Small Molecule-Induced Domain Swapping As a Mechanism for Controlling Protein Function and Assembly

Overview

Journal Sci Rep

Specialty Science

Date 2017 Mar 14

PMID 28287617

Citations 12

Authors

Joshua M Karchin

Jeung-Hoi Ha

Kevin E Namitz

Michael S Cosgrove

Stewart N Loh

Affiliations

Soon will be listed here.

Abstract

Domain swapping is the process by which identical proteins exchange reciprocal segments to generate dimers. Here we introduce induced domain swapping (INDOS) as a mechanism for regulating protein function. INDOS employs a modular design consisting of the fusion of two proteins: a recognition protein that binds a triggering molecule, and a target protein that undergoes a domain swap in response to binding of the triggering ligand. The recognition protein (FK506 binding protein) is inserted into functionally-inactivated point mutants of two target proteins (staphylococcal nuclease and ribose binding protein). Binding of FK506 to the FKBP domain causes the target domain to first unfold, then refold via domain swap. The inactivating mutations become 'swapped out' in the dimer, increasing nuclease and ribose binding activities by 100-fold and 15-fold, respectively, restoring them to near wild-type values. INDOS is intended to convert an arbitrary protein into a functional switch, and is the first example of rational design in which a small molecule is used to trigger protein domain swapping and subsequent activation of biological function.

Citing Articles

Enhancing response of a protein conformational switch by using two disordered ligand binding domains.

Sekhon H, Ha J, Loh S Front Mol Biosci. 2023; 10:1114756.

PMID: 36936990 PMC: 10018487. DOI: 10.3389/fmolb.2023.1114756.

Engineering protein and DNA tools for creating DNA-dependent protein switches.

Sekhon H, Ha J, Loh S Methods Enzymol. 2022; 675:1-32.

PMID: 36220266 PMC: 10314797. DOI: 10.1016/bs.mie.2022.07.002.

Redox- and metal-directed structural diversification in designed metalloprotein assemblies.

Kakkis A, Golub E, Choi T, Tezcan F Chem Commun (Camb). 2022; 58(49):6958-6961.

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Engineering protein activity into off-the-shelf DNA devices.

Sekhon H, Loh S Cell Rep Methods. 2022; 2(4):100202.

PMID: 35497497 PMC: 9046454. DOI: 10.1016/j.crmeth.2022.100202.

Protein Assembly by Design.

Zhu J, Avakyan N, Kakkis A, Hoffnagle A, Han K, Li Y Chem Rev. 2021; 121(22):13701-13796.

PMID: 34405992 PMC: 9148388. DOI: 10.1021/acs.chemrev.1c00308.

References

Ha J, Karchin J, Walker-Kopp N, Huang L, Berry E, Loh S . Engineering domain-swapped binding interfaces by mutually exclusive folding. J Mol Biol. 2012; 416(4):495-502. PMC: 3288482. DOI: 10.1016/j.jmb.2011.12.050. View

Vercillo N, Herald K, Fox J, Der B, Dattelbaum J . Analysis of ligand binding to a ribose biosensor using site-directed mutagenesis and fluorescence spectroscopy. Protein Sci. 2007; 16(3):362-8. PMC: 2203328. DOI: 10.1110/ps.062595707. View

Park C, Raines R . Dimer formation by a "monomeric" protein. Protein Sci. 2000; 9(10):2026-33. PMC: 2144461. DOI: 10.1110/ps.9.10.2026. View

Piccoli R, Di Gaetano S, De Lorenzo C, Grauso M, Monaco C, Spalletti-Cernia D . A dimeric mutant of human pancreatic ribonuclease with selective cytotoxicity toward malignant cells. Proc Natl Acad Sci U S A. 1999; 96(14):7768-73. PMC: 22136. DOI: 10.1073/pnas.96.14.7768. View

Cutler T, Loh S . Thermodynamic analysis of an antagonistic folding-unfolding equilibrium between two protein domains. J Mol Biol. 2007; 371(2):308-16. PMC: 2041865. DOI: 10.1016/j.jmb.2007.05.077. View

