Loop dynamics and the evolution of enzyme activity

M Corbella, GP Pinto, SCL Kamerlin - Nature Reviews Chemistry, 2023 - nature.com
In the early 2000s, Tawfik presented his 'New View'on enzyme evolution, highlighting the
role of conformational plasticity in expanding the functional diversity of limited repertoires of …

Engineering biomaterials for the recovery of rare earth elements

Q Ye, D Wang, N Wei - Trends in Biotechnology, 2023 - cell.com
The escalating global demand for rare earth elements (REEs) and the overabundance of
REE-containing waste require innovative technologies for REE recovery from waste to …

Mechanisms of protein evolution

V Jayaraman, S Toledo‐Patiño, L Noda‐García… - Protein …, 2022 - Wiley Online Library
How do proteins evolve? How do changes in sequence mediate changes in protein
structure, and in turn in function? This question has multiple angles, ranging from …

Functional roles of enzyme dynamics in accelerating active site chemistry: Emerging techniques and changing concepts

S Gao, JP Klinman - Current opinion in structural biology, 2022 - Elsevier
With the growing acceptance of the contribution of protein conformational ensembles to
enzyme catalysis and regulation, research in the field of protein dynamics has shifted toward …

Computer-aided understanding and engineering of enzymatic selectivity

L Wu, L Qin, Y Nie, Y Xu, YL Zhao - Biotechnology Advances, 2022 - Elsevier
Abstract Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric
synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally …

Exploiting enzyme evolution for computational protein design

GP Pinto, M Corbella, AO Demkiv… - Trends in Biochemical …, 2022 - cell.com
Recent years have seen an explosion of interest in understanding the physicochemical
parameters that shape enzyme evolution, as well as substantial advances in computational …

Computational design of soluble functional analogues of integral membrane proteins

CA Goverde, M Pacesa, N Goldbach, LJ Dornfeld… - BioRxiv, 2023 - biorxiv.org
De novo design of complex protein folds using solely computational means remains a
significant challenge. Here, we use a robust deep learning pipeline to design complex folds …

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 …

[HTML][HTML] The stability landscape of de novo TIM barrels explored by a modular design approach

S Romero-Romero, M Costas, DAS Manzano… - Journal of Molecular …, 2021 - Elsevier
The ability to design stable proteins with custom-made functions is a major goal in
biochemistry with practical relevance for our environment and society. Understanding and …

Exploring the protein sequence space with global generative models

S Romero-Romero, S Lindner… - Cold Spring Harbor …, 2023 - cshperspectives.cshlp.org
Recent advancements in specialized large-scale architectures for training images and
language have profoundly impacted the field of computer vision and natural language …