Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation

Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics

Protein dynamics play a crucial role in biological function, encompassing motions ranging from atomic vibrations to large-scale conformational changes. Recent advancements in experimental techniques, computational methods, and artificial intelligence have revolutionized our understanding of protein dynamics. Nuclear magnetic resonance spectroscopy provides atomic-resolution insights, while molecular dynamics simulations offer detailed trajectories of protein motions. Computational methods applied to X-ray crystallography and cryo-electron microscopy (cryo-EM) have enabled the exploration of protein dynamics, capturing conformational ensembles that were previously unattainable. The integration of machine learning, exemplified by AlphaFold2, has accelerated structure prediction and dynamics analysis. These approaches have revealed the importance of protein dynamics in allosteric regulation, enzyme catalysis, and intrinsically disordered proteins. The shift towards ensemble representations of protein structures and the application of single-molecule techniques have further enhanced our ability to capture the dynamic nature of proteins. Understanding protein dynamics is essential for elucidating biological mechanisms, designing drugs, and developing novel biocatalysts, marking a significant paradigm shift in structural biology and drug discovery.

Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites

In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.

Mutexa: A Computational Ecosystem for Intelligent Protein Engineering

Protein engineering holds immense promise in shaping the future of biomedicine and biotechnology. This Review focuses on our ongoing development of Mutexa, a computational ecosystem designed to enable "intelligent protein engineering". In this vision, researchers will seamlessly acquire sequences of protein variants with desired functions as biocatalysts, therapeutic peptides, and diagnostic proteins through a finely-tuned computational machine, akin to Amazon Alexa's role as a versatile virtual assistant. The technical foundation of Mutexa has been established through the development of a database that combines and relates enzyme structures and their respective functions (e.g., IntEnzyDB), workflow software packages that enable high-throughput protein modeling (e.g., EnzyHTP and LassoHTP), and scoring functions that map the sequence-structure-function relationship of proteins (e.g., EnzyKR and DeepLasso). We will showcase the applications of these tools in benchmarking the convergence conditions of enzyme functional descriptors across mutants, investigating protein electrostatics and cavity distributions in SAM-dependent methyltransferases, and understanding the role of nonelectrostatic dynamic effects in enzyme catalysis. Finally, we will conclude by addressing the future steps and fundamental challenges in our endeavor to develop new Mutexa applications that assist the identification of beneficial mutants in protein engineering.

Fragment-Based Calculations of Enzymatic Thermochemistry Require Dielectric Boundary Conditions

Electronic structure calculations on enzymes require hundreds of atoms to obtain converged results, but fragment-based approximations offer a cost-effective solution. We present calculations on enzyme models containing 500-600 atoms using the many-body expansion, comparing to benchmarks in which the entire enzyme-substrate complex is described at the same level of density functional theory. When the amino acid fragments contain ionic side chains, the many-body expansion oscillates under vacuum boundary conditions but rapid convergence is restored using low-dielectric boundary conditions. This implies that full-system calculations in the gas phase are inappropriate benchmarks for assessing errors in fragment-based approximations. A three-body protocol retains sub-kilocalorie per mole fidelity with respect to a supersystem calculation, as does a two-body calculation combined with a full-system correction at a low-cost level of theory. These protocols pave the way for application of high-level quantum chemistry to large systems via rigorous, ab initio treatment of many-body polarization.

Targeting the human gut microbiome with small-molecule inhibitors

The human gut microbiome is a complex microbial community that is strongly linked to both host health and disease. However, the detailed molecular mechanisms underlying the effects of these microorganisms on host biology remain largely uncharacterized. The development of non-lethal, small-molecule inhibitors that target specific gut microbial activities enables a powerful but underutilized approach to studying the gut microbiome and a promising therapeutic strategy. In this Review, we will discuss the challenges of studying this microbial community, the historic use of small-molecule inhibitors in microbial ecology, and recent applications of this strategy. We also discuss the evidence suggesting that host-targeted drugs can affect the growth and metabolism of gut microbes. Finally, we address the issues of developing and implementing microbiome-targeted small-molecule inhibitors and define important future directions for this research.

