Abstract
The scarcity, richness, and other important physiological functions of D-psicose make it crucial to increase the yield of D-psicose. The production of D-psicose can be accomplished by D-psicose 3-epimerase (DPEase) from Clostridium bolteae (CbDPEase) catalyzing the substrate D-fructose. Although the catalytic efficiency of the CbDPEase has been raised via using the site-directed mutagenesis (Y68I/G109P) technique, structure-activity relationship in the wild-type CbDPEase and Y68I/G109P mutant is currently poorly understood. In our study, a battery of molecular modeling methods [homology modeling, adaptive steered molecular dynamics (ASMD) simulations, and Molecular Mechanics/Generalized Born Surface Area (MM-GB/SA)], combined with protein structure networks, were employed to theoretically characterize the reasons for the differences in the abilities of the D-fructose catalyzed by the wild-type CbDPEase and Y68I/G109P mutant. Protein structure networks demonstrated that site-directed mutagenesis enhanced the connectivity between D-fructose and CbDPEase, leading to the increased catalytic efficiency mediated by the functional residues with high betweenness. During the dissociation of the D-fructose from the Y68I/G109P mutant, planes of benzene rings of F248 and W114 could be continuously parallel to the stretching direction of D-fructose. It made the tunnel have an open state and resulted in the stable donor-π interactions between D-fructose and the benzene rings around 18Å. The stronger substrate-protein interactions were detected in the Y68I/G109P mutant, instead of in the wild-type CbDPEase, which were consistent with the binding free energy and Potential Mean of Force (PMF) results. The theoretical results illustrated the reasons that Y68I/G109P mutations increased the catalytic efficiency of CbDPEase and could be provided the new clue for further DPEase engineering.
Highlights
D-psicose, as a C-3 epimer of D-fructose, has plentiful significant physiological functions, covering anti-hyperglycemia and antiobesity effects (Granström et al, 2004; Fukada et al, 2010; Iida et al, 2010; Zhang et al, 2016; Shintani et al, 2017)
To comprehend the structure-activity relationship in the wild-type CbDPEase and Y68I/G109P mutant, we applied molecular modeling methods with protein structure networks for the substrate D-fructose bound to the wild-type CbDPEase and Y68I/G109P mutant, correspondently
During the dissociation of the D-fructose from the Y68I/G109P mutant, the planes of benzene rings of F248 and W114 could be continuously parallel to the stretching direction of the D-fructose
Summary
D-psicose, as a C-3 epimer of D-fructose, has plentiful significant physiological functions, covering anti-hyperglycemia and antiobesity effects (Granström et al, 2004; Fukada et al, 2010; Iida et al, 2010; Zhang et al, 2016; Shintani et al, 2017). D-psicose has various physiological characteristics beneficial to health It can efficaciously reduce the accumulation of abdominal fat (Matsuo et al, 2001; Ochiai et al, 2014), remove reactive oxygen species (ROS) (Murata et al, 2003), and inhibit hepatic lipase activities (Matsuo et al, 2015). It can reduce the postprandial glycemic excursion (Matsuo and Izumori, 2006; Hayashi et al, 2010), improve the metabolism of serum lipids (Afach et al, 2008), and protect the nervous system (Takata et al, 2005). It can strengthen insulin resistance (Hossain et al, 2011, 2012), treat atherosclerotic diseases and so on (Murao et al, 2007)
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