.8384

Recent advances in the engineering and application of streptavidin-like molecules
journal, August 2019

  • Le, Quan; Nguyen, Vyncent; Park, Sheldon
  • Applied Microbiology and Biotechnology, Vol. 103, Issue 18
  • DOI: 10.1007/s00253-019-10036-5

Sodium dodecyl sulfate-polyacrylamide gel electrophoretic method for assessing the quaternary state and comparative thermostability of avidin and streptavidin
journal, January 1996

  • Bayer, Edward A.; Ehrlich-Rogozinski, Sarah; Wilchek, Meir
  • Electrophoresis, Vol. 17, Issue 8
  • DOI: 10.1002/elps.1150170808

Zinc is associated with the β subunit of DNA-dependent RNA polymerase of Bacillus subtilis
journal, June 1977

  • Halling, Shirley M.; Sanchez-Anzaldo, F. J.; Fukuda, Ryuji
  • Biochemistry, Vol. 16, Issue 13
  • DOI: 10.1021/bi00632a012

Structural Adaptation of a Thermostable Biotin-binding Protein in a Psychrophilic Environment
journal, May 2012

  • Meir, Amit; Bayer, Edward A.; Livnah, Oded
  • Journal of Biological Chemistry, Vol. 287, Issue 22
  • DOI: 10.1074/jbc.M112.357186

Structural studies of the streptavidin binding loop: Streptavidin binding loop
journal, June 1997

  • Stenkamp, Ronald E.; Trong, Isolde Le; Klumb, Lisa
  • Protein Science, Vol. 6, Issue 6
  • DOI: 10.1002/pro.5560060604

Saturation fluorescence labeling of proteins for proteomic analyses
journal, March 2008


Development of a Tetrameric Streptavidin Mutein with Reversible Biotin Binding Capability: Engineering a Mobile Loop as an Exit Door for Biotin
journal, April 2012


Dissecting Streptavidin-Biotin Interaction with a Laminar Flow Chamber
journal, June 2002


Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail
journal, August 2015


Streptavidin–biotin binding energetics
journal, December 1999


A streptavidin variant with slower biotin dissociation and increased mechanostability
journal, April 2010

  • Chivers, Claire E.; Crozat, Estelle; Chu, Calvin
  • Nature Methods, Vol. 7, Issue 5
  • DOI: 10.1038/nmeth.1450

Easily reversible desthiobiotin binding to streptavidin, avidin, and other biotin-binding proteins: uses for protein labeling, detection, and isolation
journal, September 2002


Crystal Structure of Rhizavidin: Insights into the Enigmatic High-Affinity Interaction of an Innate Biotin-Binding Protein Dimer
journal, February 2009

  • Meir, Amit; Helppolainen, Satu H.; Podoly, Erez
  • Journal of Molecular Biology, Vol. 386, Issue 2
  • DOI: 10.1016/j.jmb.2008.11.061

Rhizavidin from Rhizobium etli : the first natural dimer in the avidin protein family
journal, July 2007

  • Helppolainen, Satu H.; Nurminen, Kirsi P.; Määttä, Juha A. E.
  • Biochemical Journal, Vol. 405, Issue 3
  • DOI: 10.1042/BJ20070076

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206