Light-activated DNA Binding in a Designed Allosteric Protein

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2008 Aug 1

PMID 18667691

Citations 137

Authors

Devin Strickland

Keith Moffat

Tobin R Sosnick

Affiliations

Soon will be listed here.

Abstract

An understanding of how allostery, the conformational coupling of distant functional sites, arises in highly evolvable systems is of considerable interest in areas ranging from cell biology to protein design and signaling networks. We reasoned that the rigidity and defined geometry of an alpha-helical domain linker would make it effective as a conduit for allosteric signals. To test this idea, we rationally designed 12 fusions between the naturally photoactive LOV2 domain from Avena sativa phototropin 1 and the Escherichia coli trp repressor. When illuminated, one of the fusions selectively binds operator DNA and protects it from nuclease digestion. The ready success of our rational design strategy suggests that the helical "allosteric lever arm" is a general scheme for coupling the function of two proteins.

Citing Articles

Seesaw protein: Design of a protein that adopts interconvertible alternative functional conformations and its dynamics.

Ikeda T, Nojima T, Yamamoto S, Yamada R, Niwa T, Konno H Proc Natl Acad Sci U S A. 2025; 122(7):e2412117122.

PMID: 39928865 PMC: 11848303. DOI: 10.1073/pnas.2412117122.

Autonomous Nucleic Acid and Protein Nanocomputing Agents Engineered to Operate in Living Cells.

Panigaj M, Basu Roy T, Skelly E, Chandler M, Wang J, Ekambaram S ACS Nano. 2025; 19(2):1865-1883.

PMID: 39760461 PMC: 11757000. DOI: 10.1021/acsnano.4c13663.

SignatureFinder enables sequence mining to identify cobalamin-dependent photoreceptor proteins.

Yu Y, Jeffreys L, Poddar H, Hill A, Johannissen L, Dai F FEBS J. 2024; 292(3):635-652.

PMID: 39718193 PMC: 11796333. DOI: 10.1111/febs.17377.

A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery.

Liu Z, Gillis T, Raman S, Cui Q Elife. 2024; 12.

PMID: 38836839 PMC: 11152574. DOI: 10.7554/eLife.92262.

β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini.

Xiao S, Tarek Ibrahim M, Verkhivker G, Zoltowski B, Tao P J Comput Chem. 2024; 45(17):1493-1504.

PMID: 38476039 PMC: 11076166. DOI: 10.1002/jcc.27344.

References

Reedstrom R, Martin K, Vangala S, Mahoney S, Wilker E, ROYER C . Characterization of charge change super-repressor mutants of trp repressor: effects on oligomerization conformation, ligation and stability. J Mol Biol. 1996; 264(1):32-45. DOI: 10.1006/jmbi.1996.0621. View

Hellingwerf K . The molecular basis of sensing and responding to light in microorganisms. Antonie Van Leeuwenhoek. 2002; 81(1-4):51-9. DOI: 10.1023/a:1020521424582. View

Hilser V, Thompson E . Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins. Proc Natl Acad Sci U S A. 2007; 104(20):8311-5. PMC: 1895946. DOI: 10.1073/pnas.0700329104. View

Svergun D . Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J. 1999; 76(6):2879-86. PMC: 1300260. DOI: 10.1016/S0006-3495(99)77443-6. View

Gunsalus R, Yanofsky C . Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor. Proc Natl Acad Sci U S A. 1980; 77(12):7117-21. PMC: 350452. DOI: 10.1073/pnas.77.12.7117. View

Bhattacharyya R, Remenyi A, Yeh B, Lim W . Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem. 2006; 75:655-80. DOI: 10.1146/annurev.biochem.75.103004.142710. View

Radley T, Markowska A, Bettinger B, Ha J, Loh S . Allosteric switching by mutually exclusive folding of protein domains. J Mol Biol. 2003; 332(3):529-36. PMC: 3145375. DOI: 10.1016/s0022-2836(03)00925-2. View

Baird G, Zacharias D, Tsien R . Circular permutation and receptor insertion within green fluorescent proteins. Proc Natl Acad Sci U S A. 1999; 96(20):11241-6. PMC: 18018. DOI: 10.1073/pnas.96.20.11241. View

Sallee N, Yeh B, Lim W . Engineering modular protein interaction switches by sequence overlap. J Am Chem Soc. 2007; 129(15):4606-11. DOI: 10.1021/ja0672728. View

10.

Shao X, HENSLEY P, Matthews C . Construction and characterization of monomeric tryptophan repressor: a model for an early intermediate in the folding of a dimeric protein. Biochemistry. 1997; 36(32):9941-9. DOI: 10.1021/bi9707786. View

11.

Corchnoy S, Swartz T, Lewis J, Szundi I, Briggs W, Bogomolni R . Intramolecular proton transfers and structural changes during the photocycle of the LOV2 domain of phototropin 1. J Biol Chem. 2002; 278(2):724-31. DOI: 10.1074/jbc.M209119200. View

12.

Crosson S, Rajagopal S, Moffat K . The LOV domain family: photoresponsive signaling modules coupled to diverse output domains. Biochemistry. 2003; 42(1):2-10. DOI: 10.1021/bi026978l. View

13.

Jha A, Colubri A, Zaman M, Koide S, Sosnick T, Freed K . Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry. 2005; 44(28):9691-702. DOI: 10.1021/bi0474822. View

14.

Pawson T, Linding R . Synthetic modular systems--reverse engineering of signal transduction. FEBS Lett. 2005; 579(8):1808-14. DOI: 10.1016/j.febslet.2005.02.013. View

15.

Volkman B, Lipson D, Wemmer D, Kern D . Two-state allosteric behavior in a single-domain signaling protein. Science. 2001; 291(5512):2429-33. DOI: 10.1126/science.291.5512.2429. View

16.

Pawson T, Nash P . Assembly of cell regulatory systems through protein interaction domains. Science. 2003; 300(5618):445-52. DOI: 10.1126/science.1083653. View

17.

Gunasekaran K, Ma B, Nussinov R . Is allostery an intrinsic property of all dynamic proteins?. Proteins. 2004; 57(3):433-43. DOI: 10.1002/prot.20232. View

18.

Guex N, Peitsch M . SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1998; 18(15):2714-23. DOI: 10.1002/elps.1150181505. View

19.

Zoltowski B, Schwerdtfeger C, Widom J, Loros J, Bilwes A, Dunlap J . Conformational switching in the fungal light sensor Vivid. Science. 2007; 316(5827):1054-7. PMC: 3682417. DOI: 10.1126/science.1137128. View

20.

Zhou Z, Feng H, Zhou H, Zhou Y, Bai Y . Design and folding of a multidomain protein. Biochemistry. 2005; 44(36):12107-12. DOI: 10.1021/bi050785r. View