Comparative void-volume analysis of psychrophilic and mesophilic enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility

Abstract

Background: Psychrophiles, cold-adapted organisms, have adapted to live at low temperatures by using a variety of mechanisms. Their enzymes are active at cold temperatures by being structurally more flexible than mesophilic enzymes. Even though, there are some indications of the possible structural mechanisms by which psychrophilic enzymes are catalytic active at cold temperatures, there is not a generalized structural property common to all psychrophilic enzymes.

Results: We examine twenty homologous enzyme pairs from psychrophiles and mesophiles to investigate flexibility as a key characteristic for cold adaptation. B-factors in protein X-ray structures are one way to measure flexibility. Comparing psychrophilic to mesophilic protein B-factors reveals that psychrophilic enzymes are more flexible in 5-turn and strand secondary structures. Enzyme cavities, identified using CASTp at various probe sizes, indicate that psychrophilic enzymes have larger average cavity sizes at probe radii of 1.4-1.5 Å, sufficient for water molecules. Furthermore, amino acid side chains lining these cavities show an increased frequency of acidic groups in psychrophilic enzymes.

Conclusions: These findings suggest that embedded water molecules may play a significant role in cavity flexibility, and therefore, overall protein flexibility. Thus, our results point to the important role enzyme flexibility plays in adaptation to cold environments.

Figure 1

ΔB'-value of each secondary structure. Psychrophiles have greater atom flexibility in strands and 5-turns secondary structure (p < 0.001) compared to mesophilic proteins. * indicates outliers.

Figure 2

Average size of cavities in psychrophilic proteins subtracted from the average sizes of the mesophilic cavities. Positive ΔCavity Size indicates higher average cavity size in psychrophilic proteins at the indicated probe sizes. Red stars indicate statistically significant differences in average cavity size (p < 0.01). * indicates outliers.

Figure 3

Difference in frequency of each amino acid type on the inner cavity surface between psychrophilic and the mesophilic paired proteins. Psychrophilic enzymes have a larger number of acidic side chains on the inner surface of a cavity (p < 0.01). Mesophilic enzymes have a larger number of hydrophobic residues (p < 0.01).