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Science 317 (5844): 1544-1548

Copyright © 2007 by the American Association for the Advancement of Science

Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis

Eric A. Ortlund,1* Jamie T. Bridgham,2* Matthew R. Redinbo,1 Joseph W. Thornton2{dagger}

Abstract: The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein—the ~450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. "Permissive" mutations—substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes—played a major role in determining GR's evolutionary trajectory.

1 Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA.
2 Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403, USA.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: joet{at}

Strong Epistatic Interactions within a Single Protein.
M. Parera and M. A. Martinez (2014)
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   Abstract »    Full Text »    PDF »
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J. A. Holliday, T. Wang, and S. Aitken (2013)
g3 2, 1085-1093
   Abstract »    Full Text »    PDF »
Assessing constraints on the path of regulatory sequence evolution.
W. J. Glassford and M. Rebeiz (2013)
Phil Trans R Soc B 368, 20130026
   Abstract »    Full Text »    PDF »
Accounting for epistatic interactions improves the functional analysis of protein structures.
A. D. Wilkins, E. Venner, D. C. Marciano, S. Erdin, B. Atri, R. C. Lua, and O. Lichtarge (2013)
Bioinformatics 29, 2714-2721
   Abstract »    Full Text »    PDF »
Divergent Sequence Tunes Ligand Sensitivity in Phospholipid-regulated Hormone Receptors.
P. M. Musille, M. Pathak, J. L. Lauer, P. R. Griffin, and E. A. Ortlund (2013)
J. Biol. Chem. 288, 20702-20712
   Abstract »    Full Text »    PDF »
Experimental evidence for the thermophilicity of ancestral life.
S. Akanuma, Y. Nakajima, S.-i. Yokobori, M. Kimura, N. Nemoto, T. Mase, K.-i. Miyazono, M. Tanokura, and A. Yamagishi (2013)
PNAS 110, 11067-11072
   Abstract »    Full Text »    PDF »
Synthetic Biology of Phenotypic Adaptation in Vertebrates: The Next Frontier.
S. Yokoyama (2013)
Mol. Biol. Evol. 30, 1495-1499
   Abstract »    Full Text »    PDF »
Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin.
C. Natarajan, N. Inoguchi, R. E. Weber, A. Fago, H. Moriyama, and J. F. Storz (2013)
Science 340, 1324-1327
   Abstract »    Full Text »    PDF »
Protein Insertions and Deletions Enabled by Neutral Roaming in Sequence Space.
A. Toth-Petroczy and D. S. Tawfik (2013)
Mol. Biol. Evol. 30, 761-771
   Abstract »    Full Text »    PDF »
Functional Evolution of an Anthocyanin Pathway Enzyme during a Flower Color Transition.
S. D. Smith, S. Wang, and M. D. Rausher (2013)
Mol. Biol. Evol. 30, 602-612
   Abstract »    Full Text »    PDF »
Stability-mediated epistasis constrains the evolution of an influenza protein.
eLife Sci 2, e00631
Synthesis of Experimental Molecular Biology and Evolutionary Biology: An Example from the World of Vision.
S. Yokoyama (2012)
BioScience 62, 939-948
   Abstract »    Full Text »    PDF »
Weak Selection and Protein Evolution.
H. Akashi, N. Osada, and T. Ohta (2012)
Genetics 192, 15-31
   Abstract »    Full Text »    PDF »
Transformation of a transposon into a derived prolactin promoter with function during human pregnancy.
D. Emera and G. P. Wagner (2012)
PNAS 109, 11246-11251
   Abstract »    Full Text »    PDF »
The Rise of Chemodiversity in Plants.
J.-K. Weng, R. N. Philippe, and J. P. Noel (2012)
Science 336, 1667-1670
   Abstract »    Full Text »    PDF »
Deciphering Modern Glucocorticoid Cross-pharmacology Using Ancestral Corticosteroid Receptors.
J. A. Kohn, K. Deshpande, and E. A. Ortlund (2012)
J. Biol. Chem. 287, 16267-16275
   Abstract »    Full Text »    PDF »
The Evolution of Multimeric Protein Assemblages.
M. Lynch (2012)
Mol. Biol. Evol. 29, 1353-1366
   Abstract »    Full Text »    PDF »
Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates.
R. Huang, F. Hippauf, D. Rohrbeck, M. Haustein, K. Wenke, J. Feike, N. Sorrelle, B. Piechulla, and T. J. Barkman (2012)
PNAS 109, 2966-2971
   Abstract »    Full Text »    PDF »
InterEvol database: exploring the structure and evolution of protein complex interfaces.
G. Faure, J. Andreani, and R. Guerois (2012)
Nucleic Acids Res. 40, D847-D856
   Abstract »    Full Text »    PDF »
Cellular Effects and Epistasis among Three Determinants of Adaptation in Experimental Populations of Saccharomyces cerevisiae.
L. S. Parreiras, L. M. Kohn, and J. B. Anderson (2011)
Eukaryot. Cell 10, 1348-1356