Theoretical Kinetic Isotope Effects in Establishing the Precise Biodegradation Mechanisms of Organic Pollutants

Compound-specific isotope analysis (CSIA) for natural isotope ratios has been recognized as a promising tool to elucidate biodegradation pathways of organic pollutants by microbial enzymes by relating reported kinetic isotope effects (KIEs) to apparent KIEs (AKIEs) derived from bulk isotope fractionations (ε_bulk). However, for many environmental reactions, neither are the reference KIE ranges sufficiently narrow nor are the mechanisms elucidated to the point that rate-determining steps have been identified unequivocally. In this work, besides providing reference KIEs and rationalizing AKIEs, good relationships have been explained by DFT computations for diverse biodegradation pathways with known enzymatic models between the theoretical isotope fractionations (ε_bulk^') from intrinsic KIEs on the rate-determining steps and the observed ε_bulk. (1) To confirm the mechanistic details of previously reported pathway-dependent CSIA, it includes isotope changes in MTBE biodegradation between hydroxylation by CYP450 and S_N2 reaction by cobalamin-dependent methyltransferase, the regioselectivity of toluene biodegradation by CYP450, and the rate-determining step in toluene biodegradation by benzylsuccinate synthase. (2) To yield new fundamental insights into some unclear biodegradation pathways, it consists of the oxidative function of toluene dioxygenase in biodegradation of TCE, the epoxidation mode in biodegradation of TCE by toluene 4-monooxygenase, and the weighted average mechanism in biodegradation of cDCE by CYP450.

Alleviating the unwanted effects of oxidative stress on Aβ clearance: a review of related concepts and strategies for the development of computational modelling

Treatment for Alzheimer's disease (AD) can be more effective in the early stages. Although we do not completely understand the aetiology of the early stages of AD, potential pathological factors (amyloid beta [Aβ] and tau) and other co-factors have been identified as causes of AD, which may indicate some of the mechanism at work in the early stages of AD. Today, one of the primary techniques used to help delay or prevent AD in the early stages involves alleviating the unwanted effects of oxidative stress on Aβ clearance. 4-Hydroxynonenal (HNE), a product of lipid peroxidation caused by oxidative stress, plays a key role in the adduction of the degrading proteases. This HNE employs a mechanism which decreases catalytic activity. This process ultimately impairs Aβ clearance. The degradation of HNE-modified proteins helps to alleviate the unwanted effects of oxidative stress. Having a clear understanding of the mechanisms associated with the degradation of the HNE-modified proteins is essential for the development of strategies and for alleviating the unwanted effects of oxidative stress. The strategies which could be employed to decrease the effects of oxidative stress include enhancing antioxidant activity, as well as the use of nanozymes and/or specific inhibitors. One area which shows promise in reducing oxidative stress is protein design. However, more research is needed to improve the effectiveness and accuracy of this technique. This paper discusses the interplay of potential pathological factors and AD. In particular, it focuses on the effect of oxidative stress on the expression of the Aβ-degrading proteases through adduction of the degrading proteases caused by HNE. The paper also elucidates other strategies that can be used to alleviate the unwanted effects of oxidative stress on Aβ clearance. To improve the effectiveness and accuracy of protein design, we explain the application of quantum mechanical/molecular mechanical approach.

Data-driven enzyme engineering to identify function-enhancing enzymes

Identifying function-enhancing enzyme variants is a 'holy grail' challenge in protein science because it will allow researchers to expand the biocatalytic toolbox for late-stage functionalization of drug-like molecules, environmental degradation of plastics and other pollutants, and medical treatment of food allergies. Data-driven strategies, including statistical modeling, machine learning, and deep learning, have largely advanced the understanding of the sequence-structure-function relationships for enzymes. They have also enhanced the capability of predicting and designing new enzymes and enzyme variants for catalyzing the transformation of new-to-nature reactions. Here, we reviewed the recent progresses of data-driven models that were applied in identifying efficiency-enhancing mutants for catalytic reactions. We also discussed existing challenges and obstacles faced by the community. Although the review is by no means comprehensive, we hope that the discussion can inform the readers about the state-of-the-art in data-driven enzyme engineering, inspiring more joint experimental-computational efforts to develop and apply data-driven modeling to innovate biocatalysts for synthetic and pharmaceutical applications.

Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics

We assessed enzyme:substrate conformational dynamics and the rate-limiting glycosylation step of a human pancreatic α-amylase:maltopentose complex. Microsecond molecular dynamics simulations suggested that the distance of the catalytic Asp197 nucleophile to the anomeric carbon of the buried glucoside is responsible for most of the enzyme active site fluctuations and that both Asp197 and Asp300 interact the most with the buried glucoside unit. The buried glucoside binds either in a ⁴C₁ chair or ²S_O skew conformations, both of which can change to TS-like conformations characteristic of retaining glucosidases. Starting from four distinct enzyme:substrate complexes, umbrella sampling quantum mechanics/molecular mechanics simulations (converged within less than 1 kcal·mol^-1 within a total simulation time of 1.6 ns) indicated that the reaction occurrs with a Gibbs barrier of 13.9 kcal·mol ^-1, in one asynchronous concerted step encompassing an acid-base reaction with Glu233 followed by a loose S_N2-like nucleophilic substitution by the Asp197. The transition state is characterized by a ²H₃ half-chair conformation of the buried glucoside that quickly changes to the E₃ envelope conformation preceding the attack of the anomeric carbon by the Asp197 nucleophile. Thermodynamic analysis of the reaction supported that a water molecule tightly hydrogen bonded to the glycosidic oxygen of the substrate at the reactant state (∼1.6 Å) forms a short hydrogen bond with Glu233 at the transition state (∼1.7 Å) and lowers the Gibbs barrier in over 5 kcal·mol^-1. The resulting Asp197-glycosyl was mostly found in the ⁴C₁ conformation, although the more endergonic B_3,O conformation was also observed. Altogether, the combination of short distances for the acid-base reaction with the Glu233 and for the nucleophilic attack by the Asp197 nucleophile and the availability of water within hydrogen bonding distance of the glycosidic oxygen provides a reliable criteria to identify reactive conformations of α-amylase complexes.

Influence of the Greater Protein Environment on the Electrostatic Potential in Metalloenzyme Active Sites: The Case of Formate Dehydrogenase

The Mo/W-containing metalloenzyme formate dehydrogenase (FDH) is an efficient and selective natural catalyst that reversibly converts CO₂ to formate under ambient conditions. In this study, we investigate the impact of the greater protein environment on the electrostatic potential (ESP) of the active site. To model the enzyme environment, we used a combination of classical molecular dynamics and multiscale quantum-mechanical (QM)/molecular-mechanical (MM) simulations. We leverage charge shift analysis to systematically construct QM regions and analyze the electronic environment of the active site by evaluating the degree of charge transfer between the core active site and the protein environment. The contribution of the terminal chalcogen ligand to the ESP of the metal center is substantial and dependent on the chalcogen identity, with similar, less negative ESPs for Se and S terminal chalcogens in comparison to O regardless of whether the metal is Mo or W. The orientation of the side chains and conformations of the cofactor also affect the ESP, highlighting the importance of sampling dynamic fluctuations in the protein. Overall, our observations suggest that the terminal chalcogen ligand identity plays an important role in the enzymatic activity of FDH, suggesting opportunities for a rational bioinspired catalyst design.

Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms

We employed QM/MM molecular dynamics (MD) simulations to characterize the rate-limiting step of the glycosylation reaction of pancreatic α-amylase with combined DFT/molecular dynamics methods (PBE/def2-SVP:AMBER). Upon careful choice of four starting active site conformations based on thorough reactivity criteria, Gibbs energy profiles were calculated with umbrella sampling simulations within a statistical convergence of 1-2 kcal⋅mol -1 . Nevertheless, Gibbs activation barriers and reaction energies still varied from 11.0 to 16.8 kcal⋅mol -1 and -6.3 to +3.8 kcal⋅mol -1 depending on the starting conformations, showing that despite significant state-of-the-art QM/MM MD sampling (0.5 ns/profile) the result still depends on the starting structure. The results supported the one step dissociative mechanism of Asp197 glycosylation preceded by an acid-base reaction by the Glu233, which are qualitatively similar to those from multi-PES QM/MM studies, and thus support the use of the latter to determine enzyme reaction mechanisms.

