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Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.

Bailey LJ, Sheehy KM, Dominik PK, Liang WG, Rui H, Clark M, Jaskolowski M, Kim Y, Deneka D, Tang WJ, Kossiakoff AA
J Mol Biol 430 337-347 (2018)
Related entries: 6ayz, 6az2

Cited: 29 times
EuropePMC logo PMID: 29273204

Abstract

Antibody Fab fragments have been exploited with significant success to facilitate the structure determination of challenging macromolecules as crystallization chaperones and as molecular fiducial marks for single particle cryo-electron microscopy approaches. However, the inherent flexibility of the "elbow" regions, which link the constant and variable domains of the Fab, can introduce disorder and thus diminish their effectiveness. We have developed a phage display engineering strategy to generate synthetic Fab variants that significantly reduces elbow flexibility, while maintaining their high affinity and stability. This strategy was validated using previously recalcitrant Fab-antigen complexes where introduction of an engineered elbow region enhanced crystallization and diffraction resolution. Furthermore, incorporation of the mutations appears to be generally portable to other synthetic antibodies and may serve as a universal strategy to enhance the success rates of Fabs as structure determination chaperones.

Articles - 5cjo mentioned but not cited (2)

  1. Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination. Bailey LJ, Sheehy KM, Dominik PK, Liang WG, Rui H, Clark M, Jaskolowski M, Kim Y, Deneka D, Tang WJ, Kossiakoff AA. J Mol Biol 430 337-347 (2018)
  2. Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme. Zhang Z, Liang WG, Bailey LJ, Tan YZ, Wei H, Wang A, Farcasanu M, Woods VA, McCord LA, Lee D, Shang W, Deprez-Poulain R, Deprez B, Liu DR, Koide A, Koide S, Kossiakoff AA, Li S, Carragher B, Potter CS, Tang WJ. Elife 7 e33572 (2018)


Reviews citing this publication (2)

  1. Why recombinant antibodies - benefits and applications. Basu K, Green EM, Cheng Y, Craik CS. Curr Opin Biotechnol 60 153-158 (2019)
  2. Protein Engineering: Advances in Phage Display for Basic Science and Medical Research. Davydova EK. Biochemistry (Mosc) 87 S146-S110 (2022)