   Abstract »    Full Text »    PDF »
The reconstructed ancestral subunit a functions as both V-ATPase isoforms Vph1p and Stv1p in Saccharomyces cerevisiae.
G. C. Finnigan, V. Hanson-Smith, B. D. Houser, H. J. Park, and T. H. Stevens (2011)
Mol. Biol. Cell 22, 3176-3191
   Abstract »    Full Text »    PDF »
A method for probing the mutational landscape of amyloid structure.
C. W. O'Donnell, J. Waldispuhl, M. Lis, R. Halfmann, S. Devadas, S. Lindquist, and B. Berger (2011)
Bioinformatics 27, i34-i42
   Abstract »    Full Text »    PDF »
Lamprey endocrinology is not ancestral.
J. W. Thornton and S. M. Carroll (2011)
PNAS 108, E5
   Full Text »    PDF »
Y. Pham, B. Kuhlman, G. L. Butterfoss, H. Hu, V. Weinreb, and C. W. Carter Jr (2010)
J. Biol. Chem. 285, 38590-38601
   Abstract »    Full Text »    PDF »
Mapping of AF1 transactivation domains in duplicated rainbow trout glucocorticoid receptors.
A. Sturm, J. E. Bron, D. M. Green, and N. R. Bury (2010)
J. Mol. Endocrinol. 45, 391-404
   Abstract »    Full Text »    PDF »
Robustness of Ancestral Sequence Reconstruction to Phylogenetic Uncertainty.
V. Hanson-Smith, B. Kolaczkowski, and J. W. Thornton (2010)
Mol. Biol. Evol. 27, 1988-1999
   Abstract »    Full Text »    PDF »
Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance.
J. D. Bloom, L. I. Gong, and D. Baltimore (2010)
Science 328, 1272-1275
   Abstract »    Full Text »    PDF »
Hormone Binding and Co-regulator Binding to the Glucocorticoid Receptor are Allosterically Coupled.
S. J. Pfaff and R. J. Fletterick (2010)
J. Biol. Chem. 285, 15256-15267
   Abstract »    Full Text »    PDF »
Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region.
J. da Silva, M. Coetzer, R. Nedellec, C. Pastore, and D. E. Mosier (2010)
Genetics 185, 293-303
   Abstract »    Full Text »    PDF »
Evolutionary Expansion and Specialization of the PDZ Domains.
O. Sakarya, C. Conaco, O. Egecioglu, S. A. Solla, T. H. Oakley, and K. S. Kosik (2010)
Mol. Biol. Evol. 27, 1058-1069
   Abstract »    Full Text »    PDF »
Retracing Evolution of Red Fluorescence in GFP-Like Proteins from Faviina Corals.
S. F. Field and M. V. Matz (2010)
Mol. Biol. Evol. 27, 225-233
   Abstract »    Full Text »    PDF »
Stepwise Modification of a Modular Enhancer Underlies Adaptation in a Drosophila Population.
M. Rebeiz, J. E. Pool, V. A. Kassner, C. F. Aquadro, and S. B. Carroll (2009)
Science 326, 1663-1667
   Abstract »    Full Text »    PDF »
Predicting Virus Evolution: The Relationship between Genetic Robustness and Evolvability of Thermotolerance.
C.B. Ogbunugafor, R.C. Mcbride, and P.E. Turner (2009)
Cold Spring Harb Symp Quant Biol
   Abstract »    PDF »
Rapid Sequence Evolution of Transcription Factors Controlling Neuron Differentiation in Caenorhabditis.
R. Jovelin (2009)
Mol. Biol. Evol. 26, 2373-2386
   Abstract »    Full Text »    PDF »
Deconstructing Design: A Strategy for Defending Science.
K.R. Miller (2009)
Cold Spring Harb Symp Quant Biol
   Abstract »    PDF »
The mineralocorticoid receptor and its coregulators.
J. Yang and M. J Young (2009)
J. Mol. Endocrinol. 43, 53-64
   Abstract »    Full Text »    PDF »
In the light of directed evolution: Pathways of adaptive protein evolution.
J. D. Bloom and F. H. Arnold (2009)
PNAS 106, 9995-10000
   Abstract »    Full Text »    PDF »
Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility.
P. E. Tomatis, S. M. Fabiane, F. Simona, P. Carloni, B. J. Sutton, and A. J. Vila (2008)
PNAS 105, 20605-20610
   Abstract »    Full Text »    PDF »
Structure-function relationships in the mineralocorticoid receptor.
J. B Pippal and P. J Fuller (2008)
J. Mol. Endocrinol. 41, 405-413
   Abstract »    Full Text »    PDF »
A protein functional leap: how a single mutation reverses the function of the transcription regulator TetR.
M. Resch, H. Striegl, E. M. Henssler, M. Sevvana, C. Egerer-Sieber, E. Schiltz, W. Hillen, and Y. A. Muller (2008)
Nucleic Acids Res. 36, 4390-4401
   Abstract »    Full Text »    PDF »
Evolution of the bile salt nuclear receptor FXR in vertebrates.
E. J. Reschly, N. Ai, S. Ekins, W. J. Welsh, L. R. Hagey, A. F. Hofmann, and M. D. Krasowski (2008)
J. Lipid Res. 49, 1577-1587
   Abstract »    Full Text »    PDF »
Reconstruction of a Probable Ancestral Form of Conger Eel Galectins Revealed Their Rapid Adaptive Evolution Process for Specific Carbohydrate Recognition.
A. Konno, T. Ogawa, T. Shirai, and K. Muramoto (2007)
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   Abstract »    Full Text »    PDF »

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