Electrostatic basis for enzyme catalysis

Exploring the Linear Energy Relationships between Activation Energy and Reaction Energy under an Electric Field

Electric-field (EF)-mediated chemistry has recently garnered increasing attention partly owing to its capability to catalyze a broad range of chemical reactions. How the EF affects the kinetics and thermodynamics of target reactions is a critical question. Herein, both density functional theory (DFT) and MP2 calculations suggest that the change of activation energy ΔΔE‡ and the change of reaction energy ΔΔErxn under an EF display a linear energy relationship (LER) ΔΔE‡ = mΔΔErxn. This has been tested against several reactions such as SN2 and proton transfer reactions, including neutral and charged systems and endothermic and exothermic processes. The linear coefficient m approximates to the ratio of the dipole moment change, i.e., Δμ‡/Δμrxn, of the studied reactions. The LER holds well at EF strengths up to ≈1 V/nm but deviates from the DFT-calculated results at larger EFs. Such deviations are mainly caused by the molecular geometry changes under an EF. Systems with larger polarizability experience greater geometry changes under an EF, thus leading to larger deviations. In addition, we propose that the reaction barrier can be predicted by -Δμ‡F - 0.5Δα‡F2, while it is well approximated by -Δμ‡F for small EF strengths. The proposed LER and the field-dependent barrier estimation promise broad applicability in EF-mediated chemical reactions.

Investigation of Electrostatic Effects on Enyzme Catalysis: Insights from Computational Simulations of Monoamine Oxidase A Pathological Variants Leading to the Brunner Syndrome

Brunner syndrome is a rare genetic disorder characterized by impulsive aggressiveness and intellectual disability, which is linked to impaired function of the monoamine oxidase A (MAO-A) enzyme. Patients with specific point mutations in the MAOA gene have been reported to exhibit these symptoms, along with notably elevated serotonin levels, which suggest a decreased catalytic performance of the mutated MAO-A enzymes. In this study, we present multiscale molecular simulations focusing on the rate-limiting step of MAO-A-catalyzed serotonin degradation for the C266F and V244I variants that are reportedly associated with pathologies characteristic of the Brunner syndrome. We found that the C266F mutation causes an approximately 18,000-fold slowdown of enzymatic function, which is equivalent to a MAOA gene knockout. For the V244I mutant, a somewhat smaller, yet still significant 300-fold slowdown has been estimated. Furthermore, we conducted a comprehensive comparison of the impact of enzyme electrostatics on the catalytic function of the wild-type (WT) MAO-A and both aforementioned mutants (C266F and V244I), as well as on the E446K mutant investigated in one of our earlier studies. The results have shown that the mutation induces a noteworthy change in electrostatic interactions between the reacting moiety and its enzymatic surroundings, leading to a decreased catalytic performance in all of the considered MAO-A variants. An analysis of mutation effects supported by geometry comparison of mutants and the wild-type enzyme at a residue level suggests that a principal driving force behind the altered catalytic performance of the mutants is subtle structural changes scattered along the entire enzyme. These shifts in geometry also affect domains most relevant to catalysis, where structural offsets of few tenths of an Å can significantly change contribution to the barrier of the involved residues. These results are in full agreement with the reasoning derived from clinical observations and biochemical data. Our research represents a step forward in the attempts of using fundamental principles of chemical physics in order to explain genetically driven pathologies. In addition, our results support the view that the catalytic function of enzymes is crucially driven by electrostatic interactions.

Structure-based profiling of putative therapeutics against monkeypox virus VP39 using pharmacophore modelling and molecular dynamics simulation studies

