Potential of fragment recombination for rational design of proteins

Journal of the American Chemical Society
Simone EisenbeisBirte Höcker

Abstract

It is hypothesized that protein domains evolved from smaller intrinsically stable subunits via combinatorial assembly. Illegitimate recombination of fragments that encode protein subunits could have quickly led to diversification of protein folds and their functionality. This evolutionary concept presents an attractive strategy to protein engineering, e.g., to create new scaffolds for enzyme design. We previously combined structurally similar parts from two ancient protein folds, the (βα)(8)-barrel and the flavodoxin-like fold. The resulting "hopeful monster" differed significantly from the intended (βα)(8)-barrel fold by an extra β-strand in the core. In this study, we ask what modifications are necessary to form the intended structure and what potential this approach has for the rational design of functional proteins. Guided by computational design, we optimized the interface between the fragments with five targeted mutations yielding a stable, monomeric protein whose predicted structure was verified experimentally. We further tested binding of a phosphorylated compound and detected that some affinity was already present due to an intact phosphate-binding site provided by one fragment. The affinity could be improved quickly t...Continue Reading

References

Dec 5, 1993·Journal of Molecular Biology·A Sali, T L Blundell
Jan 3, 2001·Nature Structural Biology·B HöckerR Sterner
Sep 12, 2001·Journal of Structural Biology·N V Grishin
Jan 22, 2002·FEBS Letters·Birte HöckerReinhard Sterner
Jan 2, 2003·Nature Reviews. Genetics·Michael R Dietrich
Aug 26, 2003·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Johannes Söding, Andrei N Lupas
Apr 6, 2004·Methods in Enzymology·Carol A RohlDavid Baker
Nov 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Birte HöckerReinhard Sterner
Nov 10, 2005·Chemical Reviews·Reinhard Sterner, Birte Höcker
May 15, 1940·Proceedings of the National Academy of Sciences of the United States of America·M CalvinR Goldschmidt
May 23, 2007·Proceedings of the National Academy of Sciences of the United States of America·Gustavo Caetano-AnollésJay E Mittenthal
Jul 17, 2007·Journal of Molecular Biology·Tobias SeitzReinhard Sterner
Jul 18, 2008·Proceedings of the National Academy of Sciences of the United States of America·Tanmay A M BharatBirte Höcker
Feb 25, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jörg ClarenReinhard Sterner
Dec 3, 2010·Nature Chemistry·Vikas Nanda, Ronald L Koder
May 24, 2011·PloS One·Florian RichterDavid Baker
Oct 8, 2011·Journal of the American Chemical Society·Carie FortenberryJens Meiler

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Citations

Nov 9, 2012·Nature·Nobuyasu KogaDavid Baker
Oct 20, 2012·Protein Engineering, Design & Selection : PEDS·Sooruban ShanmugaratnamBirte Höcker
Jul 21, 2014·Nature Chemical Biology·José Arcadio Farías-RicoBirte Höcker
Jul 17, 2012·Trends in Biotechnology·Agathe UrvoasPhilippe Minard
Feb 12, 2015·Journal of Biomolecular Structure & Dynamics·Taushif Khan, Indira Ghosh
May 28, 2015·Cellular and Molecular Life Sciences : CMLS·Saligram Prabhakar BhargavInari Kursula
Aug 13, 2015·BMC Biochemistry·Deepesh NagarajanMegha Rao
Nov 5, 2013·Current Opinion in Chemical Biology·Devin L TrudeauFrances H Arnold
Sep 26, 2013·Biochemical Society Transactions·Birte Höcker
May 23, 2015·Chemistry & Biology·Hajo KriesDonald Hilvert
May 29, 2014·Current Opinion in Structural Biology·Birte Höcker
Oct 8, 2014·Proceedings of the National Academy of Sciences of the United States of America·Arnout R D VoetJeremy R H Tame
May 18, 2016·Journal of Structural Biology·Maximiliano FigueroaCécile Van de Weerdt
Jun 9, 2016·Current Opinion in Structural Biology·Aron BroomElizabeth M Meiering
Jan 30, 2016·Protein Science : a Publication of the Protein Society·Olga Khersonsky, Sarel J Fleishman
Nov 2, 2017·Protein Science : a Publication of the Protein Society·Amanda M Duran, Jens Meiler
Jul 19, 2018·Nature Communications·Gideon LapidothSarel J Fleishman
Jan 17, 2021·Current Opinion in Structural Biology·Sergio Romero-RomeroBirte Höcker
Jan 28, 2021·Molecular Biology and Evolution·Rachel KolodnyNir Ben-Tal
Apr 25, 2020·Journal of Molecular Biology·Noelia FerruzBirte Höcker
May 3, 2021·Protein Science : a Publication of the Protein Society·José M PereiraSérgio M Santos
Apr 27, 2021·Bioinformatics·Noelia FerruzBirte Höcker
Jul 25, 2019·Current Opinion in Chemical Biology·William M DawsonDerek N Woolfson

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