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Constraining protein sequence space: four amino acid alphabets are sufficient to recapitulate lambda repressor

Daniel S Maillet¹, James T Drummond

¹Indiana University, Department of Biology and Program in Biochemistry, Bloomington IN 47405, USA.

Journal of Molecular Biology

|October 13, 2007

Summary

Researchers developed a new method to explore protein sequence space using nucleic acid polymers. This approach, SynthOMIC, enables the creation of diverse protein libraries from selected amino acids, overcoming previous limitations.

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

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Published on: August 9, 2019

Area of Science:

Synthetic biology
Molecular biology
Biochemistry

Background:

Nucleic acid polymers offer diverse functions but accessing protein sequence space remains challenging.
Proteins possess greater chemical and physical diversity than nucleic acids.

Purpose of the Study:

To devise a combinatorial strategy for accessing protein sequence space using nucleic acid polymers.
To create representative libraries of proteins from selected amino acid alphabets.

Main Methods:

Developed the SynthOMIC (synthesis of ORFs by multimerizing in-frame codons) approach.
Fused nucleic acid libraries encoding selected amino acid alphabets to the lambda repressor DNA-binding domain.
Utilized in vivo selection for self-interacting proteins that reconstitute lambda repressor function.

Main Results:

The frequency of self-interactors varied significantly based on amino acid composition, spanning five orders of magnitude.
Identified sequence motifs and significant sequence identity with known proteins in generated clones.
Demonstrated the SynthOMIC approach's ability to distill protein sequence space.

Conclusions:

The SynthOMIC approach is a powerful strategy for creating combinatorial libraries of open reading frames.
This method supports selected amino acid alphabets, eliminates redundant sequences, and locally constrains amino acids.
Enables efficient exploration of protein sequence space for novel functional molecules.