The growing global health threat of the monkeypox virus (MPXV) underscores the critical need for effective antiviral agents, since there are currently no therapeutics. The MPXV VP39, a methyltransferase, is essential for viral replication, hence a potential target for anti-MPXV drug candidates. Herein, a structure-based pharmacophore modelling and molecular docking approach was employed to screen natural compounds (NCs: 581,426) from the COCONUT database for potential inhibitors of MPXV VP39. After ranking of the docking scores, an ensemble-based docking of the top-ranked 20 NCs against multiple conformations obtained from ttcluster analysis of the molecular dynamics simulation trajectory of unbound MPXV VP39 further identified five leads with favourable interaction profiles, drug-likeness, ADMET properties, and synthetic features when compared to the reference standard (sinefungin). Further analysis of the thermodynamic stability of the resulting complexes of the leads over a 100-ns MD simulation period revealed varying degrees of thermodynamic stability while maintaining the structural integrity of MPXV VP39. Furthermore, the thermodynamic binding free energy calculation, while corroborating the docking analysis, identified CNP0297833 (-39.07 kcal/mol), CNP0371756 (-25.76 kcal/mol), and CNP0402319 (-19.26 kcal/mol) as the most promising candidates, with better modulatory effect against MPXV VP39 relative to sinefungin (-3.68 kcal/mol). These leads were stabilised with hydrophobic (Phe115, Val139, and Val116) and electrostatic (Glu46 and Asp138) interactions in different conformational clusters. In addition to the observed consistent interaction patterns, favourable binding energies, pharmacokinetics, ADMET, thermodynamic stability, and molecular orbital energies of these leads, the potential for optimisation for enhanced binding features for the active site of MPXV VP39 was elucidated. Further in vitro investigation to validate these findings is suggested to establish the putative leads as therapeutics targeting the replication phase of MPXV.

Methods for Theoretical Treatment of Local Fields in Proteins and Enzymes

Electric fields generated by protein scaffolds are crucial in enzymatic catalysis. This review surveys theoretical approaches for detecting, analyzing, and comparing electric fields, electrostatic potentials, and their effects on the charge density within enzyme active sites. Pioneering methods like the empirical valence bond approach rely on evaluating ionic and covalent resonance forms influenced by the field. Strategies employing polarizable force fields also facilitate field detection. The vibrational Stark effect connects computational simulations to experimental Stark spectroscopy, enabling direct comparisons. We highlight how protein dynamics induce fluctuations in local fields, influencing enzyme activity. Recent techniques assess electric fields throughout the active site volume rather than only at specific bonds, and machine learning helps relate these global fields to reactivity. Quantum theory of atoms in molecules captures the entire electron density landscape, providing a chemically intuitive perspective on field-driven catalysis. Overall, these methodologies show protein-generated fields are highly dynamic and heterogeneous, and understanding both aspects is critical for elucidating enzyme mechanisms. This holistic view empowers rational enzyme engineering by tuning electric fields, promising new avenues in drug design, biocatalysis, and industrial applications. Future directions include incorporating electric fields as explicit design targets to enhance catalytic performance and biochemical functionalities.

Integrating Ferroelectric Fields with Active Sites for the Construction of Highly Efficient Nanozymes

Enhancing nanozymes' catalytic activity is challenging yet crucial for practical applications. Herein, inspired by the electrostatic preorganization effect in the catalytic process of natural protein enzymes, a nanozyme is constructed by decorating ferroelectric BaTiO3 nanoparticles (BTO) with hemin, which is often regarded as the active site of natural horseradish peroxidase (HRP). The Hemin-BTO nanozyme demonstrates excellent peroxidase-like (POD-like) activity with the catalytic constant (Kcat) up to 9.71 × 105 s-1 and 1.41 × 106 s-1 for TMB and H2O2 substrates, which is ca. 240-fold and 400-fold greater than that of HRP. Theoretical studies utilizing Density Functional Theory calculations revealed the underlying mechanism. The spontaneous polarization electric field of BTO adjusts the internal electrostatic field of the active site hemin, thereby enhancing the affinity between the Hemin-BTO nanozyme and the substrate. Simultaneously, the existence of hemin reduced the recombination of BTO charge carriers, accelerated electron transfer, and thus promoted the generation of reactive oxygen species, effectively enhancing its POD-like activity. In addition, Hemin-BTO has been successfully used to establish an immunoassay of human brain natriuretic peptide. This work presented a feasible strategy to construct nanozymes with highly catalytic activity by integrating the ferroelectric fields with the active site of natural enzymes.

Application of Amber Suppression To Study the Role of Tyr M210 in Electron Transfer in Rhodobacter sphaeroides Photosynthetic Reaction Centers

The initial light-induced electron transfer (ET) steps in the bacterial photosynthetic reaction center (RC) have been extensively studied and provide a paradigm for connecting structure and function. Although RCs have local pseudo-C2 symmetry, ET only occurs along the A branch of chromophores. Tyrosine M210 is a key symmetry-breaking residue adjacent to bacteriochlorophyll BA that bridges the primary electron donor P and the bacteriopheophytin acceptor HA. We used amber suppression to incorporate phenylalanine variants with different electron-withdrawing/-donating capabilities at the position M210. X-ray data generally reveal no appreciable structural changes due to the mutations. P* decay and P+HA- formation are multiexponential (∼2 to 9, ∼10 to 60, and ∼100 to 300 ps) and temperature dependent. The 1020 nm transient-absorption band of P+BA- is barely resolved for a few variants at 295 K and for none at 77 K. The results indicate a change from two-step ET for wild-type RCs to the dominance of one-step superexchange ET for the mutants. Resonance Stark spectroscopy reveals that the free energy of P+BA- changes by -57 to +66 meV among the phenylalanine variants. Because P+BA- apparently lies above P* in all phenylalanine variants, the perturbations primarily affect the energy denominator for superexchange mixing. The findings deepen insight into primary ET in the bacterial RC.

