Using multi-objective computational design to extend protein promiscuity

A journey back in time is possible at the molecular level by reconstructing proteins from extinct organisms. Here we report the reconstruction, based on sequence predicted by phylogenetic analysis, of seven Precambrian thioredoxin enzymes (Trx), dating back between ~1.4 and ~4 billion years (Gyr). The reconstructed enzymes are up to 32° C more stable than modern enzymes and the oldest show significantly higher activity than extant ones at pH 5. We probed their mechanisms of reduction using single-molecule force spectroscopy. From the force-dependency of the rate of reduction of an engineered substrate, we conclude that ancient Trxs utilize chemical mechanisms of reduction similar to those of modern enzymes. While Trx enzymes have maintained their reductase chemistry unchanged, they have adapted over a 4 Gyr time span to the changes in temperature and ocean acidity that characterize the evolution of the global environment from ancient to modern Earth.

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“…6). We found than the values of insulin precipitation rates obtained with this assay are similar than previously determined for E. coli Trx26–27.…”

Section: Resultssupporting

confidence: 86%

“…Bulk-solvent oxidoreductase activity for ancestral thioredoxins was determined using the insulin precipitation assay as described elsewhere 26–27,43. In order to further verify the activity of ancestral Trxs enzymes at acidic pH, we used DTNB (5,5′-dithiobis-(2-nitrobenzoic acid)) as substrate at pH 5.…”

Section: Methodsmentioning

confidence: 99%

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes

Pérez-Jiménez

Inglés-Prieto

Zhao

et al. 2011

Nat Struct Mol Biol

179

228

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“…In addition, GAs are often applied in bioinformatics or physical research to get approximations in adequate time. In bioinformatics, GAs are used, for instance, in peptide and protein design (Gronwald et al, 2008;Suarez et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Dynamic causal modeling with genetic algorithms

Pyka

Heider

Hauke

et al. 2011

Journal of Neuroscience Methods

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“…However, the aim of computational design methods is not finding all possible solutions, but at least one solution that fits the required properties. One of the methods that have been proposed is a multiobjective optimization, in which protein stability and catalytic activity are simultaneously optimized [4, 5]. …”

Section: Introductionmentioning

confidence: 99%

Computational Design of a DNA- and Fc-Binding Fusion Protein

Winkler

Armano

Dybowski

et al. 2011

Advances in Bioinformatics

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Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. In this work, we generated and optimized a new synthetic fusion protein using an evolutionary approach. The optimization was guided by directed evolution based on hydrophobicity scores, molecular weight, and secondary structure predictions. Several methods were used to refine the models built from the resulting sequences. We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein.

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Using multi-objective computational design to extend protein promiscuity

Cited by 18 publications

References 43 publications

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes

Dynamic causal modeling with genetic algorithms

Computational Design of a DNA- and Fc-Binding Fusion Protein

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