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  1. A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model. Kreye J, Reincke SM, Kornau HC, Sánchez-Sendin E, Corman VM, Liu H, Yuan M, Wu NC, Zhu X, Lee CD, Trimpert J, Höltje M, Dietert K, Stöffler L, von Wardenburg N, van Hoof S, Homeyer MA, Hoffmann J, Abdelgawad A, Gruber AD, Bertzbach LD, Vladimirova D, Li LY, Barthel PC, Skriner K, Hocke AC, Hippenstiel S, Witzenrath M, Suttorp N, Kurth F, Franke C, Endres M, Schmitz D, Jeworowski LM, Richter A, Schmidt ML, Schwarz T, Müller MA, Drosten C, Wendisch D, Sander LE, Osterrieder N, Wilson IA, Prüss H. Cell 183 1058-1069.e19 (2020)
  2. A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Wu NC, Yuan M, Bangaru S, Huang D, Zhu X, Lee CD, Turner HL, Peng L, Yang L, Burton DR, Nemazee D, Ward AB, Wilson IA. PLoS Pathog 16 e1009089 (2020)
  3. Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates. Cottrell CA, van Schooten J, Bowman CA, Yuan M, Oyen D, Shin M, Morpurgo R, van der Woude P, van Breemen M, Torres JL, Patel R, Gross J, Sewall LM, Copps J, Ozorowski G, Nogal B, Sok D, Rakasz EG, Labranche C, Vigdorovich V, Christley S, Carnathan DG, Sather DN, Montefiori D, Silvestri G, Burton DR, Moore JP, Wilson IA, Sanders RW, Ward AB, van Gils MJ. PLoS Pathog 16 e1008753 (2020)
  4. Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM. Uchański T, Masiulis S, Fischer B, Kalichuk V, López-Sánchez U, Zarkadas E, Weckener M, Sente A, Ward P, Wohlkönig A, Zögg T, Remaut H, Naismith JH, Nury H, Vranken W, Aricescu AR, Pardon E, Steyaert J. Nat Methods 18 60-68 (2021)
  5. Structural basis for the reaction cycle of DASS dicarboxylate transporters. Sauer DB, Trebesch N, Marden JJ, Cocco N, Song J, Koide A, Koide S, Tajkhorshid E, Wang DN. Elife 9 e61350 (2020)
  6. Structural basis for activation of voltage sensor domains in an ion channel TPC1. Kintzer AF, Green EM, Dominik PK, Bridges M, Armache JP, Deneka D, Kim SS, Hubbell W, Kossiakoff AA, Cheng Y, Stroud RM. Proc Natl Acad Sci U S A 115 E9095-E9104 (2018)
  7. Structural basis of broad HIV neutralization by a vaccine-induced cow antibody. Stanfield RL, Berndsen ZT, Huang R, Sok D, Warner G, Torres JL, Burton DR, Ward AB, Ward AB, Wilson IA, Smider VV. Sci Adv 6 eaba0468 (2020)
  8. Selection of immunoglobulin elbow region mutations impacts interdomain conformational flexibility in HIV-1 broadly neutralizing antibodies. Henderson R, Watts BE, Ergin HN, Anasti K, Parks R, Xia SM, Trama A, Liao HX, Saunders KO, Bonsignori M, Wiehe K, Haynes BF, Alam SM. Nat Commun 10 654 (2019)
  9. Diverse Antibody Responses to Conserved Structural Motifs in Plasmodium falciparum Circumsporozoite Protein. Pholcharee T, Oyen D, Torres JL, Flores-Garcia Y, Martin GM, González-Páez GE, Emerling D, Volkmuth W, Locke E, King CR, Zavala F, Ward AB, Wilson IA. J Mol Biol 432 1048-1063 (2020)
  10. Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum. Pholcharee T, Oyen D, Flores-Garcia Y, Gonzalez-Paez G, Han Z, Williams KL, Volkmuth W, Emerling D, Locke E, Richter King C, Zavala F, Wilson IA. Nat Commun 12 1063 (2021)
  11. Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins. Bloch JS, Mukherjee S, Kowal J, Filippova EV, Niederer M, Pardon E, Steyaert J, Kossiakoff AA, Locher KP. Proc Natl Acad Sci U S A 118 e2115435118 (2021)
  12. Structural basis for inhibition of the drug efflux pump NorA from Staphylococcus aureus. Brawley DN, Sauer DB, Li J, Zheng X, Koide A, Jedhe GS, Suwatthee T, Song J, Liu Z, Arora PS, Koide S, Torres VJ, Wang DN, Traaseth NJ. Nat Chem Biol 18 706-712 (2022)
  13. Delineating the mechanism of anti-Lassa virus GPC-A neutralizing antibodies. Enriquez AS, Buck TK, Li H, Norris MJ, Moon-Walker A, Zandonatti MA, Harkins SS, Robinson JE, Branco LM, Garry RF, Saphire EO, Hastie KM. Cell Rep 39 110841 (2022)
  14. Soluble T-cell receptor design influences functional yield in an E. coli chaperone-assisted expression system. Gunnarsen KS, Høydahl LS, Neumann RS, Bjerregaard-Andersen K, Nilssen NR, Sollid LM, Sandlie I, Løset GÅ. PLoS One 13 e0195868 (2018)
  15. An engineered ultra-high affinity Fab-Protein G pair enables a modular antibody platform with multifunctional capability. Slezak T, Bailey LJ, Jaskolowski M, Nahotko DA, Filippova EV, Davydova EK, Kossiakoff AA. Protein Sci 29 141-156 (2020)
  16. Repurposing off-the-shelf antihelix antibodies for enabling structural biology. Koide S. Proc Natl Acad Sci U S A 116 17611-17613 (2019)
  17. Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP. Lopez-Redondo M, Fan S, Koide A, Koide S, Beckstein O, Stokes DL. J Gen Physiol 153 e202112873 (2021)
  18. A cocktail of protective antibodies subverts the dense glycan shield of Lassa virus. Li H, Buck T, Zandonatti M, Yin J, Moon-Walker A, Fang J, Koval A, Heinrich ML, Rowland MM, Diaz Avalos R, Schendel SL, Parekh D, Zyla D, Enriquez A, Harkins S, Sullivan B, Smith V, Chukwudozie O, Watanabe R, Robinson JE, Garry RF, Branco LM, Hastie KM, Saphire EO. Sci Transl Med 14 eabq0991 (2022)
  19. Crystal structure of the Fab region of a neutralizing antibody against granulocyte-macrophage colony-stimulating factor. Angkawidjaja C, Torashima T. Acta Crystallogr F Struct Biol Commun 75 634-639 (2019)
  20. Development of a VRC01-class germline targeting immunogen derived from anti-idiotypic antibodies. Seydoux E, Wan YH, Feng J, Wall A, Aljedani S, Homad LJ, MacCamy AJ, Weidle C, Gray MD, Brumage L, Taylor JJ, Pancera M, Stamatatos L, McGuire AT. Cell Rep 35 109084 (2021)
  21. Fragment antigen binding domains (Fabs) as tools to study assembly-line polyketide synthases. Guzman KM, Khosla C. Synth Syst Biotechnol 7 506-512 (2022)
  22. Quaternary structure independent folding of voltage-gated ion channel pore domain subunits. Arrigoni C, Lolicato M, Shaya D, Rohaim A, Findeisen F, Fong LK, Colleran CM, Dominik P, Kim SS, Schuermann JP, DeGrado WF, Grabe M, Kossiakoff AA, Minor DL. Nat Struct Mol Biol 29 537-548 (2022)
  23. Rapid Discovery and Characterization of Synthetic Neutralizing Antibodies against Anthrax Edema Toxin. Farcasanu M, Wang AG, Uchański T, Bailey LJ, Yue J, Chen Z, Wu X, Kossiakoff A, Tang WJ. Biochemistry 58 2996-3004 (2019)
  24. Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA. Erramilli SK, Dominik PK, Deneka D, Tokarz P, Kim SS, Reddy BG, Skrobek BM, Dalmas O, Perozo E, Kossiakoff AA. J Mol Biol 435 168192 (2023)
  25. Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes. Bruce HA, Singer AU, Filippova EV, Blazer LL, Adams JJ, Enderle L, Ben-David M, Radley EH, Mao DYL, Pau V, Orlicky S, Sicheri F, Kurinov I, Atwell S, Kossiakoff AA, Sidhu SS. Protein Sci 33 e4824 (2024)


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