Robust enzyme discovery and engineering with deep learning using CataPro

Accurate prediction of enzyme kinetic parameters is crucial for enzyme exploration and modification. Existing models face the problem of either low accuracy or poor generalization ability due to overfitting. In this work, we first developed unbiased datasets to evaluate the actual performance of these methods and proposed a deep learning model, CataPro, based on pre-trained models and molecular fingerprints to predict turnover number (kcat), Michaelis constant (Km), and catalytic efficiency (kcat/Km). Compared with previous baseline models, CataPro demonstrates clearly enhanced accuracy and generalization ability on the unbiased datasets. In a representational enzyme mining project, by combining CataPro with traditional methods, we identified an enzyme (SsCSO) with 19.53 times increased activity compared to the initial enzyme (CSO2) and then successfully engineered it to improve its activity by 3.34 times. This reveals the high potential of CataPro as an effective tool for future enzyme discovery and modification.

Mechanisms of electrostatic interactions between two charged dielectric spheres inside a polarizable medium: an effective-dipole analysis

The mechanisms of electrostatic interactions between two charged dielectric spheres inside a polarizable medium have been investigated, in terms of hypothetical effective dipoles that depict how the positive and negative charge in each particle are separated. Our findings, which revealed that it is possible for polarization-induced opposite-charge repulsion to occur at short interparticle separations if the dielectric constant of the medium is greater than the dielectric constants of both spheres, provide insights into the physics of charge separation in each sphere and of polarization in the medium behind such counterintuitive behaviour.

Design, Synthesis, Biocompatibility, molecular docking and molecular dynamics studies of novel Benzo[b]thiophene-2-carbaldehyde derivatives targeting human IgM Fc Domains

In this study, three novel derivatives of benzo[b]thiophene-2-carbaldehyde (BTAP1, BTAP2, and BTAP3) were successfully synthesized and comprehensively characterized using spectroscopic techniques including FTIR, UV-VIS, 1HNMR, and 13CNMR. Thermal analysis through TGA and DTA demonstrated remarkable thermal stability with a maximum threshold at 270 °C. Spectroscopic investigations revealed π → π* transitions in all compounds, attributed to the conjugated system comprising benzothiophene rings connected to bromophenyl/ aminophenyl/phenol rings via α, β-unsaturated ketone bridges. Quantum chemical calculations indicated varying molecular stabilities, with BTAP3 exhibiting the highest energy gap (ΔE = 3.59 eV) and global hardness (η = 1.8), while BTAP2 showed enhanced reactivity potential with the lowest energy gap (ΔE = 3.22 eV) and highest global softness (S = 0.62). Virtual screening and molecular docking studies identified protein target 4JVW as the most favorable interaction partner, with binding energies of -8.0, -7.5, and -7.6 kcal/mol for BTAP1, BTAP2, and BTAP3, respectively. Molecular dynamics simulations revealed stable protein-ligand complexes, characterized by minimal RMSD and RMSF fluctuations, optimal Rg values, sustained hydrogen bonding networks and favorable solvent accessible surface area values. MMGBSA analysis highlighted the significance of Coulombic, van der Waals, and lipophilic interactions in complex stabilization. Toxicological evaluations demonstrated favorable safety profiles with minimal ocular and dermal irritation potential compared to allicin, coupled with low lethal dose values. These findings collectively position these novel compounds as promising candidates for pharmaceutical applications, warranting further investigation into their therapeutic potential.

