Generalized biomolecular modeling and design with RoseTTAFold All-Atom

R Krishna, J Wang, W Ahern, P Sturmfels, P Venkatesh… - Science, 2024 - science.org
Deep-learning methods have revolutionized protein structure prediction and design but are
presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which …

Opportunities and challenges for machine learning-assisted enzyme engineering

J Yang, FZ Li, FH Arnold - ACS Central Science, 2024 - ACS Publications
Enzymes can be engineered at the level of their amino acid sequences to optimize key
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …

[HTML][HTML] Strategies for designing biocatalysts with new functions

EL Bell, AE Hutton, AJ Burke, A O'Connell… - Chemical Society …, 2024 - pubs.rsc.org
The engineering of natural enzymes has led to the availability of a broad range of
biocatalysts that can be used for the sustainable manufacturing of a variety of chemicals and …

Building enzymes through design and evolution

EJ Hossack, FJ Hardy, AP Green - ACS Catalysis, 2023 - ACS Publications
Designing efficient enzymes is a formidable challenge at the forefront of modern
biocatalysis. Here, we review recent developments in the field and illustrate how the …

[HTML][HTML] Automated in vivo enzyme engineering accelerates biocatalyst optimization

E Orsi, L Schada von Borzyskowski, S Noack… - Nature …, 2024 - nature.com
Achieving cost-competitive bio-based processes requires development of stable and
selective biocatalysts. Their realization through in vitro enzyme characterization and …

Protein Design Using Structure-Prediction Networks: AlphaFold and RoseTTAFold as Protein Structure Foundation Models

J Wang, JL Watson, SL Lisanza - Cold Spring Harbor …, 2024 - cshperspectives.cshlp.org
Designing proteins with tailored structures and functions is a long-standing goal in
bioengineering. Recently, deep learning advances have enabled protein structure …

A New Age of Biocatalysis Enabled by Generic Activation Modes

S Jain, F Ospina, SC Hammer - JACS Au, 2024 - ACS Publications
Biocatalysis is currently undergoing a profound transformation. The field moves from relying
on nature's chemical logic to a discipline that exploits generic activation modes, allowing for …

Redox Engineering of Myoglobin by Cofactor Substitution to Enhance Cyclopropanation Reactivity

Y Kagawa, K Oohora, T Himiyama, A Suzuki… - Angewandte …, 2024 - Wiley Online Library
Design of metal cofactor ligands is essential for controlling the reactivity of metalloenzymes.
We investigated a carbene transfer reaction catalyzed by myoglobins containing iron …

[HTML][HTML] Nitric Oxide Binding Geometry in Heme-Proteins: Relevance for Signal Transduction

G De Simone, A di Masi, D Sbardella, P Ascenzi… - Antioxidants, 2024 - mdpi.com
Nitric oxide (NO) synthesis, signaling, and scavenging is associated to relevant
physiological and pathological events. In all tissues and organs, NO levels and related …

Synthesis of a COF-on-MOF hybrid nanomaterial for enhanced colorimetric biosensing

H Xie, L Wang, X Yu, T Zhou, M Wang, J Yang, T Gao… - Talanta, 2024 - Elsevier
The construction of hybrid materials is significant for the exploration of functionalities in
colorimetric biosensing due to its structural designability and synergy effects. In this work, a …