Dynamic Properties of a Psychrophilic α-Amylase in Comparison with a Mesophilic Homologue

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• 作者：Marco Pasi ; Laura Riccardi ; Piercarlo Fantucci ; Luca De Gioia ; Elena Papaleo
• 刊名：Journal of Physical Chemistry B
• 出版年：2009
• 出版时间：October 15, 2009
• 年：2009
• 卷：113
• 期：41
• 页码：13585-13595
• 全文大小：616K
• 年卷期：v.113,no.41(October 15, 2009)
• ISSN：1520-5207

文摘

The cold-active, chloride-dependent α-amylase from Pseudoalteromonas haloplanktis (AHA) is one of the best characterized psychrophilic enzymes, and shares high sequence and structural similarity with its mesophilic porcine counterpart (PPA). An atomic detail comparative analysis was carried out by performing more than 60 ns of multiple-replica explicit-solvent molecular dynamics simulations on the two enzymes in order to characterize the differences in ensemble properties and dynamics in solution between the two homologues. We find in both enzymes high flexibility clusters in the surroundings of the substrate-binding groove, primarily involving the long loops that protrude from the main domain’s barrel structure. These loops are longer in PPA and extend further away from the core of the barrel, where the active site is located: essential fluctuations in PPA mainly affect the highly solvent-accessible portions of these loops, whereas AHA is characterized by greater flexibility in the immediate surroundings of the active site. Furthermore, detailed analysis of active-site dynamics has revealed that elements previously identified through X-ray crystallography as involved in substrate binding in both enzymes undergo concerted motions that may be linked to catalysis.