Quantum biology. π-π entanglement signatures in Protein-DNA interactions

DNA biological functions are carried out by individual proteins that interact with specific sequences along DNA to prime molecular processes required by cellular metabolism. Protein-DNA interactions include DNA replication, gene expression and its regulation, DNA repair, DNA restriction and modification by endonucleases, generally classified as enzymatic functions, or transcription factors functions. To find specific binding target sequences and finalize their activities, proteins must operate in symbiosis with cellular crowded environment identifying extremely small cognate sequences along the DNA chain, ranging from 15-20 bps for repressors to 4-6 bps for restriction enzymes in less than one second.

Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition

To analyze the impact of various technical details on the results of quantum mechanical (QM)/molecular mechanical (MM) enzyme simulations, including the QM region size, catechol-O-methyltransferase (COMT) is studied as a model system using an approximate QM/MM method (DFTB3/CHARMM). The results show that key equilibrium and kinetic properties for methyl transfer in COMT exhibit limited variations with respect to the size of the QM region, which ranges from ∼100 to ∼500 atoms in this study. With extensive sampling, local and global structural characteristics of the enzyme are largely conserved across the studied QM regions, while the nature of the transition state (e.g., secondary kinetic isotope effect) and reaction exergonicity are largely maintained. Deviations in the free energy profile with different QM region sizes are similar in magnitude to those observed with changes in other simulation protocols, such as different initial enzyme conformations and boundary conditions. Electronic structural properties, such as the covariance matrix of residual charge fluctuations, appear to exhibit rather long-range correlations, especially when the peptide backbone is included in the QM region; this observation holds when a range-separated DFT approach is used as the QM region, suggesting that delocalization error is unlikely the origin. Overall, the analyses suggest that multiple simulation details determine the results of QM/MM enzyme simulations with comparable contributions.

The MOBH35 Metal–Organic Barrier Heights Reconsidered: Performance of Local-Orbital Coupled Cluster Approaches in Different Static Correlation Regimes

We have revisited the MOBH35 (Metal–Organic Barrier Heights, 35 reactions) benchmark [Iron, Janes, J. Phys. Chem. A, 2019, 123 ( (17), ), 3761−378130973722; ibid. 2019, 123, 6379–6380] for realistic organometallic catalytic reactions, using both canonical CCSD(T) and localized orbital approximations to it. For low levels of static correlation, all of DLPNO-CCSD(T), PNO-LCCSD(T), and LNO-CCSD(T) perform well; for moderately strong levels of static correlation, DLPNO-CCSD(T) and (T₁) may break down catastrophically, and PNO-LCCSD(T) is vulnerable as well. In contrast, LNO-CCSD(T) converges smoothly to the canonical CCSD(T) answer with increasingly tight convergence settings. The only two reactions for which our revised MOBH35 reference values differ substantially from the original ones are reaction 9 and to a lesser extent 8, both involving iron. For the purpose of evaluating density functional theory (DFT) methods for MOBH35, it would be best to remove reaction 9 entirely as its severe level of static correlation makes it just too demanding for a test. The magnitude of the difference between DLPNO-CCSD(T) and DLPNO-CCSD(T₁) is a reasonably good predictor for errors in DLPNO-CCSD(T₁) compared to canonical CCSD(T); otherwise, monitoring all of T₁, D₁, max|t_i^A|, and 1/(ε_LUMO – ε_HOMO) should provide adequate warning for potential problems. Our conclusions are not specific to the def2-SVP basis set but are largely conserved for the larger def2-TZVPP, as they are for the smaller def2-SV(P): the latter may be an economical choice for calibrating against canonical CCSD(T). Finally, diagnostics for static correlation are statistically clustered into groups corresponding to (1) importance of single excitations in the wavefunction; (2a) the small band gap, weakly separated from (2b) correlation entropy; and (3) thermochemical importance of correlation energy, as well as the slope of the DFT reaction energy with respect to the percentage of HF exchange. Finally, a variable reduction analysis reveals that much information on the multireference character is provided by T₁, I_ND/I_tot, and the exchange-based diagnostic A₁₀₀[TPSS].

