How synonymous mutations alter enzyme structure and function over long timescales.

Area of Science:

• Biochemistry
• Molecular Biology
• Computational Biology

Background:

• Synonymous mutations, which do not change the amino acid sequence, can alter enzyme activity over long cellular timescales.
• The molecular mechanisms underlying these changes in enzyme specific activity remain largely unknown.

Purpose of the Study:

• To elucidate the molecular mechanisms by which synonymous mutations impact enzyme specific activity.
• To investigate the role of protein folding pathways and kinetics in mediating these effects.

Main Methods:

• Multiscale modeling incorporating coarse-grained simulations, all-atom simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations.
• Analysis of three Escherichia coli enzymes: type III chloramphenicol acetyltransferase, D-alanine-D-alanine ligase B, and dihydrofolate reductase.

Main Results:

• Synonymous mutations alter codon translation rates, shifting co-translational and post-translational folding pathways.
• This leads to kinetic partitioning into subpopulations of molecules that slowly interconvert to the native state.
• These long-lived states exhibit localized misfolding near active sites and reduced catalytic activity due to increased activation energies.

Conclusions:

• Synonymous mutations can induce long-term functional changes in enzymes by altering folding kinetics and creating kinetically trapped states.
• These findings provide a molecular explanation for how changes in mRNA sequence, without altering protein primary structure, affect enzyme activity.