Zachary D. Nagel

Update 1 of: Tunneling and Dynamics in Enzymatic Hydride Transfer

Enzymes continue to be the subject of intensive research efforts because of their ability to accelerate chemical reactions by factors as large as 1020 with extraordinary selectivity.1 Despite enormous advances, on both experimental and theoretical fronts, our understanding of how proteins catalyze reactions remains incomplete. Biomimetic and engineered protein catalysts have failed to reach the catalytic efficiency of naturally occurring enzymes. In addition, computational methods continue to fall short of predicting with precision the catalytic properties of known structures, and the more ambitious goal of generating de novo enzymes with desired function. A recent advance combines computational design with directed evolution to achieve a 105-fold rate acceleration.2 Nevertheless, the ultimate goal of using and engineering enzymes for biomedical and industrial applications still demands a deeper understanding of how the primary sequence of a protein determines its catalytic properties. This review is intended to provide insight into recent advances in the field of enzymology, with emphasis on experiments illuminating the role of protein dynamics from the richly informative perspective of hydride transfer. 1.1. Properties of Hydrogen and Protein Motion A very large number of the known enzymatic reactions involve the transfer of hydrogen (where hydrogen can refer to a proton, hydrogen atom, or hydride). Because of the unique properties of the periodic table’s lightest element, these reactions present at once a difficulty and an opportunity in terms of our understanding of biological catalysis: while hydrogen chemistry demands some special theoretical considerations, it also offers sensitivity of the reaction to environmental effects that can serve as a valuable probe of the subtle ways in which enzymes catalyze reactions. 1.1.1. Properties of Hydrogen Several features distinguish hydrogen transfer from chemistry involving the exchange of bonds between heavier atoms. First, because of its small mass, hydrogen has a de Broglie wavelength on the order of the distances over which it is expected to be transferred. It is, therefore, anticipated that quantum mechanical behavior will play a significant role in the chemical dynamics of hydrogen chemistry.3 Second, there are three isotopes of hydrogen: protium, deuterium, and tritium with atomic mass 1, 2, and 3, respectively. Since the heavier isotopes will have the same chemical properties but significantly smaller de Broglie wavelengths, they can serve as a direct probe of quantum effects; this contrasts with electron transfer, where particles of variable mass are not available for kinetic studies.4 Third, because the hydrogen donor and acceptor wave function overlap will be a very sensitive function of the donor–acceptor distance, environmental dynamics on a subangstrom scale can have a significant impact on the quantum mechanical aspects of hydrogen transfer.5 Indeed, a picture is emerging wherein the quantum properties of hydrogen and the motions of enzymes are deeply connected in the mechanism of enzyme-catalyzed hydrogen transfer.

Multiplexed DNA repair assays for multiple lesions and multiple doses via transcription inhibition and transcriptional mutagenesis

Significance DNA, the blueprint of the cell, is constantly damaged by chemicals and radiation. Because DNA damage may cause cell death or mutations that may lead to diseases such as cancer, cells are armed with an arsenal of several distinct mechanisms for repairing the many types of DNA damage that occur. DNA repair capacity (DRC) varies among individuals, and reduced DRC is associated with disease risk; however, the available DRC assays are labor intensive and measure only one pathway at a time. Herein, we present powerful new assays that measure DRC in multiple pathways in a single assay. We use the assays to measure interindividual DRC differences and inhibition of DNA repair, and to uncover unexpected error-prone transcriptional bypass of a thymine dimer. The capacity to repair different types of DNA damage varies among individuals, making them more or less susceptible to the detrimental health consequences of damage exposures. Current methods for measuring DNA repair capacity (DRC) are relatively labor intensive, often indirect, and usually limited to a single repair pathway. Here, we describe a fluorescence-based multiplex flow-cytometric host cell reactivation assay (FM-HCR) that measures the ability of human cells to repair plasmid reporters, each bearing a different type of DNA damage or different doses of the same type of DNA damage. FM-HCR simultaneously measures repair capacity in any four of the following pathways: nucleotide excision repair, mismatch repair, base excision repair, nonhomologous end joining, homologous recombination, and methylguanine methyltransferase. We show that FM-HCR can measure interindividual DRC differences in a panel of 24 cell lines derived from genetically diverse, apparently healthy individuals, and we show that FM-HCR may be used to identify inhibitors or enhancers of DRC. We further develop a next-generation sequencing-based HCR assay (HCR-Seq) that detects rare transcriptional mutagenesis events due to lesion bypass by RNA polymerase, providing an added dimension to DRC measurements. FM-HCR and HCR-Seq provide powerful tools for exploring relationships among global DRC, disease susceptibility, and optimal treatment.