Current and emerging tools of computational biology to improve the detoxification of mycotoxins

Biological organisms carry a rich potential for removing toxins from our environment, but identifying suitable candidates and improving them remain challenging. We explore the use of computational tools to discover strains and enzymes that detoxify harmful compounds. In particular, we will focus on mycotoxins-fungi-produced toxins that contaminate food and feed-and biological enzymes that are capable of rendering them less harmful. We discuss the use of established and novel computational tools to complement existing empirical data in three directions: discovering the prospect of detoxification among underexplored organisms, finding important cellular processes that contribute to detoxification, and improving the performance of detoxifying enzymes. We hope to create a synergistic conversation between researchers in computational biology and those in the bioremediation field. We showcase open bioremediation questions where computational researchers can contribute and highlight relevant existing and emerging computational tools that could benefit bioremediation researchers.

Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery

Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.

Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins

Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have reduced the cost of high-accuracy models. Tradeoffs between sampling and accuracy have motivated modeling with molecular mechanics (MM) in a multiscale QM/MM or iterative approach. Limitations to both conventional density-functional theory and classical MM force fields remain for describing noncovalent interactions in comparison to experiment or wavefunction theory. Because predictions of enzyme action (i.e. electrostatics), free energy barriers, and mechanisms are sensitive to the protocol and embedding method in QM/MM, convergence tests and systematic methods for quantifying QM-level interactions are a needed, active area of development.

Cheminformatic quantum mechanical enzyme model design: A catechol-O-methyltransferase case study

To accurately simulate the inner workings of an enzyme active site with quantum mechanics (QM), not only must the reactive species be included in the model but also important surrounding residues, solvent, or coenzymes involved in crafting the microenvironment. Our lab has been developing the Residue Interaction Network Residue Selector (RINRUS) toolkit to utilize interatomic contact network information for automated, rational residue selection and QM-cluster model generation. Starting from an x-ray crystal structure of catechol-O-methyltransferase, RINRUS was used to construct a series of QM-cluster models. The reactant, product, and transition state of the methyl transfer reaction were computed for a total of 550 models, and the resulting free energies of activation and reaction were used to evaluate model convergence. RINRUS-designed models with only 200-300 atoms are shown to converge. RINRUS will serve as a cornerstone for improved and automated cheminformatics-based enzyme model design.

Protein Dynamics and Substrate Protonation States Mediate the Catalytic Action of trans-4-Hydroxy-l-Proline Dehydratase

The enzyme trans-4-hydroxy-l-proline (Hyp) dehydratase (HypD) is among the most abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is considered a promising antibiotic target for the prominent antibiotic-resistant pathogen Clostridium difficile. Although an enzymatic mechanism has been proposed, the role of the greater HypD protein environment in mediating radical reactivity is not well understood. To fill this gap in understanding, we investigate HypD across multiple time- and length-scales using electronic structure modeling and classical molecular dynamics. We observe that the Hyp substrate protonation state significantly alters both its enzyme-free reactivity and its dynamics within the enzyme active site. Accurate coupled-cluster modeling suggests the deprotonated form of Hyp to be the most reactive protonation state for C5-H_pro-S activation. In the protein environment, hydrophobic interactions modulate the positioning of the Cys434 radical to enhance the reactivity of C5-H_pro-S abstraction. Long-time dynamics reveal that changing Hyp protonation states triggers the switching of a Leu643-gated water tunnel, a functional feature that has not yet been observed for members of the GRE superfamily.

