The road to fully programmable protein catalysis

SL Lovelock, R Crawshaw, S Basler, C Levy, D Baker… - Nature, 2022 - nature.com
The ability to design efficient enzymes from scratch would have a profound effect on
chemistry, biotechnology and medicine. Rapid progress in protein engineering over the past …

Biocatalysis

EL Bell, W Finnigan, SP France, AP Green… - Nature Reviews …, 2021 - nature.com
Biocatalysis has become an important aspect of modern organic synthesis, both in
academia and across the chemical and pharmaceutical industries. Its success has been …

Improving protein expression, stability, and function with ProteinMPNN

KH Sumida, R Núñez-Franco, I Kalvet… - Journal of the …, 2024 - ACS Publications
Natural proteins are highly optimized for function but are often difficult to produce at a scale
suitable for biotechnological applications due to poor expression in heterologous systems …

Direct generation of protein conformational ensembles via machine learning

G Janson, G Valdes-Garcia, L Heo, M Feig - Nature Communications, 2023 - nature.com
Dynamics and conformational sampling are essential for linking protein structure to
biological function. While challenging to probe experimentally, computer simulations are …

Machine learning for chemical reactions

M Meuwly - Chemical Reviews, 2021 - ACS Publications
Machine learning (ML) techniques applied to chemical reactions have a long history. The
present contribution discusses applications ranging from small molecule reaction dynamics …

Enhanced active-site electric field accelerates enzyme catalysis

C Zheng, Z Ji, II Mathews, SG Boxer - Nature Chemistry, 2023 - nature.com
The design and improvement of enzymes based on physical principles remain challenging.
Here we demonstrate that the principle of electrostatic catalysis can be leveraged to …

A backbone-centred energy function of neural networks for protein design

B Huang, Y Xu, X Hu, Y Liu, S Liao, J Zhang, C Huang… - Nature, 2022 - nature.com
A protein backbone structure is designable if a substantial number of amino acid sequences
exist that autonomously fold into it,. It has been suggested that the designability of …

Ratcheting synthesis

S Borsley, JM Gallagher, DA Leigh… - Nature Reviews …, 2024 - nature.com
Synthetic chemistry has traditionally relied on reactions between reactants of high chemical
potential and transformations that proceed energetically downhill to either a global or local …

Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B

TS Mehlman, JT Biel, SM Azeem, ER Nelson… - Elife, 2023 - elifesciences.org
Much of our current understanding of how small-molecule ligands interact with proteins
stems from X-ray crystal structures determined at cryogenic (cryo) temperature. For proteins …

Catalytic cycle of formate dehydrogenase captured by single-molecule conductance

A Zhang, X Zhuang, J Liu, J Huang, L Lin, Y Tang… - Nature Catalysis, 2023 - nature.com
Understanding the mechanisms and kinetics of enzymatic reactions is essential for studies
of life science and for bioengineering. Here the different reaction states in the catalytic cycle …