Unusual depolymerization mechanism of Poly(ethylene terephthalate) by hydrolase 202

Polyethylene terephthalate (PET) waste significantly contributes to the global plastic crisis, but enzymatic conversion has become an efficient and environmentally friendly strategy to combat it. Therefore, this study explored the Re-face selective depolymerization mechanisms of a novel PET-degradation peptidase, hydrolase 202. Theoretical calculations revealed that the first step, a catalytic triad-assisted nucleophilic attack, is the rate-determining step. The corresponding Boltzmann-weighted average barrier was 21.6 kcal/mol. Furthermore, hydrolase 202 degraded Re-face PET more effectively than FAST-PETase, whereas other reported PET hydrolases (e.g., FAST-PETase) degraded Si-face PET more effectively. The hydrogen bond network significantly influenced the depolymerization efficiency. We also identified correlations between 24 important structural and charge features and energy barriers. Key charge, distance, and angle features were responsible for the superiority of the Re-face depolymerization. Finally, we identified residues that may affect the depolymerization efficiency of hydrolase 202, such as Glu215. These findings offer new insights into the potential engineering of PETases and may enhance enzymatic PET waste recycling.

Advanced molecular modeling of proteins: Methods, breakthroughs, and future prospects

The contemporary advancements in molecular modeling of proteins have significantly enhanced our comprehension of biological processes and the functional roles of proteins on a global scale. The application of advanced methodologies, including homology modeling, molecular dynamics simulations, and quantum mechanics/molecular mechanics strategies, has empowered numerous researchers to forecast the behavior of protein macromolecules, elucidate drug-protein interactions, and develop drugs with enhanced precision. This chapter elucidates the advent of deep learning algorithms such as AlphaFold, a notable advancement that has significantly improved the precision of intricate protein structure predictions. The recent advancements have significantly enhanced the precision of protein predictions and expedited drug discovery and development processes. Integrating approaches like multi-scale modeling and hybrid methods incorporating reliable experimental data is anticipated to revolutionize and offer more significant implications for precision medicine and targeted treatments.

CHARMM-GUI EnzyDocker for Protein-Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes

Enzymes play crucial roles in all biological systems by catalyzing a myriad of chemical reactions. These reactions range from simple one-step processes to intricate multistep cascades. Predicting mechanistically appropriate binding modes along a reaction pathway for substrate, product, and all reaction intermediates and transition states is a daunting task. To address this challenge, special docking programs like EnzyDock have been developed. Yet, running such docking simulations is complicated due to the nature of multistep enzyme processes. This work presents CHARMM-GUI EnzyDocker, a web-based cyberinfrastructure designed to streamline the preparation and running of EnzyDock docking simulations. The development of EnzyDocker has been achieved through integration of existing CHARMM-GUI modules, such as PDB Reader and Manipulator, Ligand Designer, and QM/MM Interfacer. In addition, new functionalities have been developed to facilitate a one-stop preparation of multistate and multiscale docking systems and enable interactive and intuitive ligand modifications and flexible protein residues selections. A simple setup related to multiligand docking is automatized through intuitive user interfaces. EnzyDocker offers support for standard classical docking and QM/MM docking with CHARMM built-in semiempirical engines. Automated consensus restraints for incorporating experimental knowledge into the docking are facilitated via a maximum common substructure algorithm. To illustrate the robustness of EnzyDocker, we conducted docking simulations of three enzyme systems: dihydrofolate reductase, SARS-CoV-2 Mpro, and the diterpene synthase CotB2. In addition, we have created four tutorial videos about these systems, which can be found at https://www.charmm-gui.org/demo/enzydock. EnzyDocker is expected to be a valuable and accessible web-based tool that simplifies and accelerates the setup process for multistate docking for enzymes.

Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages

The bespoke environments in enzyme active sites can selectively accelerate chemical reactions by as much as 1019. Macromolecular and supramolecular chemists have been inspired to understand and mimic these accelerations and selectivities for applications in catalysis for sustainable synthesis. Over the past 60+ years, mimicry strategies have evolved with changing interests, understanding, and synthetic advances but, ubiquitously, research has focused on use of a molecular "cavity". The activities of different cavities vary with the subset of features available to a particular cavity type. Unsurprisingly, without synthetic access to mimics able to encompass more/all of the functional features of enzyme active sites, examples of cavity-catalyzed processes demonstrating enzyme-like rate accelerations remain rare. This perspective will briefly highlight some of the key advances in traditional cavity catalysis, by cavity type, in order to contextualize the recent development of robust organic cage catalysts, which can exploit stability, functionality, and reduced symmetry to enable promising catalytic modes.