Computational analysis of deleterious single nucleotide polymorphisms in catechol O-Methyltransferase conferring risk to post-traumatic stress disorder

Post-traumatic stress disorder (PTSD) is one of the prevalent neurological disorder which is drawing increased attention over the past few decades. Major risk factors for PTSD can be categorized into environmental and genetic factors. Among the genetic risk factors, polymorphisms in the catechol-O-methyltransferase (COMT) gene is known to be associated with the risk for PTSD. In the present study, we analysed the impact of deleterious single nucleotide polymorphisms (SNPs) in the COMT gene conferring risk to PTSD using computational based approaches followed by molecular dynamic simulations. The data on COMT gene associated with PTSD were collected from several databases including Online Mendelian Inheritance in Man (OMIM) search. Datasets related to SNP were downloaded from the dbSNP database. To study the structural and dynamic effects of COMT wild type and mutant forms, we performed molecular dynamics simulations (MD simulations) at a time scale of 300 ns. Results from screening the SNPs using the computational tools SIFT and Polyphen-2 demonstrated that the SNP rs4680 (V158M) in COMT has a deleterious effect with phenotype in PTSD. Results from the MD simulations showed that there is some major fluctuations in the structural features including root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuation (RMSF) and secondary structural elements including α-helices, sheets and turns between wild-type (WT) and mutant forms of COMT protein. In conclusion, our study provides novel insights into the deleterious effects and impact of V158M mutation on COMT protein structure which plays a key role in PTSD.

Combined MD and QM/MM Investigations of Hydride Reduction of 5α-Dihydrotestosterone Catalyzed by Human 3α-Hydroxysteroid Dehydrogenase Type 3: Importance of Noncovalent Interactions

3α-Hydroxysteroid dehydrogenase (3α-HSD) is an enzyme that is essential in the regulation of the concentration of 5α-dihydrotestosterone (5α-DHT) in the prostate. It catalyzes the hydride reduction of 5α-DHT to 3α-androstanediol, which activates androgen receptors. Elucidating details about the hydride reduction of 5α-DHT by 3α-HSD and the environment around the active site of the enzyme could lead to the development of effective drugs for the treatment of prostate cancer. In this study, the X-ray crystal structure of human 3α-HSD type 3 was comprehensively evaluated. Moreover, molecular dynamics (MD) simulations and hybrid ONIOM-type quantum mechanics/molecular mechanics (QM/MM) calculations were performed using a large QM region (maximum 232 atoms). It was determined that the reaction proceeded in a single step without the formation of an alkoxide ion owing to the direct hydride reduction of the substrate by nicotinamide adenine dinucleotide phosphate (NADPH) and concerted proton transfer by Tyr55 and Lys84. Noncovalent interaction (NCI) analysis highlighted the roles of Tyr216 and Trp227 in 3α-HSD. Specifically, Tyr216 assisted the reaction by π/π interactions with the neighboring nicotinamide ring of NADP(H), whereas Trp227 played an important role in recognition of the size of the substrate by CH/π interactions.

Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase

Desulfonation of isethionate by the bacterial glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslA) generates sulfite, a substrate for respiration that in turn produces the disease-associated metabolite hydrogen sulfide. Here, we present a 2.7 Å resolution X-ray structure of wild-type IslA from Bilophila wadsworthia with isethionate bound. In comparison with other GREs, alternate positioning of the active site β strands allows for distinct residue positions to contribute to substrate binding. These structural differences, combined with sequence variations, create a highly tailored active site for the binding of the negatively charged isethionate substrate. Through the kinetic analysis of 14 IslA variants and computational analyses, we probe the mechanism by which radical chemistry is used for C-S bond cleavage. This work further elucidates the structural basis of chemistry within the GRE superfamily and will inform structure-based inhibitor design of IsIA and thus of microbial hydrogen sulfide production.

When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins

Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computationally demanding electronic structure methods from correlated wavefunction theory for predictive accuracy. Numerous amino acid sidechains contain functional groups (e.g., hydroxyls in Ser/Thr or Tyr and amides in Asn/Gln) that can act as either HB acceptors or donors (HBA/HBD) and even form simultaneous, ambifunctional HB interactions. To understand the relative energetic benefit of each interaction, we characterize the potential energy surfaces of representative model systems with accurate coupled cluster theory calculations. To reveal the relationship of these energetics to the balance of these interactions in proteins, we curate a set of 4000 HBs, of which >500 are ambifunctional HBs, in high-resolution protein structures. We show that our model systems accurately predict the favored HB structural properties. Differences are apparent in HBA/HBD preference for aromatic Tyr versus aliphatic Ser/Thr hydroxyls because Tyr forms significantly stronger O–H⋯O HBs than N–H⋯O HBs in contrast to comparable strengths of the two for Ser/Thr. Despite this residue-specific distinction, all models of residue pairs indicate an energetic benefit for simultaneous HBA and HBD interactions in an ambifunctional HB. Although the stabilization is less than the additive maximum due both to geometric constraints and many-body electronic effects, a wide range of ambifunctional HB geometries are more favorable than any single HB interaction.

