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How adding a single methylene to dihydrofolate reductase can change its conformational dynamics
Ryan W Penhallurick1, Alliyah Harold1, Maya D Durnal1
1Department of Chemistry, Georgetown University, Washington, District of Columbia 20057, USA.
Abstract:
Studies of the effects of pressure on proteins from piezophilic (pressure-loving) microbes compared with homologous proteins from mesophilic microbes have been relatively rare. Interestingly, such studies of dihydrofolate reductase show that a single-site mutation from an aspartic acid to a glutamic acid can reverse the pressure-dependent monotonic decrease in activity to that in a monotonic pressure-dependent activation. This residue is near the active site but is not thought to directly participate in the catalytic mechanism. Here, the ways that addition of one carbon to the entire protein could lead to such a profound difference in pressure effects are explored using molecular dynamics simulations. The results indicate that the glutamate changes the coupling between a helix and the β-sheet due to the extra flexibility of the side chain, which further changes correlated motions of other regions of the protein.
Insights
A single amino acid change in dihydrofolate reductase (an enzyme) can alter how protein activity responds to pressure. This mutation impacts protein flexibility and motion, affecting pressure adaptation in microbes.
Area of Science:
- Biochemistry
- Molecular Biology
- Microbial Physiology
Background:
- Piezophilic microbes thrive under high pressure, but their proteins' pressure responses are understudied compared to mesophilic counterparts.
- Dihydrofolate reductase (DHFR) is crucial for folate metabolism in all organisms.
- Previous studies on DHFR revealed a single amino acid substitution (aspartic acid to glutamic acid) can invert pressure-dependent activity profiles.
Purpose of the Study:
- To investigate how a single amino acid mutation in dihydrofolate reductase influences protein behavior under varying hydrostatic pressure.
- To elucidate the molecular mechanisms by which this mutation alters pressure-dependent activity using computational simulations.
Main Methods:
- Comparative analysis of homologous dihydrofolate reductase proteins from piezophilic and mesophilic organisms.
- Molecular dynamics simulations were employed to model protein behavior.
- Analysis of residue-level interactions and correlated motions within the protein structure.
Main Results:
- The substitution of aspartic acid with glutamic acid significantly alters the pressure response of DHFR activity.
- Molecular dynamics simulations revealed that the glutamic acid side chain's increased flexibility impacts helix-sheet coupling.
- This change in flexibility propagates, altering correlated motions in distant protein regions, thereby modulating pressure sensitivity.
Conclusions:
- A single amino acid substitution can profoundly alter a protein's response to hydrostatic pressure.
- The observed changes in pressure effects are linked to altered intramolecular communication and flexibility, not direct active site involvement.
- This highlights the subtle yet significant role of specific residues in protein adaptation to extreme environments.
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