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Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty.

Geeta N Eick1,2, Jamie T Bridgham1, Douglas P Anderson1,3

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Molecular Biology and Evolution
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Ancestral protein reconstruction (APR) helps study ancient protein functions. Researchers found that protein functions are generally robust to uncertainty in ancestral sequences, even with many possible amino acid changes.

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Area of Science:

  • Evolutionary biology
  • Biochemistry
  • Molecular biology

Background:

  • Ancestral protein reconstruction (APR) is used to infer functions of ancient proteins and historical mutations.
  • Ambiguities in sequence reconstruction can affect the reliability of functional inferences.

Purpose of the Study:

  • To systematically investigate the robustness of inferred ancestral protein functions and mutational effects to sequence uncertainty.
  • To evaluate different methods for incorporating sequence uncertainty into experimental characterization.

Main Methods:

  • Reconstruction of ancestral proteins from three diverse domain families.
  • Experimental characterization of reconstructed proteins, incorporating sequence uncertainty through posterior distribution sampling and a "worst plausible case" approach.

Main Results:

  • Qualitative conclusions about ancestral protein functions and historical mutation effects were robust to sequence uncertainty.
  • Similar functions were observed across plausible ancestral sequences, even with numerous amino acid variations.
  • Quantitative functional descriptors showed some variation, highlighting the need for experimental robustness checks.

Conclusions:

  • Ancestral protein functions are largely robust to sequence uncertainty.
  • The "worst plausible case" method is an efficient strategy for assessing robustness to significant sequence ambiguity.
  • Experimental characterization is crucial for accurate quantitative estimates of ancient biochemical parameters.