Correlated wavefunction theory predicts and high-resolution crystal structure analysis confirms the important, stabilizing effect of simultaneous hydrogen bond donor and acceptor interactions in proteins.

Hydrogen deuterium exchange defines catalytically linked regions of protein flexibility in the catechol O-methyltransferase reaction

Human catechol O-methyltransferase (COMT) has emerged as a model for understanding enzyme-catalyzed methyl transfer from S-adenosylmethionine (AdoMet) to small-molecule catecholate acceptors. Mutation of a single residue (tyrosine 68) behind the methyl-bearing sulfonium of AdoMet was previously shown to impair COMT activity by interfering with methyl donor-acceptor compaction within the activated ground state of the wild type enzyme [J. Zhang, H. J. Kulik, T. J. Martinez, J. P. Klinman, Proc. Natl. Acad. Sci. U.S.A. 112, 7954-7959 (2015)]. This predicts the involvement of spatially defined protein dynamical effects that further tune the donor/acceptor distance and geometry as well as the electrostatics of the reactants. Here, we present a hydrogen/deuterium exchange (HDX)-mass spectrometric study of wild type and mutant COMT, comparing temperature dependences of HDX against corresponding kinetic and cofactor binding parameters. The data show that the impaired Tyr68Ala mutant displays similar breaks in Arrhenius plots of both kinetic and HDX properties that are absent in the wild type enzyme. The spatial resolution of HDX below a break point of 15-20 °C indicates changes in flexibility across ∼40% of the protein structure that is confined primarily to the periphery of the AdoMet binding site. Above 20 °C, Tyr68Ala behaves more like WT in HDX, but its rate and enthalpic barrier remain significantly altered. The impairment of catalysis by Tyr68Ala can be understood in the context of a mutationally induced alteration in protein motions that becomes manifest along and perpendicular to the primary group transfer coordinate.

Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase

Quantum-mechanical/molecular-mechanical (QM/MM) methods are essential to the study of metalloproteins, but the relative importance of sampling and degree of QM treatment in achieving quantitative predictions is poorly understood. We study the relative magnitude of configurational and QM-region sensitivity of energetic and electronic properties in a representative Zn²⁺ metal binding site of a DNA methyltransferase. To quantify property variations, we analyze snapshots extracted from 250 ns of molecular dynamics simulation. To understand the degree of QM-region sensitivity, we perform analysis using QM regions ranging from a minimal 49-atom region consisting only of the Zn²⁺ metal and its four coordinating Cys residues up to a 628-atom QM region that includes residues within 12 Å of the metal center. Over the configurations sampled, we observe that illustrative properties (e.g., rigid Zn²⁺ removal energy) exhibit large fluctuations that are well captured with even minimal QM regions. Nevertheless, for both energetic and electronic properties, we observe a slow approach to asymptotic limits with similarly large changes in absolute values that converge only with larger (ca. 300-atom) QM region sizes. For the smaller QM regions, the electronic description of Zn²⁺ binding is incomplete: the metal binds too tightly and is too stabilized by the strong electrostatic potential of MM point charges, and the Zn-S bond covalency is overestimated. Overall, this work suggests that efficient sampling with QM/MM in small QM regions is an effective method to explore the influence of enzyme structure on target properties. At the same time, accurate descriptions of electronic and energetic properties require a larger QM region than the minimal metal-coordinating residues in order to converge treatment of both metal-local bonding and the overall electrostatic environment.

Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme

The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, trans-4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to (S)-Δ1-pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen Clostridioides difficile with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.

