De Novo Design of a Hyperstable Non-natural Protein-ligand Complex with Sub-Å Accuracy

Overview

Journal Nat Chem

Specialty Chemistry

Date 2017 Nov 24

PMID 29168496

Citations 50

Authors

Nicholas F Polizzi

Yibing Wu

Thomas Lemmin

Alison M Maxwell

Shao-Qing Zhang

Jeff Rawson

David N Beratan

Michael J Therien

William F DeGrado

Affiliations

Soon will be listed here.

Abstract

Protein catalysis requires the atomic-level orchestration of side chains, substrates and cofactors, and yet the ability to design a small-molecule-binding protein entirely from first principles with a precisely predetermined structure has not been demonstrated. Here we report the design of a novel protein, PS1, that binds a highly electron-deficient non-natural porphyrin at temperatures up to 100 °C. The high-resolution structure of holo-PS1 is in sub-Å agreement with the design. The structure of apo-PS1 retains the remote core packing of the holoprotein, with a flexible binding region that is predisposed to ligand binding with the desired geometry. Our results illustrate the unification of core packing and binding-site definition as a central principle of ligand-binding protein design.

Citing Articles

Emergence of binding and catalysis from a designed generalist binding protein.

Chen Y, Bhattacharya S, Bergmann L, Correy G, Tan S, Hou K bioRxiv. 2025; .

PMID: 39975260 PMC: 11838529. DOI: 10.1101/2025.01.30.635804.

De novo design of transmembrane fluorescence-activating proteins.

Zhu J, Liang M, Sun K, Wei Y, Guo R, Zhang L Nature. 2025; .

PMID: 39972138 DOI: 10.1038/s41586-025-08598-8.

Design of a light and Ca switchable organic-peptide hybrid.

Khaleel Z, No Y, Kim N, Bae D, Wu Y, Kim S Proc Natl Acad Sci U S A. 2025; 122(5):e2411316122.

PMID: 39883844 PMC: 11804555. DOI: 10.1073/pnas.2411316122.

Confinement and Catalysis within Designed Peptide Barrels.

Petrenas R, Hawkins O, Jones J, Scott D, Fletcher J, Obst U J Am Chem Soc. 2025; 147(4):3796-3803.

PMID: 39813445 PMC: 11783595. DOI: 10.1021/jacs.4c16633.

A de novo designed coiled coil-based switch regulates the microtubule motor kinesin-1.

Cross J, Dawson W, Shukla S, Weijman J, Mantell J, Dodding M Nat Chem Biol. 2024; 20(7):916-923.

PMID: 38849529 PMC: 11213707. DOI: 10.1038/s41589-024-01640-2.

References

Huang P, Boyken S, Baker D . The coming of age of de novo protein design. Nature. 2016; 537(7620):320-7. DOI: 10.1038/nature19946. View

Rubtsov I, Susumu K, Rubtsov G, Therien M . Ultrafast singlet excited-state polarization in electronically asymmetric ethyne-bridged bis[(porphinato)zinc(II)] complexes. J Am Chem Soc. 2003; 125(9):2687-96. DOI: 10.1021/ja021157p. View

Peacock A . Incorporating metals into de novo proteins. Curr Opin Chem Biol. 2013; 17(6):934-9. DOI: 10.1016/j.cbpa.2013.10.015. View

Cornilescu G, Delaglio F, Bax A . Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR. 1999; 13(3):289-302. DOI: 10.1023/a:1008392405740. View

Guntert P, Mumenthaler C, Wuthrich K . Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol. 1997; 273(1):283-98. DOI: 10.1006/jmbi.1997.1284. View

Friedland G, Lakomek N, Griesinger C, Meiler J, Kortemme T . A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol. 2009; 5(5):e1000393. PMC: 2682763. DOI: 10.1371/journal.pcbi.1000393. View

Lombardi A, NASTRI F, Pavone V . Peptide-based heme-protein models. Chem Rev. 2001; 101(10):3165-89. DOI: 10.1021/cr000055j. View

Koulechova D, Tripp K, Horner G, Marqusee S . When the Scaffold Cannot Be Ignored: The Role of the Hydrophobic Core in Ligand Binding and Specificity. J Mol Biol. 2015; 427(20):3316-3326. PMC: 4938156. DOI: 10.1016/j.jmb.2015.08.014. View

Reedy C, Gibney B . Heme protein assemblies. Chem Rev. 2004; 104(2):617-49. DOI: 10.1021/cr0206115. View

10.

Sela-Culang I, Kunik V, Ofran Y . The structural basis of antibody-antigen recognition. Front Immunol. 2013; 4:302. PMC: 3792396. DOI: 10.3389/fimmu.2013.00302. View

11.

Schwieters C, Kuszewski J, Tjandra N, Clore G . The Xplor-NIH NMR molecular structure determination package. J Magn Reson. 2003; 160(1):65-73. DOI: 10.1016/s1090-7807(02)00014-9. View

12.

Kuhlman B, Dantas G, Ireton G, Varani G, Stoddard B, Baker D . Design of a novel globular protein fold with atomic-level accuracy. Science. 2003; 302(5649):1364-8. DOI: 10.1126/science.1089427. View

13.

North B, Summa C, Ghirlanda G, Degrado W . D(n)-symmetrical tertiary templates for the design of tubular proteins. J Mol Biol. 2001; 311(5):1081-90. DOI: 10.1006/jmbi.2001.4900. View

14.

Bender G, Lehmann A, Zou H, Cheng H, Fry H, Engel D . De novo design of a single-chain diphenylporphyrin metalloprotein. J Am Chem Soc. 2007; 129(35):10732-40. PMC: 2542652. DOI: 10.1021/ja071199j. View

15.

Bollen Y, Westphal A, Lindhoud S, van Berkel W, van Mierlo C . Distant residues mediate picomolar binding affinity of a protein cofactor. Nat Commun. 2012; 3:1010. PMC: 3432467. DOI: 10.1038/ncomms2010. View

16.

Woolfson D, Bartlett G, Burton A, Heal J, Niitsu A, Thomson A . De novo protein design: how do we expand into the universe of possible protein structures?. Curr Opin Struct Biol. 2015; 33:16-26. DOI: 10.1016/j.sbi.2015.05.009. View

17.

Ulas G, Lemmin T, Wu Y, Gassner G, DeGrado W . Designed metalloprotein stabilizes a semiquinone radical. Nat Chem. 2016; 8(4):354-9. PMC: 4857601. DOI: 10.1038/nchem.2453. View

18.

Prier C, Arnold F . Chemomimetic biocatalysis: exploiting the synthetic potential of cofactor-dependent enzymes to create new catalysts. J Am Chem Soc. 2015; 137(44):13992-4006. DOI: 10.1021/jacs.5b09348. View

19.

Thomson A, Wood C, Burton A, Bartlett G, Sessions R, Brady R . Computational design of water-soluble α-helical barrels. Science. 2014; 346(6208):485-8. DOI: 10.1126/science.1257452. View

20.

Fry H, Lehmann A, Saven J, DeGrado W, Therien M . Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological (porphinato)zinc chromophore. J Am Chem Soc. 2010; 132(11):3997-4005. PMC: 2856663. DOI: 10.1021/ja907407m. View