Investigation of an “alternate water supply system” in enzymatic hydrolysis in the processive endocellulase Cel7A from Rasamsonia emersonii by molecular dynamics simulation

Cel7A from Rasamsonia emersonii is one of the processive endocellulases classified under family 7 glycoside hydrolase. Molecular dynamics simulations were carried out to obtain the optimized sliding and hydrolyzing conformations, in which the reducing ends of sugar chains are located on different sites. Hydrogen bonds are investigated to clarify the interactions between protein and substrate in either conformation. Nine hydrogen bonding interactions are identified in the sliding conformation, and six similar interactions are also found correspondingly in the hydrolyzing conformation. In addition, four strong hydrophobic interactions are also determined. The domain cross‐correlation map analysis shows movement correlation of protein including autocorrelation between residues. The root mean square fluctuations analysis represents the various flexibilities of different fragment in the two conformations. Comparing the two conformations reveals the water‐supply mechanism of selective hydrolysis of cellulose in Cel7A. The mechanism can be described as follow. When the reducing end of substrate slides from the unhydrolyzing site (sliding conformation) to the hydrolyzing site (hydrolyzing conformation), His225 is pushed down and rotated, the rotation leads to the movement of Glu209 with the interstrand hydrogen bonding in β‐sheet. It further makes Asp211 close to the hydrolysis center and provides a water molecule bounding on its carboxyl in the previous unhydrolyzing site. After the hydrolysis takes place and the product is excluded from the enzyme, the Asp211 comes back to its initial position. In summary, Asp211 acts as an elevator to transport outer water molecules into the hydrolysis site for every other glycosidic bond.     

Departure from naturalized to invasive stage: a disturbance-induced mechanism and associated interacting factors

Aims Within a habitat of multiple plant species, increased resource availabilities and altered species abundances following disturbances create opportunities for exotic species to successfully establish and subsequently naturalize into its non-native environment. Such post-disturbance changes in abiotic and biotic environments may also promote a naturalized exotic species (or invading species) to become invasive through rapid colonization of the habitat sites by reducing the extent and size of resident plant species. By combining species life history traits with that of the disturbance-induced changes in habitat characteristics, we aimed to determine those interacting factors and associated mechanism allowing an exotic invasion to start off.Methods We used a modified version of the classic competition–colonization (CC) model which was formulated first by Hastings (1980) and studied later by Tilman (1994) to explain spatial coexistence of multiple species. Within this model framework, recruitment-limited spatial competition has explicitly been linked with interspecific resource competition without altering the basic assumptions and structure of the original CC model.Important findings The model results showed that at a constant rate of resource supply, invading species can stably coexist with native species via trade-offs between species competitive ability and colonizing ability. On the other hand, the model predicted that with a fluctuating resource condition, invading species can successfully invade a habitat following continuous reductions in the size and extent of native species. Whether or not invading species holds competitive superiority over the native species for limiting resource, we showed that there exists a range of variation in available resource that allows an exotic invasion to start off in post-disturbance habitat. The associated disturbance-induced mechanism promoting invading species to become invasive has been identified. It states that occurrences of disturbances such as fire or clear-cutting influence variation in resource availability, and in addition open up many vacant microsites; given these disturbance-induced changes, invading species with a higher rate of propagule production and with a higher survival rate of adults particularly in low-resource condition recruits microsites at faster rate relative to native competitor species, and with a given range of variation in resource availabilities, it maintains continued expansions following reductions in size and extent of native species. Moreover, we identified those interacting factors and their specific roles that drive this mechanism. These factors include propagule supply, variable resource level and vacant microsite availability. Increased availability of vacant microsites following disturbances creates an opportunity for rapid colonization. Given this opportunity, higher number of propagules supplied by the invading species enhances the rate of colonization success, whereas the resource variation within a range of given thresholds maintains enhanced colonization rate of the invading species while it depresses native competitor species. Owing to the each factor's invasion regulatory ability, controlling one or all of them may have strong negative impact on the occurrence of exotic invasion.     

The influence of pre‐settlement and early post‐settlement processes on the adult distribution and relative dominance of two invasive mussel species

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