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Comparing mutagenesis and simulations as tools for identifying functionally important sequence changes for protein

Ming-Ling Liao¹, George N Somero², Yun-Wei Dong³

¹State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, 361102 Xiamen, China.

Proceedings of the National Academy of Sciences of the United States of America

|December 26, 2018

Summary

Marine molluscs show how amino acid changes in cytosolic malate dehydrogenase (cMDH) adapt to different temperatures. Surface residue interactions outside the active site modulate enzyme flexibility and thermal stability, aiding evolutionary adaptation.

Keywords:

adaptation cytosolic malate dehydrogenase evolution molecular dynamics simulations protein evolution

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Area of Science:

Biochemistry
Evolutionary Biology
Structural Biology

Background:

Comparative studies show protein thermal stability varies with species' adaptation temperatures.
Mechanisms linking sequence variation to adaptive thermal changes in proteins are not well understood.

Purpose of the Study:

To investigate how amino acid sequence variations in cytosolic malate dehydrogenase (cMDH) from marine molluscs correlate with adaptation to different temperatures.
To elucidate the precise molecular mechanisms by which these sequence variations influence enzyme thermal stability and function.

Main Methods:

Comparative analysis of cMDH orthologs from molluscs adapted to a wide temperature range (-1.9 °C to 55 °C).
Site-directed mutagenesis (SDM) and in vitro protein experimentation.
In silico mutagenesis using molecular dynamics simulation (MDS).

Main Results:

Amino acid usage in cMDH varies across enzyme regions (surface, core) with adaptation temperature.
SDM and MDS methods generally agreed on the effects of substitutions on protein stability.
MDS revealed that substitutions outside mobile regions (MRs) can alter their flexibility through surface residue interactions, impacting enzyme function.

Conclusions:

Evolutionary adaptation of enzyme thermal responses involves amino acid substitutions outside the active site.
Protein surface residues play a critical role in transmitting flexibility changes to functionally important regions, thereby influencing thermal adaptation.