Proton Occupancies in Histidine Side Chains of Carbonic Anhydrase II by Neutron Crystallography and NMR - Differences, Similarities and Opportunities

Histidine is a key amino-acid residues in proteins that can exist in three different protonation states: two different neutral tautomeric forms and a protonated, positively charged one. It can act as both donor and acceptor of hydrogen bonds, coordinate metal ions, and engage in acid/base catalysis. Human Carbonic Anhydrase II (HCA II) is a pivotal enzyme catalyzing the reversible hydration of carbon dioxide. It contains 12 histidine residues: six are surface exposed, two buried, three are active site zinc ion ligands, and one is a proton shuttle. Comparing results from NMR spectroscopy with previously determined neutron protein crystal structures enabled a side-by-side investigation of the proton occupancies and preferred tautomeric states of the histidine residues in HCA II. Buried and zinc coordinating histidines remain in one neutral tautomeric state across the entire pH range studied, as validated by both methods. In contrast, solvent-exposed histidines display high variability in proton occupancies. While the data were overall remarkably consistent between methods, some discrepancies were observed, shedding light on the limitations of each technique. Therefore, combining these methods with full awareness of the advantages and drawbacks of each, provides insights into the dynamic protonation landscape of HCA II histidines, crucial for elucidating enzyme catalytic mechanisms.

Supramolecularly Built Local Electric Field Microenvironment around Cobalt Phthalocyanine in Covalent Organic Frameworks for Enhanced Photocatalysis

The local electric field (LEF) plays an important role in the catalytic process; however, the precise construction and manipulation of the electric field microenvironment around the active site remains a significant challenge. Here, we have developed a supramolecular strategy for the implementation of a LEF by introducing the host macrocycle 18-crown-6 (18C6) into a cobalt phthalocyanine (CoPc)-containing covalent organic framework (COF). Utilizing the supramolecular interaction between 18C6 and potassium ion (K+), a locally enhanced K+ concentration around CoPc can be built to generate a LEF microenvironment around the catalytically active Co site. The COF with this supramolecularly built LEF realizes an activity of up to 7.79 mmol mmolCo-1 h-1 in the photocatalytic CO2 reduction reaction (CO2RR), which is a 180% improvement compared to its counterpart without 18C6 units. The effect of LEF can be subtly controlled by fully harnessing the K+@18C6 interaction by changing the potassium salts with different counterions. In situ spectroscopy and density functional theory calculations show that the complexation of K+ by 18C6 creates a positive electric field that stabilizes the critical intermediate *COOH involved in CO2RR, which can be tuned by the halide ion-mediated K+@18C6 interaction and hydrogen-bonding interaction, consequently leading to improved catalytic performance to varying degrees.

Evolution Enhances Kemp Eliminase Activity by Optimizing Oxyanion Stabilization and Conformational Flexibility

The base-promoted Kemp elimination reaction has been used as a model system for enzyme design. Among the multiple computationally designed and evolved Kemp eliminases generated along the years, the HG3-to-HG3.17 evolutionary trajectory is particularly interesting due to the high catalytic efficiency of HG3.17 and the debated role of glutamine 50 (Gln50) as potential oxyanion stabilizer. This study aims to elucidate the structural and dynamic changes along the evolutionary pathway from HG3 to HG3.17 that contribute to improved catalytic efficiency. In particular, we evaluate key variants along the HG3 evolutionary trajectory via molecular dynamics simulations coupled to non-covalent interactions and water analysis. Our computational study indicates that HG3.17 can adopt a catalytically competent conformation promoted by a water-mediated network of non-covalent interactions, in which aspartate 127 (Asp127) is properly positioned for proton abstraction and Gln50 and to some extent mutation cysteine 84 (Cys84) contribute to oxyanion stabilization. We find that HG3.17 exhibits a rather high flexibility of Gln50, which is regulated by the conformation adopted by the active site residue tryptophan 44 (Trp44). This interplay between Gln50 and Trp44 positioning induced by distal active site mutations affects the water-mediated network of non-covalent interactions, Gln50 preorganization, and water content of the active site pocket.