Impaired protein conformational landscapes as revealed in anomalous Arrhenius prefactors

A growing body of data supports a role for protein motion in enzyme catalysis. In particular, the ability of enzymes to sample catalytically relevant conformational substates has been invoked to model kinetic and spectroscopic data. However, direct experimental links between rapidly interconverting conformations and the chemical steps of catalysis remain rare. We report here on the kinetic analysis and characterization of the hydride transfer step catalyzed by a series of mutant thermophilic alcohol dehydrogenases (ht-ADH), presenting evidence for Arrhenius prefactor values that become enormously elevated above an expected value of approximately 1013 s-1 when the enzyme operates below its optimal temperature range. Restoration of normal Arrhenius behavior in the ht-ADH reaction occurs at elevated temperatures. A simple model, in which reduced temperature alters the ability of the ht-ADH variants to sample the catalytically relevant region of conformational space, can reproduce the available data. These findings indicate an impaired landscape that has been generated by the combined condition of reduced temperature and mutation at a single, active-site hydrophobic side chain. The broader implication is that optimal enzyme function requires the maintenance of a relatively smooth landscape that minimizes low energy traps.

Minor Changes in Expression of the Mismatch Repair Protein MSH2 Exert a Major Impact on Glioblastoma Response to Temozolomide

Glioblastoma (GBM) is often treated with the cytotoxic drug temozolomide, but the disease inevitably recurs in a drug-resistant form after initial treatment. Here, we report that in GBM cells, even a modest decrease in the mismatch repair (MMR) components MSH2 and MSH6 have profound effects on temozolomide sensitivity. RNAi-mediated attenuation of MSH2 and MSH6 showed that such modest decreases provided an unexpectedly strong mechanism of temozolomide resistance. In a mouse xenograft model of human GBM, small changes in MSH2 were sufficient to suppress temozolomide-induced tumor regression. Using The Cancer Genome Atlas to analyze mRNA expression patterns in tumors from temozolomide-treated GBM patients, we found that MSH2 transcripts in primary GBM could predict patient responses to initial temozolomide therapy. In recurrent disease, the absence of microsatellite instability (the standard marker for MMR deficiency) suggests a lack of involvement of MMR in the resistant phenotype of recurrent disease. However, more recent studies reveal that decreased MMR protein levels occur often in recurrent GBM. In accordance with our findings, these reported decreases may constitute a mechanism by which GBM evades temozolomide sensitivity while maintaining microsatellite stability. Overall, our results highlight the powerful effects of MSH2 attenuation as a potent mediator of temozolomide resistance and argue that MMR activity offers a predictive marker for initial therapeutic response to temozolomide treatment.

Active Site Hydrophobic Residues Impact Hydrogen Tunneling Differently in a Thermophilic Alcohol Dehydrogenase at Optimal versus Nonoptimal Temperatures

