DNA glycosylases safeguard the genome by locating and excising a diverse array of aberrant nucleobases created from oxidation, alkylation, and deamination of DNA. Since the discovery 28years ago that these enzymes employ a base flipping mechanism to trap their substrates, six different protein architectures have been identified to perform the same basic task. Work over the past several years ha...

In enzymology, as in organic chemistry, many transformations revolve around the chemistry of the carbonyl group. A carbonyl group is electrophilic how can it be made more so? Hydrogens next to a carbonyl group have a reduced pK, how can this reactivity be promoted? Nature has found several ways to address these mechanistic challenges, the most important of which is the use of imines. Studies on...

One of the most controversial questions in enzymology today is whether protein dynamics are significant in enzyme catalysis. A particular issue in these debates is the unusual temperature-dependence of some kinetic isotope effects for enzyme-catalysed reactions. In the present paper, we review our recent model [Glowacki, Harvey and Mulholland (2012) Nat. Chem. 4, 169-176] that is capable of rep...

Simulations and modelling [e.g. with combined QM/MM (quantum mechanics/molecular mechanics) methods] are increasingly important in investigations of enzyme-catalysed reaction mechanisms. Calculations offer the potential of uniquely detailed, atomic-level insight into the fundamental processes of biological catalysis. Highly accurate methods promise quantitative comparison with experiments, and ...

BACKGROUND Chemistry and particularly enzymology at surfaces is a topic of rapidly growing interest, both in terms of its role in biological systems and its application in biocatalysis. Existing protein immobilization approaches, including noncovalent or covalent attachments to solid supports, have difficulties in controlling protein orientation, reducing nonspecific absorption and preventing p...

This study offers a detailed mechanistic investigation of host-guest encapsulation behavior in a new enzyme-mimetic metal-ligand host and provides the first observation of a conformational selection mechanism (as opposed to induced fit) in a supramolecular system. The Ga4L4 host described features a C3-symmetric ligand motif with meta-substituted phenyl spacers, which enables the host to initia...

Mechanistic models for biochemical systems are frequently proposed from structural data. Site-directed mutagenesis can be used to test the importance of proposed functional sites, but these data do not necessarily indicate how these sites contribute to function. In this study, we applied an alternative approach to the catalytic mechanism of alkaline phosphatase (AP), a widely studied prototypic...

Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix...

Reflections on advances and retreats in biochemistry have, over the years, generated several maxims. The late Efraim Racker’s ‘don’t waste clean thinking on dirty enzymes’ has been one of the most durable. On the occasion of a lecture in Jerusalem a decade ago, I framed a list of the ten ‘best’ maxims as ‘commandments’, which were later published as a ‘Guest Commentary’ in the Journal of Bacter...

In this improved method for rapid enzymatic determination of total cholesterol, the lipid extracts from tissues are dissolved in an equal volume of peroxide-free dioxane/isopropanol (50/50 by vol) solution, and are reacted directly with the aqueous enzymatic reagent, without further treatment. The presence of organic solvents, such as dioxane and isopropanol, does not interfere with enzymatic a...