Origins of the Superiority of Oscillating Electric Fields for Disrupting Senile Plaques: Insights from the 7-Residue Fragment and the Full-length Aβ-42 Peptide

Our recent molecular dynamics simulations of decomposing Alzheimer's disease plaques, under oscillating- and static external electric fields (Os-EEFs and St-EEFs), revealed the superiority of Os-EEF for decomposing plaques consisting of the 7-residue peptide segment. This conclusion is now reinforced by studying the dimers of the short peptides and trimers of the full-length Aβ-42 peptide. Thus, the dispersed peptides obtained following St-EEF applications reformed the plaques once the St-EEF subsided. In contrast, plaques originating from the application of Os-EEF remained dispersed for long time scales. The present study provides insights into these results by modeling the decomposition modes that transpire under both field types. Additionally, this study provides insights into the frequency effects on the decomposition processes within the THz-MHz regions. The simulation shows that the Os-EEF in the lower frequency range (≤GHz) decomposes the plaque on a time scale of ∼50 ns, whereas the higher frequency Os-EEFs (≥THz) are less effective. As such, Os-EEFs with moderate-to-low frequencies (≤GHz) lead to an "explosion," whereby the peptides fly distantly apart and inhibit plaque reformation. By contrast, St-EEFs form parallel peptide pairs, which are stabilized by the EEF due to the large dipole moment of the ensemble. Thus, St-EEF applications lead to sluggish and reversible plaque decomposition processes. We further conclude that the Os-EEF impact is maximal for short pulses, which prevents the EEF propensity to arrange the peptides in parallel pairs. The superiority of the Os-EEF over the St-EEF is maintained irrespective of the peptides' length. A model is formulated that predicts the dependence of the decomposition time scale on the EEF.

Reversible Isomerization of Stiff-Stilbene by an Oriented External Electric Field

Understanding and effectively controlling molecular conformational changes are essential for developing responsive and dynamic molecular systems. Here, we report that an oriented external electric field (OEEF) is an effective catalyst for the cis-trans isomerization of stiff-stilbene, a key component of overcrowded alkene-based rotary motors. This reversible isomerization occurs under ambient conditions, is free from side reactions, and has been verified using ultraperformance liquid chromatography and UV-vis absorption spectroscopy. Low electric field promotes cis-to-trans conversion, and high electric field enables the reverse trans-to-cis process, demonstrating the precise reaction control through electric field manipulation. Density functional theory calculations reveal the mechanism of the electric-field-catalyzed cis-trans carbon-carbon double bond isomerization. Our findings provide a novel perspective on constructing OEEF-catalyzed, reversible molecular systems and pave the way for fully electrically driven artificial molecular machines.

Biochemical and Computational Characterization of Haloalkane Dehalogenase Variants Designed by Generative AI: Accelerating the SN2 Step

Generative artificial intelligence (AI) models trained on natural protein sequences have been used to design functional enzymes. However, their ability to predict individual reaction steps in enzyme catalysis remains unclear, limiting the potential use of sequence information for enzyme engineering. In this study, we demonstrated that sequence information can predict the rate of the SN2 step of a haloalkane dehalogenase using a generative maximum-entropy (MaxEnt) model. We then designed lower-order protein variants of haloalkane dehalogenase using the model. Kinetic measurements confirmed the successful design of protein variants that enhance catalytic activity, above that of the wild type, in the overall reaction and in particular in the SN2 step. On the simulation side, we provided molecular insights into these designs for the SN2 step using the empirical valence bond (EVB) and metadynamics simulations. The EVB calculations showed activation barriers consistent with experimental reaction rates, while examining the effect of amino acid replacements on the electrostatic effect on the activation barrier and the consequence of water penetration, as well as the extent of ground state destabilization/stabilization. Metadynamics simulations emphasize the importance of the substrate positioning in enzyme catalysis. Overall, our AI-guided approach successfully enabled the design of a variant with a faster rate for the SN2 step than the wild-type enzyme, despite haloalkane dehalogenase being extensively optimized through natural evolution.

Electric-Field Catalysis on Carbon Nanotubes in Electromicrofluidic Reactors: Monoterpene Cyclizations

The control over the movement of electrons during chemical reactions with oriented external electric fields (OEEFs) has been predicted to offer a general approach to catalysis. Recently, we suggested that many problems to realize electric-field catalysis in practice under scalable bulk conditions could possibly be solved on multiwalled carbon nanotubes in electromicrofluidic reactors. Here, we selected monoterpene cyclizations to assess the scope of our system in organic synthesis. We report that electric-field catalysis can function by stabilizing both anionic and cationic transition states, depending on the orientation of the applied field. Moreover, electric-field catalysis can promote reactions which are barely accessible by general Brønsted and Lewis acids and field-free anion-π and cation-π interactions, and drive chemoselectivity toward intrinsically disfavored products without the need for pyrene interfacers attached to the substrate to prolong binding to the carbon nanotubes. Finally, interfacing with chiral organocatalysts is explored and evidence against contributions from redox chemistry is provided.