A growing body of data suggests that protein motion plays an important role in enzyme catalysis. Two highly conserved hydrophobic active site residues in the cofactor-binding pocket of ht-ADH (Leu176 and V260) have been mutated to a series of hydrophobic side chains of smaller size, as well as one deletion mutant, L176Δ. Mutations decrease k(cat) and increase K(M)(NAD(+)). Most of the observed decreases in effects on k(cat) at pH 7.0 are due to an upward shift in the optimal pH for catalysis; a simple electrostatic model is invoked that relates the change in pK(a) to the distance between the positively charged nicotinamide ring and bound substrate. Structural modeling of the L176Δ and V260A variants indicates the development of a cavity behind the nicotinamide ring without any significant perturbation of the secondary structure of the enzyme relative to that of the wild type. Primary kinetic isotope effects (KIEs) are modestly increased for all mutants. Above the dynamical transition at 30 °C for ht-ADH [Kohen, A., et al. (1999) Nature 399, 496], the temperature dependence of the KIE is seen to increase with a decrease in side chain volume at positions 176 and 260. Additionally, the relative trends in the temperature dependence of the KIE above and below 30 °C appear to be reversed for the cofactor-binding pocket mutants in relation to wild-type protein. The aggregate results are interpreted in the context of a full tunneling model of enzymatic hydride transfer that incorporates both protein conformational sampling (preorganization) and active site optimization of tunneling (reorganization). The reduced temperature dependence of the KIE in the mutants below 30 °C indicates that at low temperatures, the enzyme adopts conformations refractory to donor-acceptor distance sampling.

Inter-individual variation in DNA repair capacity: a need for multi-pathway functional assays to promote translational DNA repair research.

Why does a constant barrage of DNA damage lead to disease in some individuals, while others remain healthy? This article surveys current work addressing the implications of inter-individual variation in DNA repair capacity for human health, and discusses the status of DNA repair assays as potential clinical tools for personalized prevention or treatment of disease. In particular, we highlight research showing that there are significant inter-individual variations in DNA repair capacity (DRC), and that measuring these differences provides important biological insight regarding disease susceptibility and cancer treatment efficacy. We emphasize work showing that it is important to measure repair capacity in multiple pathways, and that functional assays are required to fill a gap left by genome wide association studies, global gene expression and proteomics. Finally, we discuss research that will be needed to overcome barriers that currently limit the use of DNA repair assays in the clinic.

Identification of a Long-range Protein Network That Modulates Active Site Dynamics in Extremophilic Alcohol Dehydrogenases

Background: The role of protein flexibility in the C-H activation step, catalyzed by homologous thermophilic and psychrophilic alcohol dehydrogenases, is addressed. Results: Mutation at the substrate-binding site, or at a dimer interface, alters kinetic properties and protein oligomeric structure. Conclusion: Active site flexibility is correlated with subunit interactions 20 Å away. Significance: A long-range network of catalytically relevant, dynamical communication is identified. A tetrameric thermophilic alcohol dehydrogenase from Bacillus stearothermophilus (ht-ADH) has been mutated at an aromatic side chain in the active site (Trp-87). The ht-W87A mutation results in a loss of the Arrhenius break seen at 30 °C for the wild-type enzyme and an increase in cold lability that is attributed to destabilization of the active tetrameric form. Kinetic isotope effects (KIEs) are nearly temperature-independent over the experimental temperature range, and similar in magnitude to those measured above 30 °C for the wild-type enzyme. This suggests that the rigidification in the wild-type enzyme below 30 °C does not occur for ht-W87A. A mutation at the dimer-dimer interface in a thermolabile psychrophilic homologue of ht-ADH, ps-A25Y, leads to a more thermostable enzyme and a change in the rate-determining step at low temperature. The reciprocal mutation in ht-ADH, ht-Y25A, results in kinetic behavior similar to that of W87A. Collectively, the results indicate that flexibility at the active site is intimately connected to a subunit interaction 20 Å away. The convex Arrhenius curves previously reported for ht-ADH (Kohen, A., Cannio, R., Bartolucci, S., and Klinman, J. P. (1999) Nature 399, 496–499) are proposed to arise, at least in part, from a change in subunit interactions that rigidifies the substrate-binding domain below 30 °C, and impedes the ability of the enzyme to sample the catalytically relevant conformational landscape. These results implicate an evolutionarily conserved, long-range network of dynamical communication that controls C-H activation in the prokaryotic alcohol dehydrogenases.