Liu Y, Eisenberg D . 3D domain swapping: as domains continue to swap. Protein Sci. 2002; 11(6):1285-99. PMC: 2373619. DOI: 10.1110/ps.0201402. View

Carey J, Lindman S, Bauer M, Linse S . Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency. Protein Sci. 2007; 16(11):2317-33. PMC: 2211703. DOI: 10.1110/ps.072985007. View

Jensson O, Gudmundsson G, Arnason A, BLONDAL H, Petursdottir I, Thorsteinsson L . Hereditary cystatin C (gamma-trace) amyloid angiopathy of the CNS causing cerebral hemorrhage. Acta Neurol Scand. 1987; 76(2):102-14. DOI: 10.1111/j.1600-0404.1987.tb03553.x. View

Stratton M, Mitrea D, Loh S . A Ca2+-sensing molecular switch based on alternate frame protein folding. ACS Chem Biol. 2008; 3(11):723-32. PMC: 2769504. DOI: 10.1021/cb800177f. View

10.

Ha J, Shinsky S, Loh S . Stepwise conversion of a binding protein to a fluorescent switch: application to Thermoanaerobacter tengcongensis ribose binding protein. Biochemistry. 2013; 52(4):600-12. PMC: 5966831. DOI: 10.1021/bi301105u. View

11.

Baker M, Hynson R, Ganuelas L, Shah Mohammadi N, Liew C, Rey A . Domain-swap polymerization drives the self-assembly of the bacterial flagellar motor. Nat Struct Mol Biol. 2016; 23(3):197-203. DOI: 10.1038/nsmb.3172. View

12.

Stratton M, Loh S . On the mechanism of protein fold-switching by a molecular sensor. Proteins. 2010; 78(16):3260-9. PMC: 3145374. DOI: 10.1002/prot.22833. View

13.

Thakur S, Cattoni D, Nollmann M . The fluorescence properties and binding mechanism of SYTOX green, a bright, low photo-damage DNA intercalating agent. Eur Biophys J. 2015; 44(5):337-48. DOI: 10.1007/s00249-015-1027-8. View

14.

Hafner-Bratkovic I, Bester R, Pristovsek P, Gaedtke L, Veranic P, Gaspersic J . Globular domain of the prion protein needs to be unlocked by domain swapping to support prion protein conversion. J Biol Chem. 2011; 286(14):12149-56. PMC: 3069419. DOI: 10.1074/jbc.M110.213926. View

15.

Nagarkar R, Hule R, Pochan D, Schneider J . Domain swapping in materials design. Biopolymers. 2010; 94(1):141-55. DOI: 10.1002/bip.21332. View

16.

Reis J, Burns D, Woolley G . Optical control of protein-protein interactions via blue light-induced domain swapping. Biochemistry. 2014; 53(30):5008-16. PMC: 4372075. DOI: 10.1021/bi500622x. View

17.

Hayashi Y, Yamanaka M, Nagao S, Komori H, Higuchi Y, Hirota S . Domain swapping oligomerization of thermostable c-type cytochrome in E. coli cells. Sci Rep. 2016; 6:19334. PMC: 4738263. DOI: 10.1038/srep19334. View

18.

Dwyer J, Gittis A, Lattman E, Spencer D, Stites W . Experimental measurement of the effective dielectric in the hydrophobic core of a protein. Biophys Chem. 1997; 64(1-3):211-24. DOI: 10.1016/s0301-4622(96)02238-7. View

19.

Brasch J, Harrison O, Honig B, Shapiro L . Thinking outside the cell: how cadherins drive adhesion. Trends Cell Biol. 2012; 22(6):299-310. PMC: 3385655. DOI: 10.1016/j.tcb.2012.03.004. View

20.

Meeker A, Shortle D . Contributions of the ionizable amino acids to the stability of staphylococcal nuclease. Biochemistry. 1996; 35(20):6443-9. DOI: 10.1021/bi960171+. View