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Switching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity

View ORCID ProfileVictor Y. Zhao, Joao V. Rodrigues, Elena R. Lozovsky, View ORCID ProfileDaniel L. Hartl, View ORCID ProfileEugene I. Shakhnovich
doi: https://doi.org/10.1101/2021.06.18.448971
Victor Y. Zhao
1Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
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Joao V. Rodrigues
1Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
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Elena R. Lozovsky
2Department Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
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Daniel L. Hartl
2Department Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
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Eugene I. Shakhnovich
1Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
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  • For correspondence: shakhnovich@chemistry.harvard.edu
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Abstract

To what degree are individual structural elements within proteins modular such that similar structures from unrelated proteins can be interchanged? We study sub-domain modularity by creating 20 chimeras of an enzyme, E. coli dihydrofolate reductase (DHFR), in which a catalytically important, 10-residue α-helical sequence is replaced by α-helical sequences from a diverse set of proteins. The chimeras stably fold but have a range of diminished thermal stabilities and catalytic activities. Evolutionary coupling analysis indicates that the residues of this α-helix are under selection pressure to maintain catalytic activity in DHFR. We performed molecular dynamics simulations using replica exchange with solute-tempering. Chimeras with low catalytic activity exhibit non-helical conformations that block the binding site and disrupt the positioning of the catalytically essential residue D27. Simulation observables and in vitro measurements of thermal stability and substrate binding affinity are strongly correlated. Several E. coli strains with chromosomally integrated chimeric DHFRs can grow, with growth rates that follow predictions from a kinetic flux model that depends on the intracellular abundance and catalytic activity of DHFR. Our findings show that although α-helices are not universally substitutable, the molecular and fitness effects of modular segments can be predicted by the biophysical compatibility of the replacement segment.

Statement of Significance α-helices are ubiquitous components of protein structure that exhibit a degree of independent folding behavior, making them plausible structural modules within proteins. Here, we assess the effects of switching the sequence of an α-helix in an essential enzyme for α-helical sequences from evolutionarily unrelated proteins. The resultant chimeric proteins can still fold but enzymatic activity, stability, and cellular growth rates are negatively affected. Computational investigations reveal how residues in an α-helix have been shaped by selection pressure to maintain catalytic activity and a specific, helical conformation of the protein. More broadly, we illustrate how molecular and fitness effects of switching protein segments depend on the protein and cellular context.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 02, 2021.
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Switching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity
Victor Y. Zhao, Joao V. Rodrigues, Elena R. Lozovsky, Daniel L. Hartl, Eugene I. Shakhnovich
bioRxiv 2021.06.18.448971; doi: https://doi.org/10.1101/2021.06.18.448971
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Switching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity
Victor Y. Zhao, Joao V. Rodrigues, Elena R. Lozovsky, Daniel L. Hartl, Eugene I. Shakhnovich
bioRxiv 2021.06.18.448971; doi: https://doi.org/10.1101/2021.06.18.448971

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