Psychrophilic alpha-amylase from the antarctic bacterium pseudoalteromonas haloplanktis (AHA) and its mesophilic homologue, porcine pancreatic alpha-amylase (PPA) are theoretically investigated with molecular dynamics (MD) simulations. We carried out 240-ns MD simulations for four systems, AHA and PPA with/without the bound substrate, and examined protein conformational entropy changes upon the substrate binding. We developed an analysis that decomposes the entropy changes into contributions of individual amino acids, and successfully identified protein regions responsible for the entropy changes. The results provide a molecular insight into the structural flexibilities of those enzymes related to the temperature dependences of the enzymatic activity. (C) 2010 Elsevier B. V. All rights reserved.