We can't find the internet
Attempting to reconnect
Something went wrong!
Hang in there while we get back on track
Assessment of Kaistella jeonii esterase conformational dynamics in response to poly(ethylene terephthalate) binding
AI summary Read the abstract
Researchers used molecular dynamics simulations to characterize how a cold-active esterase enzyme from Kaistella jeonii changes shape when it binds PET plastic, revealing conformational flexibility in its active site that may explain its ability to break down polyethylene terephthalate at low temperatures.
The pervasive presence of plastic in the environment has reached a concerning scale, being identified in many ecosystems. Bioremediation is the cheapest and most eco-friendly alternative to remove this polymer from affected areas. Recent work described that a novel cold-active esterase enzyme extracted from the bacteria Kaistella jeonii could promiscuously degrade PET. Compared to the well-known PETase from Ideonella sakaiensis, this novel esterase presents a low sequence identity yet has a remarkably similar folding. However, enzymatic assays demonstrated a lower catalytic efficiency. In this work, we employed a strict computational approach to investigate the binding mechanism between the esterase and PET. Understanding the underlying mechanism of binding can shed light on the evolutive mechanism of how enzymes have been evolving to degrade these artificial molecules and help develop rational engineering approaches to improve PETase-like enzymes. Our results indicate that this esterase misses a disulfide bridge, keeping the catalytic residues closer and possibly influencing its catalytic efficiency. Moreover, we describe the structural response to the interaction between enzyme and PET, indicating local and global effects. Our results aid in deepening the knowledge behind the mechanism of biological catalysis of PET degradation and as a base for the engineering of novel PETases.
More Papers Like This
In silico structural analysis and biochemical characterization of a novel PETase from Antarctic Streptomyces sp .
AI summary Read the abstract
Researchers characterized a novel PET-degrading enzyme (SsPETase) from Antarctic Streptomyces bacteria, using AlphaFold structural prediction and molecular dynamics simulations to reveal key catalytic residues and a substrate-dependent conformational shift that activates the enzyme, providing a foundation for engineering more efficient plastic-degrading enzymes.
The effect of ionic strength on PETase enzymes: an experimental and computational study
AI summary Read the abstract
Researchers used molecular dynamics simulations and lab assays to compare two PET-degrading enzymes at different salt concentrations, finding that the marine-derived PETaseSM14 maintains activity under high-salt conditions due to a rigid binding pocket, while the commonly studied IsPETase is deactivated by high ionic strength, offering insights for engineering enzymes suited to diverse environments.
Discovering Novel PETase Enzymes for Enhanced PET Plastic Degradation Using in Silico Approaches
AI summary Read the abstract
This comprehensive review found that freshwater biodiversity faces extinction rates 100 times above background levels, driven by habitat fragmentation, chemical pollution, invasive species, and hydrological alteration, with molluscs, fishes, and crustaceans among the most threatened groups. Microplastic pollution is among the chemical stressors contributing to this crisis, making freshwater biodiversity monitoring frameworks directly relevant to assessing microplastic ecological impacts.
Identification of Prospective PETases Across Prokaryotes Using an in silico Approach
AI summary Read the abstract
Researchers used computational methods to screen prokaryotic protein sequences for PET-degrading enzyme candidates, identifying 27 potential PETases across diverse bacterial species and shortlisting three from Halopseudomonas pertucinogena, Halopseudomonas bauzanensis, and Ketobacter sp. as the most structurally and functionally similar to the well-characterized PETase from Ideonella sakaiensis.
From Bulk to Binding: Decoding the Entry of PET into Hydrolase Binding Pockets
AI summary Read the abstract
Researchers used computational and structural analyses to decode how PET polymer chains enter and bind within the active sites of plastic-degrading hydrolase enzymes, providing mechanistic insights that could guide engineering of more efficient PETase variants for industrial recycling applications.
Research digests by email
When a large batch of papers lands in the Atlas, we read through it and send a short write-up of what stood out.