What makes a protein fold amenable to functional innovation? fold polarity and stability trade-offs

Eynat Dellus-Gur, Agnes Toth-Petroczy, Mikael Elias, Dan S. Tawfik

Research output: Contribution to journalArticlepeer-review

108 Scopus citations

Abstract

Protein evolvability includes two elements - robustness (or neutrality, mutations having no effect) and innovability (mutations readily inducing new functions). How are these two conflicting demands bridged? Does the ability to bridge them relate to the observation that certain folds, such as TIM barrels, accommodate numerous functions, whereas other folds support only one? Here, we hypothesize that the key to innovability is polarity - an active site composed of flexible, loosely packed loops alongside a well-separated, highly ordered scaffold. We show that highly stabilized variants of TEM-1 β-lactamase exhibit selective rigidification of the enzyme's scaffold while the active-site loops maintained their conformational plasticity. Polarity therefore results in stabilizing, compensatory mutations not trading off, but instead promoting the acquisition of new activities. Indeed, computational analysis indicates that in folds that accommodate only one function throughout evolution, for example, dihydrofolate reductase, ≥ 60% of the active-site residues belong to the scaffold. In contrast, folds associated with multiple functions such as the TIM barrel show high scaffold-active-site polarity (~ 20% of the active site comprises scaffold residues) and > 2-fold higher rates of sequence divergence at active-site positions. Our work suggests structural measures of fold polarity that appear to be correlated with innovability, thereby providing new insights regarding protein evolution, design, and engineering.

Original languageEnglish (US)
Pages (from-to)2609-2621
Number of pages13
JournalJournal of Molecular Biology
Volume425
Issue number14
DOIs
StatePublished - Jul 24 2013

Bibliographical note

Funding Information:
The notion of local versus global compensation stemmed from an inspiring symposium at New England BioLabs, and following discussions with Joe Thornton. We are very grateful to Ruth Nussinov, Devin Trudeau, Evandro Ferrada, and Emmanuel Levy for valuable discussions and comments. We thank Prof. J. Pelletier for the TEM-1 expression plasmid. Financial support by the Israel Science Foundation and the Meil de Botton Fund is gratefully acknowledged. D.S.T. is the incumbent of the Nella and Leon Benoziyo Professorial Chair.

Keywords

  • enzyme evolution
  • protein disorder
  • protein evolution
  • protein folds

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