Using nature's blueprint to expand catalysis with Earth-abundant metals

RM Bullock, JG Chen, L Gagliardi, PJ Chirik, OK Farha… - Science, 2020 - science.org
BACKGROUND Catalysis has had a transformative impact on society, playing a crucial role
in the production of modern materials, medicines, fuels, and chemicals. Precious metals …

Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W Xi, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

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 …

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015 - pubs.rsc.org
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

Differentially evolved glucosyltransferases determine natural variation of rice flavone accumulation and UV-tolerance

M Peng, R Shahzad, A Gul, H Subthain, S Shen… - Nature …, 2017 - nature.com
Decoration of phytochemicals contributes to the majority of metabolic diversity in nature,
whereas how this process alters the biological functions of their precursor molecules …

The challenge of predicting distal active site mutations in computational enzyme design

S Osuna - Wiley Interdisciplinary Reviews: Computational …, 2021 - Wiley Online Library
Many computational enzyme design approaches have been developed in recent years that
focus on a reduced set of key enzymatic features. Initial protocols mostly focused on the …

Machine learning-guided acyl-ACP reductase engineering for improved in vivo fatty alcohol production

JC Greenhalgh, SA Fahlberg, BF Pfleger… - Nature …, 2021 - nature.com
Alcohol-forming fatty acyl reductases (FARs) catalyze the reduction of thioesters to alcohols
and are key enzymes for microbial production of fatty alcohols. Many metabolic engineering …

The role of conformational dynamics and allostery in modulating protein evolution

P Campitelli, T Modi, S Kumar… - Annual review of …, 2020 - annualreviews.org
Advances in sequencing techniques and statistical methods have made it possible not only
to predict sequences of ancestral proteins but also to identify thousands of mutations in the …

Accurate prediction of enzyme thermostabilization with Rosetta using AlphaFold ensembles

F Peccati, S Alunno-Rufini… - Journal of chemical …, 2023 - ACS Publications
Thermostability enhancement is a fundamental aspect of protein engineering as a
biocatalyst's half-life is key for its industrial and biotechnological application, particularly at …

Role of conformational dynamics in the evolution of novel enzyme function

MA Maria-Solano, E Serrano-Hervás… - Chemical …, 2018 - pubs.rsc.org
The free energy landscape concept that describes enzymes as an ensemble of differently
populated conformational sub-states in dynamic equilibrium is key for evaluating enzyme …