Endo- and exo-inulinases: enzyme-substrate interaction and rational immobilization.
Three-dimensional models of exoinulinase from Bacillus stearothermophilus and endoinulinase from Aspergillus niger were built up by means of homology modeling. The crystal structure of exoinulinase from Aspergillus awamori was used as a template, which is the sole structure of inulinase resolved so far. Docking and molecular dynamics simulations were performed to investigate the differences between the two inulinases in terms of substrate selectivity. The analysis of the structural differences between the two inulinases provided the basis for the explanation of their different regio-selectivity and for the understanding of enzyme-substrate interactions. Surface analysis was performed to point out structural features that can affect the efficiency of enzymes also after immobilization. The computational analysis of the three-dimensional models proved to be an effective tool for acquiring information and allowed to formulate an optimal immobilized biocatalyst even more active that the native one, thus enabling the full exploitation of the catalytic potential of these enzymes.
Basso
Alessandra
A
Laboratory of Applied and Computational Biocatalysis, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Trieste, Piazzale Europa, Trieste 1-34127, Italy.
Spizzo
Patrizia
P
Ferrario
Valerio
V
Knapic
Lorena
L
Savko
Nina
N
Braiuca
Paolo
P
Ebert
Cynthia
C
Ricca
Emanuele
E
Calabrò
Vincenza
V
Gardossi
Lucia
L
D001234:Aspergillus niger / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D004800:Enzymes, Immobilized / Q000737:chemistry* / Q000378:metabolism; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism; D001411:Geobacillus stearothermophilus / Q000201:enzymology; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000378:metabolism; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D013499:Surface Properties
D001426:Bacterial Proteins; D004800:Enzymes, Immobilized; D005656:Fungal Proteins; D006026:Glycoside Hydrolases; C023086:inulinase