[HTML][HTML] Insertions and deletions in protein evolution and engineering

S Savino, T Desmet, J Franceus - Biotechnology Advances, 2022 - Elsevier
Protein evolution or engineering studies are traditionally focused on amino acid
substitutions and the way these contribute to fitness. Meanwhile, the insertion and deletion …

Sourcing thermotolerant poly (ethylene terephthalate) hydrolase scaffolds from natural diversity

E Erickson, JE Gado, L Avilán, F Bratti… - Nature …, 2022 - nature.com
Enzymatic deconstruction of poly (ethylene terephthalate)(PET) is under intense
investigation, given the ability of hydrolase enzymes to depolymerize PET to its constituent …

Enzyme function and evolution through the lens of bioinformatics

AJM Ribeiro, IG Riziotis, N Borkakoti… - Biochemical …, 2023 - portlandpress.com
Enzymes have been shaped by evolution over billions of years to catalyse the chemical
reactions that support life on earth. Dispersed in the literature, or organised in online …

Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt

AT Nottingham, JJ Scott, K Saltonstall, K Broders… - Nature …, 2022 - nature.com
Perturbation of soil microbial communities by rising temperatures could have important
consequences for biodiversity and future climate, particularly in tropical forests where high …

FLIP: Benchmark tasks in fitness landscape inference for proteins

C Dallago, J Mou, KE Johnston, BJ Wittmann… - bioRxiv, 2021 - biorxiv.org
Abstract Machine learning could enable an unprecedented level of control in protein
engineering for therapeutic and industrial applications. Critical to its use in designing …

Unlocking the stereoselectivity and substrate acceptance of enzymes: Proline‐induced loop engineering test

G Qu, Y Bi, B Liu, J Li, X Han, W Liu… - Angewandte Chemie …, 2022 - Wiley Online Library
Protein stability and evolvability influence each other. Although protein dynamics play
essential roles in various catalytically important properties, their high flexibility and diversity …

Protein conformational ensembles in function: roles and mechanisms

R Nussinov, Y Liu, W Zhang, H Jang - RSC Chemical Biology, 2023 - pubs.rsc.org
The sequence-structure-function paradigm has dominated twentieth century molecular
biology. The paradigm tacitly stipulated that for each sequence there exists a single, well …

Ensemble-function relationships to dissect mechanisms of enzyme catalysis

F Yabukarski, T Doukov, MM Pinney, JT Biel… - Science …, 2022 - science.org
Decades of structure-function studies have established our current extensive understanding
of enzymes. However, traditional structural models are snapshots of broader conformational …

Photosynthetic adaptation to polar life: Energy balance, photoprotection and genetic redundancy

NPA Hüner, DR Smith, M Cvetkovska, X Zhang… - Journal of Plant …, 2022 - Elsevier
The persistent low temperature that characterize polar habitats combined with the
requirement for light for all photoautotrophs creates a conundrum. The absorption of too …

Dual-function biomimetic carrier based facilitated transport mixed matrix membranes with high stability for efficient CO2/N2 separation

W Zheng, Z Tian, Z Wang, D Peng, Y Zhang… - Separation and …, 2022 - Elsevier
Realizing efficient carbon capture by high-performance CO 2 separation membrane is
significant to mitigate the increasing emissions of greenhouse gas CO 2. Inspired by the …