Home LiteratureArticle Details
PMID: 18927392 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Surface sites for engineering allosteric control in proteins.

Science (New York, N.Y.) ·Vol. 322 ·No. 5900 ·2008-10-17 ·Pages 438-42

Lee J, Natarajan M, Nashine VC, Socolich M, Vo T, Russ WP, Benkovic SJ, Ranganathan R

Abstract

Statistical analyses of protein families reveal networks of coevolving amino acids that functionally link distantly positioned functional surfaces. Such linkages suggest a concept for engineering allosteric control into proteins: The intramolecular networks of two proteins could be joined across their surface sites such that the activity of one protein might control the activity of the other. We tested this idea by creating PAS-DHFR, a designed chimeric protein that connects a light-sensing signaling domain from a plant member of the Per/Arnt/Sim (PAS) family of proteins with Escherichia coli dihydrofolate reductase (DHFR). With no optimization, PAS-DHFR exhibited light-dependent catalytic activity that depended on the site of connection and on known signaling mechanisms in both proteins. PAS-DHFR serves as a proof of concept for engineering regulatory activities into proteins through interface design at conserved allosteric sites.

MeSH Terms
Allosteric Regulation Allosteric Site Binding Sites Catalysis Cryptochromes Escherichia coli/enzymology Flavoproteins/chemistry,metabolism Kinetics Ligands Light Models, Molecular NADP/metabolism Protein Conformation Protein Engineering Protein Structure, Secondary Protein Structure, Tertiary Recombinant Fusion Proteins/chemistry,metabolism Tetrahydrofolate Dehydrogenase/chemistry,metabolism
Chemicals
Cryptochromes Flavoproteins Ligands Recombinant Fusion Proteins NADP Tetrahydrofolate Dehydrogenase
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Lee Jeeyeon
Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
Natarajan Madhusudan
Nashine Vishal C
Socolich Michael
Vo Tina
Russ William P
Benkovic Stephen J
Ranganathan Rama
References (35)
35 references, click to expand
  1. Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity.
    Biochemistry. 2004 Dec 28;43(51):16184-92 PMID: 15610012
  2. Structural basis of a phototropin light switch.
    Science. 2003 Sep 12;301(5639):1541-4 PMID: 12970567
  3. Structural determinants of allosteric ligand activation in RXR heterodimers.
    Cell. 2004 Feb 6;116(3):417-29 PMID: 15016376
  4. Relating protein motion to catalysis.
    Annu Rev Biochem. 2006;75:519-41 PMID: 16756501
  5. The packing density in proteins: standard radii and volumes.
    J Mol Biol. 1999 Jul 2;290(1):253-66 PMID: 10388571
  6. Signal transduction pathway of TonB-dependent transporters.
    Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):513-8 PMID: 17197416
  7. The linkage between protein folding and functional cooperativity: two sides of the same coin?
    Annu Rev Biophys Biomol Struct. 2002;31:235-56 PMID: 11988469
  8. Estimation of the available free energy in a LOV2-J alpha photoswitch.
    Nat Chem Biol. 2008 Aug;4(8):491-7 PMID: 18604202
  9. Probing the functional role of phenylalanine-31 of Escherichia coli dihydrofolate reductase by site-directed mutagenesis.
    Biochemistry. 1987 Jun 30;26(13):4093-100 PMID: 3307917
  10. The PAS superfamily: sensors of environmental and developmental signals.
    Annu Rev Pharmacol Toxicol. 2000;40:519-61 PMID: 10836146
  11. Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity protein, Par6.
    EMBO J. 2003 Mar 3;22(5):1125-33 PMID: 12606577
  12. The origin of protein interactions and allostery in colocalization.
    Nature. 2007 Dec 13;450(7172):983-90 PMID: 18075577
  13. An analysis of packing in the protein folding problem.
