Designing better enzymes: Insights from directed evolution
Highlights•Enzymes can be created by computational design and directed
evolution.•Insights from directed evolution:•Active-site organization by H-bonding networks …
evolution.•Insights from directed evolution:•Active-site organization by H-bonding networks …
How directed evolution reshapes the energy landscape in an enzyme to boost catalysis
The advent of biocatalysts designed computationally and optimized by laboratory evolution
provides an opportunity to explore molecular strategies for augmenting catalytic function …
provides an opportunity to explore molecular strategies for augmenting catalytic function …
Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico
The creation of artificial enzymes is a key objective of computational protein design.
Although de novo enzymes have been successfully designed, these exhibit low catalytic …
Although de novo enzymes have been successfully designed, these exhibit low catalytic …
Epistasis arises from shifting the rate-limiting step during enzyme evolution of a β-lactamase
Epistasis, the non-additive effect of mutations, can provide combinatorial improvements to
enzyme activity that substantially exceed the gains from individual mutations. Yet the …
enzyme activity that substantially exceed the gains from individual mutations. Yet the …
Enriching productive mutational paths accelerates enzyme evolution
D Patsch, T Schwander, M Voss, D Schaub… - Nature Chemical …, 2024 - nature.com
Darwinian evolution has given rise to all the enzymes that enable life on Earth. Mimicking
natural selection, scientists have learned to tailor these biocatalysts through recursive cycles …
natural selection, scientists have learned to tailor these biocatalysts through recursive cycles …
Using high-throughput molecular dynamics simulation to enhance the computational design of kemp elimination enzymes
Computational enzyme design has been successfully applied to identify new alternatives to
natural enzymes for the biosynthesis of important compounds. However, the moderate …
natural enzymes for the biosynthesis of important compounds. However, the moderate …
A novel 3D Zn-coordination polymer based on a multiresponsive fluorescent sensor demonstrating outstanding sensitivities and selectivities for the efficient detection …
Y Liu, Y Wang, XS Zhang, YS Sheng, WZ Li… - Dalton …, 2021 - pubs.rsc.org
A novel and unusual 3D luminescent coordination polymer (CP)[Zn2 (3-bpah)(bpta)(H2O)]·
3H2O (1), where 3-bpah denotes N, N′-bis (3-pyridinecarboxamide)-1, 2-cyclohexane and …
3H2O (1), where 3-bpah denotes N, N′-bis (3-pyridinecarboxamide)-1, 2-cyclohexane and …
Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening
VA Risso, A Romero-Rivera, LI Gutierrez-Rus… - Chemical …, 2020 - pubs.rsc.org
Directed evolution has revolutionized protein engineering. Still, enzyme optimization by
random library screening remains sluggish, in large part due to futile probing of mutations …
random library screening remains sluggish, in large part due to futile probing of mutations …
Interplay Between Substrate Polarity and Protein Dynamics in Evolved Kemp Eliminases
Extensive molecular dynamics (MD) simulations on designed and evolved enzymes for the
Kemp Elimination were performed. Over thirty different systems including combinations of …
Kemp Elimination were performed. Over thirty different systems including combinations of …
Decoded fingerprints of hyperresponsive, expanding product space: polyether cascade cyclizations as tools to elucidate supramolecular catalysis
H Chen, TR Li, N Sakai, C Besnard, L Guénée… - Chemical …, 2022 - pubs.rsc.org
Simple enough to be understood and complex enough to be revealing, cascade cyclizations
of diepoxides are introduced as new tools to characterize supramolecular catalysis …
of diepoxides are introduced as new tools to characterize supramolecular catalysis …