Protein rethreading: A novel approach to protein design

Agah, Sayeh; Poulos, Sandra; Yu, Austin; Kucharska, Iga; Faham, Salem

doi:10.1038/srep26847

Title: Protein rethreading: A novel approach to protein design

Journal Article · Fri May 27 00:00:00 EDT 2016 · Scientific Reports

DOI:https://doi.org/10.1038/srep26847· OSTI ID:1256349

Agah, Sayeh ^[1]; Poulos, Sandra ^[1]; Yu, Austin ^[1]; Kucharska, Iga ^[1]; Faham, Salem ^[1]

Univ. of Virginia School of Medicine, Charlottesville, VA (United States)

Protein engineering is an important tool for the design of proteins with novel and desirable features. Templates from the protein databank (PDB) are often used as initial models that can be modified to introduce new properties. We examine whether it is possible to reconnect a protein in a manner that generates a new topology yet preserves its structural integrity. Here, we describe the rethreading of dihydrofolate reductase (DHFR) from E. coli (wtDHFR). The rethreading process involved the removal of three native loops and the introduction of three new loops with alternate connections. The structure of the rethreaded DHFR (rDHFR-1) was determined to 1.6 Å, demonstrating the success of the rethreading process. Both wtDHFR and rDHFR-1 exhibited similar affinities towards methotrexate. However, rDHFR-1 showed no reducing activity towards dihydrofolate and exhibited about ~6-fold lower affinity towards NADPH than wtDHFR. This work demonstrates that protein rethreading can be a powerful tool for the design of a large array of proteins with novel structures and topologies and that by careful rearrangement of a protein sequence, the sequence to structure relationship can be expanded substantially.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

OSTI ID:: 1256349

Journal Information:: Scientific Reports, Vol. 6, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 3 works

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References (45)