    Q Rev Biophys. 1993 Nov;26(4):423-98 PMID: 8058892
  14. FamClash: a method for ranking the activity of engineered enzymes.
    Proc Natl Acad Sci U S A. 2004 Mar 23;101(12):4142-7 PMID: 14981242
  15. A perspective on enzyme catalysis.
    Science. 2003 Aug 29;301(5637):1196-202 PMID: 12947189
  16. Structural basis for PAS domain heterodimerization in the basic helix--loop--helix-PAS transcription factor hypoxia-inducible factor.
    Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15504-9 PMID: 14668441
  17. Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition.
    Mol Cell. 2004 Mar 12;13(5):665-76 PMID: 15023337
  18. Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant.
    Biochemistry. 1997 Dec 16;36(50):15792-800 PMID: 9398309
  19. Evolutionarily conserved networks of residues mediate allosteric communication in proteins.
    Nat Struct Biol. 2003 Jan;10(1):59-69 PMID: 12483203
  20. Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli.
    Biochemistry. 1987 Jun 30;26(13):4085-92 PMID: 3307916
  21. Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence.
    Biochemistry. 1997 Jan 21;36(3):586-603 PMID: 9012674
  22. N- and C-terminal flanking regions modulate light-induced signal transduction in the LOV2 domain of the blue light sensor phototropin 1 from Avena sativa.
    Biochemistry. 2007 Dec 11;46(49):14001-9 PMID: 18001137
  23. The changing landscape of protein allostery.
    Curr Opin Struct Biol. 2006 Feb;16(1):102-8 PMID: 16423525
  24. Dynamic personalities of proteins.
    Nature. 2007 Dec 13;450(7172):964-72 PMID: 18075575
  25. Phototropin LOV domains exhibit distinct roles in regulating photoreceptor function.
    Plant J. 2002 Oct;32(2):205-19 PMID: 12383086
  26. Preorganization and protein dynamics in enzyme catalysis.
    Chem Rec. 2002;2(1):24-36 PMID: 11933259
  27. Allosteric determinants in guanine nucleotide-binding proteins.
    Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14445-50 PMID: 14623969
  28. Dynamics of the dihydrofolate reductase-folate complex: catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features.
    Biochemistry. 1995 Sep 5;34(35):11037-48 PMID: 7669761
  29. An optomechanical transducer in the blue light receptor phototropin from Avena sativa.
    Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12357-61 PMID: 11606742
  30. Evolutionarily conserved pathways of energetic connectivity in protein families.
    Science. 1999 Oct 8;286(5438):295-9 PMID: 10514373
  31. Photochemical and mutational analysis of the FMN-binding domains of the plant blue light receptor, phototropin.
    Biochemistry. 2000 Aug 8;39(31):9401-10 PMID: 10924135
  32. Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism.
    Biochemistry. 2003 May 6;42(17):4759-70 PMID: 12718516
  33. PAS domains: internal sensors of oxygen, redox potential, and light.
    Microbiol Mol Biol Rev. 1999 Jun;63(2):479-506 PMID: 10357859
  34. LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): binding sites for the chromophore flavin mononucleotide.
    Proc Natl Acad Sci U S A. 1999 Jul 20;96(15):8779-83 PMID: 10411952
  35. PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry.
    J Mol Biol. 2006 Oct 13;363(1):148-60 PMID: 16952373
Article Info
Journal
Science (New York, N.Y.)
Abbr.
Science
ISSN
1095-9203
DOI
10.1126/science.1159052
Published
2008-10-17
Pages
438-42
Language
English
Region
United States
NLM ID
0404511
PMCID
PMC3071530
Subset
IM
Grants
NEI NIH HHS · R01 EY018720 · United States
NEI NIH HHS · R01 EY018720-01 · United States
NEI NIH HHS · R01 EY018720-02 · United States
NEI NIH HHS · R01 EY018720-03 · United States
External Links
PubMed source DOI: 10.1126/science.1159052 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2