Tuning Bro̷nsted Acidity by up to 12 pKa Units in a Redox-Active Nanopore Lined with Multifunctional Metal Sites

Electrostatic interactions, hydrogen bonding, and solvation effects can alter the free energies of ionizable functional groups in proteins and other nanoporous architectures, allowing such structures to tune acid-base chemistry to support specific functions. Herein, we expand on this theme to examine how metal sites (M = H2, ZnII, CoII, CoI) affect the pKa of benzoic acid guests bound in discrete porphyrin nanoprisms (M3TriCage) in CD3CN. These host-guest systems were chosen to model how porous metalloporphyrin electrocatalysts might influence H+ transfer processes that are needed to support important electrochemical reactions (e.g., reductions of H+, O2, or CO2). Usefully, the cavities of the host-guest complexes become hydrated at low water concentrations (10-40 mM), providing a good representation of the active sites of porous electrocatalysts in water. Under these conditions, Lewis acidic CoII and ZnII ions increase the Bro̷nsted acidities of the guests by 4 and 8 pKa units, respectively, while reduction of the CoII sites to anionic CoI sites produces an electrostatic potential that lowers acidity by ca. 4 units (8 units relative to the CoII state). Lacking functional metal sites, H6TriCage increases the acidity of the guests by just 2.5 pKa units despite the 12+ charge of this host and contributions from other factors (hydrogen bonding, hydration) that might stabilize the deprotonated guests. Thus, the metal sites have dominant effects on acid-base chemistry in the M3TriCages, providing a larger pKa range (12.75 to ≥24.5) for an encapsulated acid than attained via other confinement effects in proteins and artificial porous materials.

Electrostatically Dominated Pre-Organization in Cyclodextrin Metal-Organic Frameworks

Electrostatic interactions between oppositely charged entities play a key role in pre-organizing substrates and stabilizing transition states of reactions in enzymes. The use of electrostatic interactions to pre-organize ions in nanoconfined pores, however, has not been investigated to its full potential. Herein, we describe how carboxylate anions can be pre-organized at the behest of their electrostatic interactions with K+ cations in nanoconfined tunnels present in γ-cyclodextrin metal-organic frameworks, i.e., CD-MOFs. Several carboxylate anions, which are all much smaller than the cavities of the tunnels, were visualized by X-ray crystallography when nanoconfined in CD-MOFs, despite the large voids present in the tunnels. These anions were found to be aligned within a planar array defined by four K+ cations, positioned around the periphery of the tunnels. The strong electrostatic interactions between the carboxylate anions and the K+ cations dictate the orientation of the anions and override the influence of all other possible noncovalent bonding interactions between them and the tunnels. Consequently, the aligned pairs of γ-cyclodextrin rings constituting the tunnels become distorted, resulting in them having lower symmetry and fewer disordered carboxylate anions in the solid state. Our findings offer a transformative strategy for controlling the packing and orientation of ions in nanoconfined environments.

Origins of Catalysis in Non-Heme Fe(II)/2-Oxoglutarate-Dependent Histone Lysine Demethylase KDM4A with Differently Methylated Histone H3 Peptides

Histone lysine demethylase 4 A (KDM4A), a non-heme Fe(II)/2-oxoglutarate (2OG) dependent oxygenase that catalyzes the demethylation of tri-methylated lysine residues at the 9, 27, and 36 positions of histone H3 (H3 K9me3, H3 K27me3, and H3 K36me3). These methylated residues show contrasting transcriptional roles; therefore, understanding KDM4A's catalytic mechanisms with these substrates is essential to explain the factors that control the different sequence-dependent demethylations. In this study, we use molecular dynamics (MD)-based combined quantum mechanics/molecular mechanics (QM/MM) methods to investigate determinants of KDM4A catalysis with H3 K9me3, H3 K27me3 and H3 K36me3 substrates. In KDM4A-H3(5-14)K9me3 and KDM4A-H3(23-32)K27me3 ferryl complexes, the O-H distance positively correlates with the activation barrier of the rate-limiting step, however in the KDM4A-H3(32-41)K36me3, no direct one-to-one relationship was found implying that the synergistic effects between the geometric parameters, second sphere interactions and the intrinsic electric field contribute for the effective catalysis for this substrate. The intrinsic electric field along the Fe-O bond changes between the three complexes and shows a positive correlation with the HAT activation barrier, suggesting that modulating electric field can be used for fine engineering KDM catalysis with a specific substrate. The results reveal how KDM4A uses a combination of strategies to enable near equally efficient demethylation of different H3Kme3 residues.

