Flexibility and enzymatic cold-adaptation: a comparative molecular dynamics investigation of the elastase family.
Molecular dynamics simulations of representative mesophilic and psycrophilic elastases have been carried out at different temperatures to explore the molecular basis of cold adaptation inside a specific enzymatic family. The molecular dynamics trajectories have been compared and analyzed in terms of secondary structure, molecular flexibility, intramolecular and protein-solvent interactions, unravelling molecular features relevant to rationalize the efficient catalytic activity of psychrophilic elastases at low temperature. The comparative molecular dynamics investigation reveals that modulation of the number of protein-solvent interactions is not the evolutionary strategy followed by the psycrophilic elastase to enhance catalytic activity at low temperature. In addition, flexibility and solvent accessibility of the residues forming the catalytic triad and the specificity pocket are comparable in the cold- and warm-adapted enzymes. Instead, loop regions with different amino acid composition in the two enzymes, and clustered around the active site or the specificity pocket, are characterized by enhanced flexibility in the cold-adapted enzyme. Remarkably, the psycrophilic elastase is characterized by reduced flexibility, when compared to the mesophilic counterpart, in some scattered regions distant from the functional sites, in agreement with hypothesis suggesting that local rigidity in regions far from functional sites can be beneficial for the catalytic activity of psychrophilic enzymes.
Papaleo
Elena
E
Department of Biotechnology and Bioscience, University of Milano-Bicocca, P.za della Scienza 2, 20126, Milan, Italy.
Riccardi
Laura
L
Villa
Chiara
C
Fantucci
Piercarlo
P
De Gioia
Luca
L
D000064:Acclimatization; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis; D000818:Animals; D020134:Catalytic Domain; D003081:Cold Climate; D004795:Enzyme Stability; D066298:In Vitro Techniques; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010196:Pancreatic Elastase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011487:Protein Conformation; D020317:Salmo salar / Q000235:genetics / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity; D013552:Swine / Q000235:genetics / Q000378:metabolism; D013816:Thermodynamics
D000596:Amino Acids; D010196:Pancreatic Elastase