Ensemble-function relationships to dissect mechanisms of enzyme catalysis

Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (P-effects) and changing the reactivity of each state (k-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.

Parallel molecular mechanisms for enzyme temperature adaptation

The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.

Serum electrolytes can promote hydroxyl radical-initiated biomolecular damage from inflammation

Chronic inflammatory disorders are associated with biomolecular damage attributed partly to reactions with Reactive Oxygen Species (ROS), particularly hydroxyl radicals (^•OH). However, the impacts of serum electrolytes on ROS-associated damage has received little attention. We demonstrate that the conversion of ^•OH to carbonate and halogen radicals via reactions with serum-relevant carbonate and halide concentrations fundamentally alters the targeting of amino acids and loss of enzymatic activity in catalase, albumin and carbonic anhydrase, three important blood proteins. Chemical kinetic modeling indicated that carbonate and halogen radical concentrations should exceed ^•OH concentrations by 6 and 2 orders of magnitude, respectively. Steady-state γ-radiolysis experiments demonstrated that serum-level carbonates and halides increased tyrosine, tryptophan and enzymatic activity losses in catalase up to 6-fold. These outcomes were specific to carbonates and halides, not general ionic strength effects. Serum carbonates and halides increased the degradation of tyrosines and methionines in albumin, and increased the degradation of histidines while decreasing enzymatic activity loss in carbonic anhydrase. Serum electrolytes increased the degradation of tyrosines, tryptophans and enzymatic activity in the model enzyme, ketosteroid isomerase, predominantly due to carbonate radical reactions. Treatment of a mutant ketosteroid isomerase indicated that preferential targeting of the active site tyrosine accounted for half of the total tyrosine loss. The results suggest that carbonate and halogen radicals may be more significant than ^•OH as drivers for protein degradation in serum. Accounting for the selective targeting of biomolecules by these daughter radicals is important for developing a mechanistic understanding of the consequences of oxidative stress.

Hydrogen Bonds: Simple after All?

Hydrogen bonds play integral roles in biological structure, function, and conformational dynamics and are fundamental to life as it has evolved on Earth. However, our understanding of these fundamental and ubiquitous interactions has seemed fractured and incomplete, and it has been difficult to extract generalities and principles about hydrogen bonds despite thousands of papers published on this topic, perhaps in part because of the expanse of this subject and the density of studies. Fortunately, recent hydrogen bond proposals, discussions, and debates have stimulated new tests and models and have led to a remarkably simple picture of the structure of hydrogen bonds. This knowledge also provides clarity concerning hydrogen bond energetics, limiting and simplifying the factors that need be considered. Herein we recount the advances that have led to this simpler view of hydrogen bond structure, dynamics, and energetics. A quantitative predictive model for hydrogen bond length can now be broadly and deeply applied to evaluate current proposals and to uncover structural features of proteins, their conformational restraints, and their correlated motions. In contrast, a quantitative energetic description of molecular recognition and catalysis by proteins remains an important ongoing challenge, although our improved understanding of hydrogen bonds may aid in testing predictions from current and future models. We close by codifying our current state of understanding into five "Rules for Hydrogen Bonding" that may provide a foundation for understanding and teaching about these vital interactions and for building toward a deeper understanding of hydrogen bond energetics.

Electron transfer and proton-coupled electron transfer reactivity and self-exchange of synthetic [2Fe-2S] complexes: models for Rieske and mitoNEET clusters

This report describes the thermochemistry, proton-coupled electron transfer (PCET) reactions and self-exchange rate constants for a set of bis-benzimidazolate-ligated [2Fe–2S] clusters. These clusters serve as a model for the chemistry of biological Rieske and mitoNEET clusters. PCET from [Fe₂S₂(^Prbbim)(^PrbbimH)]^2– (4) and [Fe₂S₂(^Prbbim)(^PrbbimH₂)]^1– (5) to TEMPO occurs via concerted proton–electron transfer (CPET) mechanisms (^PrbbimH₂ = 4,4-bis-(benzimidazol-2-yl)heptane). Intermolecular electron transfer (ET) self-exchange between [Fe₂S₂(^Prbbim)₂]^2– (1) and [Fe₂S₂(^Prbbim)₂]^3– (2) occurs with a rate constant of (1.20 ± 0.06) × 10⁵ M^–1 s^–1 at 26 °C. A similar self-exchange rate constant is found for the related [2Fe–2S] cluster [Fe₂S₂(SArO)₂]^2–/3–, SArO^2– = thiosalicylate. These are roughly an order of magnitude slower than that reported for larger [4Fe–4S] clusters and 1 order of magnitude faster than that reported for N-ligated high-spin iron complexes. These results suggest that the rate of intermolecular ET to/from [Fe–S] clusters is modulated by cluster size. The measured PCET self-exchange rate constant for 1 and 4 at −30 °C is (3.8 ± 0.7) × 10⁴ M^–1 s^–1. Analysis of rate constants using the Marcus cross-relation suggests that this process likely occurs via a concerted proton–electron transfer (CPET) mechanism. The implications of these findings to biological systems are also discussed, including the conclusion that histidine-ligated [2Fe–2S] clusters should not have a strong bias to undergo concerted e^–/H⁺ transfers.

[Fe₂S₂(^Prbbim)(^PrbbimH_x)]^y- clusters have been generated in multiple redox and protonation states. Their PCET and ET thermochemistry and reactivity are described. The PCET self-exchange reaction occurs by concerted e⁻/H⁺ exchange, and the ET self-exchange barriers for different clusters are shown to scale with [Fe−S] cluster size. The implications of these results for the reactivity of biochemical imidazole-ligated clusters is discussed.