Engineering strictosidine synthase: Rational design of a small, focused circular permutation library of the β-propeller fold enzyme Fischereder, Eva; Pressnitz, Desiree; Kroutil, Wolfgang Bioorganic & Medicinal Chemistry, Vol. 22, Issue 20 https://doi.org/10.1016/j.bmc.2014.06.023	journal	October 2014
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/S0907444996012255	journal	May 1997
Novel protein folds and their nonsequential structural analogs Guerler, Aysam; Knapp, Ernst-Walter Protein Science, Vol. 17, Issue 8 https://doi.org/10.1110/ps.035469.108	journal	August 2008
Accurate design of co-assembling multi-component protein nanomaterials King, Neil P.; Bale, Jacob B.; Sheffler, William Nature, Vol. 510, Issue 7503 https://doi.org/10.1038/nature13404	journal	May 2014
A multiple-template approach to protein threading Peng, Jian; Xu, Jinbo Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue 6 https://doi.org/10.1002/prot.23016	journal	April 2011
Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding Bystroff, Christopher; Kraut, Joseph Biochemistry, Vol. 30, Issue 8 https://doi.org/10.1021/bi00222a028	journal	February 1991
Dali server: conservation mapping in 3D Holm, Liisa; Rosenstrï¿½m, Pï¿½ivi Nucleic Acids Research, Vol. 38, Issue suppl_2 https://doi.org/10.1093/nar/gkq366	journal	May 2010
Raptorx: Exploiting structure information for protein alignment by statistical inference Peng, Jian; Xu, Jinbo Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue S10 https://doi.org/10.1002/prot.23175	journal	January 2011
A method to identify protein sequences that fold into a known three-dimensional structure Bowie, J.; Luthy, R.; Eisenberg, D. Science, Vol. 253, Issue 5016 https://doi.org/10.1126/science.1853201	journal	July 1991
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information Wu, Sitao; Zhang, Yang Proteins: Structure, Function, and Bioinformatics, Vol. 72, Issue 2 https://doi.org/10.1002/prot.21945	journal	February 2008
Circular permutation: a different way to engineer enzyme structure and function Yu, Ying; Lutz, Stefan Trends in Biotechnology, Vol. 29, Issue 1 https://doi.org/10.1016/j.tibtech.2010.10.004	journal	January 2011
Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate .cntdot. NADP+ ternary complex. substrate binding and a model for the transition state Bystroff, Christopher; Oatley, Stuart J.; Kraut, Joseph Biochemistry, Vol. 29, Issue 13 https://doi.org/10.1021/bi00465a018	journal	April 1990
Improved Biocatalysts from a Synthetic Circular Permutation Library of the Flavin-Dependent Oxidoreductase Old Yellow Enzyme Daugherty, Ashley B.; Govindarajan, Sridhar; Lutz, Stefan Journal of the American Chemical Society, Vol. 135, Issue 38 https://doi.org/10.1021/ja4074886	journal	September 2013
Circular permutation of T4 lysozyme Zhang, Tao; Bertelsen, Eric; Benvegnu, Dominic Biochemistry, Vol. 32, Issue 46 https://doi.org/10.1021/bi00097a006	journal	November 1993
Circular permutation of E. coli EPSP synthase: increased inhibitor resistance, improved catalytic activity, and an indicator for protein fragment complementation Dai, Xiongfeng; Zhu, Manlu; Wang, Yi-Ping Chem. Commun., Vol. 50, Issue 15 https://doi.org/10.1039/C3CC48722A	journal	January 2014
Structure and dynamics in solution of the complex of lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate Polshakov, Vladimir I.; Birdsall, Berry; Frenkiel, Thomas A. Protein Science, Vol. 8, Issue 3 https://doi.org/10.1110/ps.8.3.467	journal	January 1999
Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase Liu, C. Tony; Layfield, Joshua P.; Stewart, Robert J. Journal of the American Chemical Society, Vol. 136, Issue 29 https://doi.org/10.1021/ja5038947	journal	July 2014
I-TASSER server for protein 3D structure prediction Zhang, Yang BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-40	journal	January 2008
Protein design by fusion: implications for protein structure prediction and evolution Skorupka, Katarzyna; Han, Seong Kyu; Nam, Hyun-Jun Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 12 https://doi.org/10.1107/S0907444913022701	journal	November 2013
Protein structure prediction on the Web: a case study using the Phyre server Kelley, Lawrence A.; Sternberg, Michael J. E. Nature Protocols, Vol. 4, Issue 3 https://doi.org/10.1038/nprot.2009.2	journal	February 2009
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy Kuhlman, Brian; Dantas, Gautam; Ireton, Gregory C. Science, Vol. 302, Issue 5649 https://doi.org/10.1126/science.1089427	journal	November 2003
