Biocatalysis in organic chemistry and biotechnology: past, present, and future

MT Reetz - Journal of the American Chemical Society, 2013 - ACS Publications
Enzymes as catalysts in synthetic organic chemistry gained importance in the latter half of
the 20th century, but nevertheless suffered from two major limitations. First, many enzymes …

Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology

MW van der Kamp, AJ Mulholland - Biochemistry, 2013 - ACS Publications
Computational enzymology is a rapidly maturing field that is increasingly integral to
understanding mechanisms of enzyme-catalyzed reactions and their practical applications …

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 …

On the temperature dependence of enzyme-catalyzed rates

VL Arcus, EJ Prentice, JK Hobbs, AJ Mulholland… - Biochemistry, 2016 - ACS Publications
One of the critical variables that determine the rate of any reaction is temperature. For
biological systems, the effects of temperature are convoluted with myriad (and often …

Design of biomimetic catalysts by molecular imprinting in synthetic polymers: the role of transition state stabilization

GU Wulff, J Liu - Accounts of chemical research, 2012 - ACS Publications
The impressive efficiency and selectivity of biological catalysts has engendered a long-
standing effort to understand the details of enzyme action. It is widely accepted that enzymes …

[HTML][HTML] Gates of enzymes

A Gora, J Brezovsky, J Damborsky - Chemical reviews, 2013 - ACS Publications
Enzymes are very efficient catalysts that are essential for the functioning of living organisms.
The low efficiency of biocatalysts produced de novo relative to those that have evolved …

Good vibrations in enzyme-catalysed reactions

S Hay, NS Scrutton - Nature chemistry, 2012 - nature.com
Fast motions (femtosecond to picosecond) and their potential involvement during enzyme-
catalysed reactions have ignited considerable interest in recent years. Their influence on …

Hydrogen tunneling in enzymes and biomimetic models

JP Layfield, S Hammes-Schiffer - Chemical reviews, 2014 - ACS Publications
Hydrogen transfer reactions play an important role throughout chemistry and biology. In
general, hydrogen transfer reactions encompass proton and hydride transfer, which are …

Drug design in the exascale era: a perspective from massively parallel QM/MM simulations

B Raghavan, M Paulikat, K Ahmad… - Journal of chemical …, 2023 - ACS Publications
The initial phases of drug discovery–in silico drug design–could benefit from first principle
Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations …

Catalytic enzymes are active matter

AY Jee, YK Cho, S Granick… - Proceedings of the …, 2018 - National Acad Sciences
Using a microscopic theory to analyze experiments, we demonstrate that enzymes are active
matter. Superresolution fluorescence measurements—performed across four orders of …