S-State Dependence of the Calcium Requirement and Binding Characteristics in the Oxygen-Evolving Complex of Photosystem II †

The functional role of the Ca (2+) ion in the oxygen-evolving complex of photosystem II is not yet clear. Current models explain why the redox cycle of the complex would be interrupted after the S 3 state without Ca (2+), but the literature shows that it is interrupted after the S 2 state. Reinterpretation of the literature on methods of Ca (2+) depletion [Miqyass, M., van Gorkom, H. J., and Yocum, C. F. (2007) Photosynth. Res. 92, 275-287] led us to propose that all S-state transitions require Ca (2+). Here we confirm that interpretation by measurements of flash-induced S-state transitions in UV absorbance. The results are explained by a cation exchange at the Ca (2+) binding site that, in the absence of the extrinsic PsbP and PsbQ polypeptides, can occur in minutes in low S-states and in seconds in high S-states, depending on the concentration of the substituting cation. In the S 2(K (+)) or S 2(Na (+)) state a slow conformational change occurs that prevents recovery of the slow-exchange situation on return to a lower S-state but does not inhibit the S-state cycle in the presence of Ca (2+). The ratio of binding affinities for monovalent vs divalent cations increases dramatically in the higher S-states. With the possible exception of S 0 to S 1, all S-state transitions specifically require Ca (2+), suggesting that Ca (2+)-bound H 2O plays an essential role in a H (+) transfer network required for H (+)-coupled electron transfer from the Mn cluster to tyrosine Z.

DNA repair capacity in multiple pathways predicts chemoresistance in glioblastoma multiforme

Cancer cells can resist the effects of DNA-damaging therapeutic agents via utilization of DNA repair pathways, suggesting that DNA repair capacity (DRC) measurements in cancer cells could be used to identify patients most likely to respond to treatment. However, the limitations of available technologies have so far precluded adoption of this approach in the clinic. We recently developed fluorescence-based multiplexed host cell reactivation (FM-HCR) assays to measure DRC in multiple pathways. Here we apply a mathematical model that uses DRC in multiple pathways to predict cellular resistance to killing by DNA-damaging agents. This model, developed using FM-HCR and drug sensitivity measurements in 24 human lymphoblastoid cell lines, was applied to a panel of 12 patient-derived xenograft (PDX) models of glioblastoma to predict glioblastoma response to treatment with the chemotherapeutic DNA-damaging agent temozolomide. This work showed that, in addition to changes in O6-methylguanine DNA methyltransferase (MGMT) activity, small changes in mismatch repair (MMR), nucleotide excision repair (NER), and homologous recombination (HR) capacity contributed to acquired temozolomide resistance in PDX models and led to reduced relative survival prolongation following temozolomide treatment of orthotopic mouse models in vivo Our data indicate that measuring the combined status of MMR, HR, NER, and MGMT provided a more robust prediction of temozolomide resistance than assessments of MGMT activity alone. Cancer Res; 77(1); 198-206. ©2016 AACR.

ARID1A deficiency promotes mutability and potentiates therapeutic antitumor immunity unleashed by immune checkpoint blockade

ARID1A (the AT-rich interaction domain 1A, also known as BAF250a) is one of the most commonly mutated genes in cancer1,2. The majority of ARID1A mutations are inactivating mutations and lead to loss of ARID1A expression3, which makes ARID1A a poor therapeutic target. Therefore, it is of clinical importance to identify molecular consequences of ARID1A deficiency that create therapeutic vulnerabilities in ARID1A-mutant tumors. In a proteomic screen, we found that ARID1A interacts with mismatch repair (MMR) protein MSH2. ARID1A recruited MSH2 to chromatin during DNA replication and promoted MMR. Conversely, ARID1A inactivation compromised MMR and increased mutagenesis. ARID1A deficiency correlated with microsatellite instability genomic signature and a predominant C>T mutation pattern and increased mutation load across multiple human cancer types. Tumors formed by an ARID1A-deficient ovarian cancer cell line in syngeneic mice displayed increased mutation load, elevated numbers of tumor-infiltrating lymphocytes, and PD-L1 expression. Notably, treatment with anti-PD-L1 antibody reduced tumor burden and prolonged survival of mice bearing ARID1A-deficient but not ARID1A-wild-type ovarian tumors. Together, these results suggest ARID1A deficiency contributes to impaired MMR and mutator phenotype in cancer, and may cooperate with immune checkpoint blockade therapy.Loss of mismatch-repair protein ARID1A in cancer correlates with high mutation load & checkpoint blockade response, complementing MSI-based prognosis.