Tying up the loose ends: circular permutation decreases the proteolytic susceptibility of recombinant proteins Whitehead, T. A.; Bergeron, L. M.; Clark, D. S. Protein Engineering Design and Selection, Vol. 22, Issue 10 https://doi.org/10.1093/protein/gzp034	journal	July 2009
Loop and Subdomain Movements in the Mechanism of Escherichia coli Dihydrofolate Reductase: Crystallographic Evidence ^† ^, ^‡ Sawaya, Michael R.; Kraut, Joseph Biochemistry, Vol. 36, Issue 3 https://doi.org/10.1021/bi962337c	journal	January 1997
Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography Wan, Qun; Bennett, Brad C.; Wilson, Mark A. Proceedings of the National Academy of Sciences, Vol. 111, Issue 51 https://doi.org/10.1073/pnas.1415856111	journal	December 2014
Protein structure prediction and analysis using the Robetta server Kim, D. E.; Chivian, D.; Baker, D. Nucleic Acids Research, Vol. 32, Issue Web Server https://doi.org/10.1093/nar/gkh468	journal	July 2004
Characterizing the Existing and Potential Structural Space of Proteins by Large-Scale Multiple Loop Permutations Dai, Liang; Zhou, Yaoqi Journal of Molecular Biology, Vol. 408, Issue 3 https://doi.org/10.1016/j.jmb.2011.02.056	journal	May 2011
Decoy Models for Protein Structure Comparison Score Normalisation Taylor, William R. Journal of Molecular Biology, Vol. 357, Issue 2 https://doi.org/10.1016/j.jmb.2005.12.084	journal	March 2006
Computational Design of Enzymes Sterner, Reinhard; Merkl, Rainer; Raushel, Frank M. Chemistry & Biology, Vol. 15, Issue 5 https://doi.org/10.1016/j.chembiol.2008.04.007	journal	May 2008
Protein design: Past, present, and future: Protein Design: Past, Present, and Future Regan, Lynne; Caballero, Diego; Hinrichsen, Michael R. Biopolymers, Vol. 104, Issue 4 https://doi.org/10.1002/bip.22639	journal	July 2015
Circular Permutation in the Ω-Loop of TEM-1 β-Lactamase Results in Improved Activity and Altered Substrate Specificity Guntas, Gurkan; Kanwar, Manu; Ostermeier, Marc PLoS ONE, Vol. 7, Issue 4 https://doi.org/10.1371/journal.pone.0035998	journal	April 2012
Improving the Catalytic Activity of Candida antarctica Lipase B by Circular Permutation Qian, Zhen; Lutz, Stefan Journal of the American Chemical Society, Vol. 127, Issue 39 https://doi.org/10.1021/ja053932h	journal	October 2005
Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces Gonen, S.; DiMaio, F.; Gonen, T. Science, Vol. 348, Issue 6241 https://doi.org/10.1126/science.aaa9897	journal	June 2015
TopDraw: a sketchpad for protein structure topology cartoons Bond, C. S. Bioinformatics, Vol. 19, Issue 2 https://doi.org/10.1093/bioinformatics/19.2.311	journal	January 2003
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/s0907444910007493	journal	March 2010
2D protein lattices by design Doerr, Allison Nature Methods, Vol. 12, Issue 8 https://doi.org/10.1038/nmeth.3513	journal	July 2015
De Novo Protein Design: Fully Automated Sequence Selection Dahiyat, Bassil I.; Mayo, Stephen L. Science, Vol. 278, Issue 5335 https://doi.org/10.1126/science.278.5335.82	journal	October 1997
Circular permutation and receptor insertion within green fluorescent proteins Baird, G. S.; Zacharias, D. A.; Tsien, R. Y. Proceedings of the National Academy of Sciences, Vol. 96, Issue 20 https://doi.org/10.1073/pnas.96.20.11241	journal	September 1999
A 2.13 Å Structure of E. coli Dihydrofolate Reductase Bound to a Novel Competitive Inhibitor Reveals a New Binding Surface Involving the M20 Loop Region Summerfield, Rachael L.; Daigle, Denis M.; Mayer, Stanislas Journal of Medicinal Chemistry, Vol. 49, Issue 24 https://doi.org/10.1021/jm060570v	journal	November 2006
De novo design of a transmembrane Zn ²⁺ -transporting four-helix bundle Joh, Nathan H.; Wang, Tuo; Bhate, Manasi P. Science, Vol. 346, Issue 6216 https://doi.org/10.1126/science.1261172	journal	December 2014
De Novo Computational Design of Retro-Aldol Enzymes Jiang, L.; Althoff, E. A.; Clemente, F. R. Science, Vol. 319, Issue 5868 https://doi.org/10.1126/science.1152692	journal	March 2008
Automated prediction of CASP-5 structures using the Robetta server Chivian, Dylan; Kim, David E.; Malmstr�m, Lars Proteins: Structure, Function, and Genetics, Vol. 53, Issue S6 https://doi.org/10.1002/prot.10529	journal	January 2003
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Proteins from Scratch DeGrado, William F. Science, Vol. 278, Issue 5335 https://doi.org/10.1126/science.278.5335.80	journal	October 1997
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Computational protein design enables a novel one-carbon assimilation pathway Siegel, Justin B.; Smith, Amanda Lee; Poust, Sean Proceedings of the National Academy of Sciences https://doi.org/10.1073/pnas.1500545112	journal	March 2015

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