Predicting the functional motions of p97 using symmetric normal modes

p97 is a protein complex of the AAA+ family. Although functions of p97 are well understood, the mechanism by which p97 performs its unfolding activities remains unclear. In this work, we present a novel way of applying normal mode analysis to study this six‐fold symmetric molecular machine. By selecting normal modes that are axial symmetric and give the largest movements at D1 or D2 pore residues, we are able to predict the functional motions of p97, which are then validated by experimentally observed conformational changes. Our results shed light and provide new understandings on several key steps of the p97 functional process that were previously unclear or controversial, and thus are able to reconcile multiple previous findings. Specifically, our results reveal that (i) a venous valve‐like mechanism is used at D2 pore to ensure a one‐way exit‐only traffic of substrates; (ii) D1 pore remains shut during the functional process; (iii) the “swing‐up” motion of the N domain is closely coupled with the vertical motion of the D1 pore along the pore axis; (iv) because of the shut D1 pore and the one‐way traffic at D2 pore, it is highly likely that substrates enter the chamber through the gaps at the D1/D2 interface. The limited chamber volume inside p97 suggests that a substrate may be pulling out from D2 while at the same time being pulling in at the interface; (v) lastly, p97 uses a series of actions that alternate between twisting and pulling to remove the substrate. Proteins 2016; 84:1823–1835. © 2016 Wiley Periodicals, Inc.     

Changes of physiological rhythms of N-methyl-d-aspartate receptors in the chum salmon Oncorhynchus keta: effect of seawater acclimation during the parr-smolt transformation

We examined changes on N-methyl-d-aspartate receptors (NRs) in different growth stages (early parr, parr, and early smolt) of chum salmon, Oncorhynchus keta, during parr-smolt transformation from freshwater to seawater. Expression levels of NR genes mRNA and concentration of cortisol, T₃, T₄, dopamine and Na⁺/K⁺-ATPase activity significantly increased at salinity change condition. Moreover, in cultured brain cells, NRs were significantly lower in all groups treated with MK-801 (an antagonist of NRs) than in the early parr stage group in the FW treatment. We confirmed that the reduction in mRNA expression levels of NRs increased from the early parr to the early smolt stage. The information reported here should be taken into account in future studies on the relationship between memory factors of natal streams and homing mechanisms in Salmonidae.     

Differential daily rhythms of melatonin in the pineal gland and gut of goldfish Carassius auratus in response to light

The objectives of this study were to test the effects of light on melatonin rhythms in the pineal gland and gut of goldfish Carassius auratus and to investigate whether melatonin function differed in these two tissues, which are photosensitive and non-photosensitive respectively. Rhythms were evaluated by measuring arylalkylamine N-acetyltransferase (AANAT2) and melatonin receptor 1 (MT-R1) mRNA expression and melatonin concentration in the pineal gland, gut (in vivo), and cell cultures of the two tissues (in vitro). Compared to control, pineal gland melatonin secretion was higher at night, whereas the 24-h dark and ophthalmectomy groups maintained higher AANAT2 and MT-R1 mRNA expression during the day. Melatonin levels and AANAT2 and MT-R1 mRNA expression in the gut were also the highest at night, but the 24-h light, dark, and ophthalmectomy groups did not significantly differ from control. Furthermore, we measured AANAT2 and MT-R1 mRNA expression in high temperature water (30 °C) to investigate differences in the antioxidant capacity of pineal gland vs. gut melatonin. Melatonin and H₂O₂ levels, as well as AANAT2 and MT-R1 mRNA expression, were all higher in the two tissues under thermal stress, compared with their levels at 22 °C. Taken together, our results suggest that light has no effect on melatonin patterns in the gut, which appears to exhibit its own circadian rhythm, but both gut and pineal gland melatonin exhibit similar antioxidant function.