Using Atomic Confining Potentials for Geometry Optimization and Vibrational Frequency Calculations in Quantum-Chemical Models of Enzyme Active Sites

Quantum-chemical studies of enzymatic reaction mechanisms sometimes use truncated active-site models as simplified alternatives to mixed quantum mechanics molecular mechanics (QM/MM) procedures. Eliminating the MM degrees of freedom reduces the complexity of the sampling problem, but the trade-off is the need to introduce geometric constraints in order to prevent structural collapse of the model system during geometry optimizations that do not contain a full protein backbone. These constraints may impair the efficiency of the optimization, and care must be taken to avoid artifacts such as imaginary vibrational frequencies. We introduce a simple alternative in which terminal atoms of the model system are placed in soft harmonic confining potentials rather than being rigidly constrained. This modification is simple to implement and straightforward to use in vibrational frequency calculations, unlike iterative constraint-satisfaction algorithms, and allows the optimization to proceed without constraint even though the practical result is to fix the anchor atoms in space. The new approach is more efficient for optimizing minima and transition states, as compared to the use of fixed-atom constraints, and also more robust against unwanted imaginary frequencies. We illustrate the method by application to several enzymatic reaction pathways where entropy makes a significant contribution to the relevant reaction barriers. The use of confining potentials correctly describes reaction paths and facilitates calculation of both vibrational zero-point and finite-temperature entropic corrections to barrier heights.

Harnessing fluoroacetate dehalogenase for defluorination of fluorocarboxylic acids: in silico and in vitro approach

Widely distributed fluorocarboxylic acids have aroused worldwide environmental concerns due to its toxicity, persistence, and bioaccumulation. Enzyme-based eco-friendly biodegradation techniques have become increasingly important in treating fluorocarboxylic acids. Here we utilized in silico and in vitro approaches to investigate the defluorination mechanism of fluoroacetate dehalogenase (FAcD) toward monofluoropropionic acids at atomic-level. The experimentally determined k_cat and k_M for defluorination of 2-fluoropropionic acid are 330 ± 60 min^-1 and 6.12 ± 0.13 mM. The in silico results demonstrated positive/negative correlations between activation barriers and structural parameters (e.g. distance and angle) under different enzymatic conformations. We also screened computationally and tested in vitro (enzyme assay and kinetic study) the catalytic proficiency of FAcD toward polyfluoropropionic acids and perfluoropropionic acids which are known to be challenging for enzymatic degradation. The results revealed potential degradation activity of FAcD enzyme toward 2,3,3,3-tetrafluoropropionic acids. Our work will initiate the development of a new "integrated approach" for enzyme engineering to degrade environmentally persistent fluorocarboxylic acids.

Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases

Methyl transferases (MTases) are a well-studied class of enzymes for which competing enzymatic enhancement mechanisms have been suggested, ranging from structural methyl group CH···X hydrogen bonds (HBs) to electrostatic- and charge-transfer-driven stabilization of the transition state (TS). We identified all Class I MTases for which reasonable resolution (<2.0 Å) crystal structures could be used to form catalytically competent ternary complexes for multiscale (i.e., quantum-mechanical/molecular-mechanical or QM/MM) simulation of the S_N2 methyl transfer reaction coordinate. The four Class I MTases studied have both distinct functions (e.g., protein repair or biosynthesis) and substrate nucleophiles (i.e., C, N, or O). While CH···X HBs stabilize all reactant complexes, no universal TS stabilization role is found for these interactions in MTases. A consistent picture is instead obtained through analysis of charge transfer and electrostatics, wherein much of cofactor-substrate charge separation is maintained in the TS region, and electrostatic potential is correlated with substrate nucleophilicity (i.e., intrinsic reactivity).

Linear Response Functions of Densities and Spin Densities for Systematic Modeling of the QM/MM Approach for Mono- and Poly-Nuclear Transition Metal Systems

We applied our analysis, based on a linear response function of density and spin density, to two typical transition metal complex systems-the reaction centers of P450, and oxygen evolving center in Photosystem II, both of which contain open-shell transition metal ions. We discuss the relationship between LRF of electron density and spin density and the types of units and interactions of the systems. The computational results are discussed in relation to quantum mechanics (QM) cluster and quantum mechanics/molecular mechanics (QM/MM) modeling that are employed to compute the reaction centers of enzymes.