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 …

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 …

Advances in ultrahigh-throughput screening for directed enzyme evolution

U Markel, KD Essani, V Besirlioglu, J Schiffels… - Chemical Society …, 2020 - pubs.rsc.org
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long
time. In order to exploit their full potential, enzymes often need to be re-engineered or …

Biomolecular QM/MM simulations: What are some of the “burning issues”?

Q Cui, T Pal, L Xie - The Journal of Physical Chemistry B, 2021 - ACS Publications
QM/MM simulations have become an indispensable tool in many chemical and biochemical
investigations. Considering the tremendous degree of success, including recognition by a …

Evolution of dynamical networks enhances catalysis in a designer enzyme

HA Bunzel, JLR Anderson, D Hilvert, VL Arcus… - Nature Chemistry, 2021 - nature.com
Activation heat capacity is emerging as a crucial factor in enzyme thermoadaptation, as
shown by the non-Arrhenius behaviour of many natural enzymes. However, its physical …

Designing better enzymes: Insights from directed evolution

HA Bunzel, JLR Anderson, AJ Mulholland - Current Opinion in Structural …, 2021 - Elsevier
Highlights•Enzymes can be created by computational design and directed
evolution.•Insights from directed evolution:•Active-site organization by H-bonding networks …

Temperature, dynamics, and enzyme-catalyzed reaction rates

VL Arcus, AJ Mulholland - Annual review of biophysics, 2020 - annualreviews.org
We review the adaptations of enzyme activity to different temperatures. Psychrophilic (cold-
adapted) enzymes show significantly different activation parameters (lower activation …

Computational enzyme redesign: large jumps in function

Y Cui, J Sun, B Wu - Trends in Chemistry, 2022 - cell.com
Rising demands for enzymes in biotechnological applications have fueled efforts to tailor
their properties towards desired functions, such as activity, selectivity, and stability …

Enzyme evolution and the temperature dependence of enzyme catalysis

VL Arcus, MW Van Der Kamp, CR Pudney… - Current Opinion in …, 2020 - Elsevier
Experiments and biomolecular simulations are revealing new and unexpected details of
how enzymes are adapted to specific temperatures. These findings are elucidating enzyme …

From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics

SS Chaturvedi, D Bím, CZ Christov… - Chemical Science, 2023 - pubs.rsc.org
Enzymes are versatile and efficient biological catalysts that drive numerous cellular
processes, motivating the development of enzyme design approaches to tailor catalysts for …