Utilization of Electric Fields to Modulate Molecular Activities on the Nanoscale: From Physical Properties to Chemical Reactions

As a primary energy source, electricity drives broad fields from everyday electronic circuits to industrial chemical catalysis. From a chemistry viewpoint, studying electric field effects on chemical reactivity is highly important for revealing the intrinsic mechanisms of molecular behaviors and mastering chemical reactions. Recently, manipulating the molecular activity using electric fields has emerged as a new research field. In addition, because integration of molecules into electronic devices has the natural complementary metal-oxide-semiconductor compatibility, electric field-driven molecular devices meet the requirements for both electronic device miniaturization and precise regulation of chemical reactions. This Review provides a timely and comprehensive overview of recent state-of-the-art advances, including theoretical models and prototype devices for electric field-based manipulation of molecular activities. First, we summarize the main approaches to providing electric fields for molecules. Then, we introduce several methods to measure their strengths in different systems quantitatively. Subsequently, we provide detailed discussions of electric field-regulated photophysics, electron transport, molecular movements, and chemical reactions. This review intends to provide a technical manual for precise molecular control in devices via electric fields. This could lead to development of new optoelectronic functions, more efficient logic processing units, more precise bond-selective control, new catalytic paradigms, and new chemical reactions.

Conformational ensembles reveal the origins of serine protease catalysis

Enzymes exist in ensembles of states that encode the energetics underlying their catalysis. Conformational ensembles built from 1231 structures of 17 serine proteases revealed atomic-level changes across their reaction states. By comparing the enzymatic and solution reaction, we identified molecular features that provide catalysis and quantified their energetic contributions to catalysis. Serine proteases precisely position their reactants in destabilized conformers, creating a downhill energetic gradient that selectively favors the motions required for reaction while limiting off-pathway conformational states. The same catalytic features have repeatedly evolved in proteases and additional enzymes across multiple distinct structural folds. Our ensemble-function analyses revealed previously unknown catalytic features, provided quantitative models based on simple physical and chemical principles, and identified motifs recurrent in nature that may inspire enzyme design.

Electrostatic interactions of enzymes in non-aqueous conditions: insights from molecular dynamics simulations

Electrostatic interactions of enzymes and their effects on enzyme activity and stability are poorly understood in non-aqueous conditions. Here, we investigate the contribution of the electrostatic interactions on the stability and activity of enzymes in the non-aqueous environment using molecular dynamics simulations. Lipase was selected as active and lysozyme as inactive model enzymes in non-aqueous media. Hexane was used as a common non-aqueous solvent model. In agreement with the previous experiments, simulations show that lysozyme has more structural instabilities than lipase in hexane. The number of hydrogen bonds and salt bridges of both enzymes is dramatically increased in hexane. In contrast to the other opinions, we show that the increase of the electrostatic interactions in non-aqueous media is not so favorable for enzymatic function and stability. In this condition, the newly formed hydrogen bonds and salt bridges can partially denature the local structure of the enzymes. For lysozyme, the changes in electrostatic interactions occur in all domains including the active site cleft, which leads to enzyme inactivation and destabilization. Interestingly, most of the changes in electrostatic interactions of lipase occur far from the active site regions. Therefore, the active site entrance regions remain functional in hexane. The results of this study reveal how the changes in electrostatic interactions can affect enzyme stability and activity in non-aqueous conditions. Moreover, we show for the first time how some enzymes, such as lipase, remain active in a non-aqueous environment.Communicated by Ramaswamy H. Sarma.

Electric Field-Induced Sequential Prototropic Tautomerism in Enzyme-like Nanopocket Created by Single Molecular Break Junction

Mastering the control of external stimuli-induced chemical transformations with detailed insights into the mechanistic pathway is the key for developing efficient synthetic strategies and designing functional molecular systems. Enzymes, the most potent biological catalysts, efficiently utilize their built-in electric field to catalyze and control complex chemical reactions within the active site. Herein, we have demonstrated the interfacial electric field-induced prototropic tautomerization reaction in acylhydrazone entities by creating an enzymatic-like nanopocket within the atomically sharp gold electrodes using a mechanically controlled break junction (MCBJ) technique. In addition to that, the molecular system used here contains two coupled acylhydrazone reaction centers, hence demonstrating a cooperative stepwise electric field-induced reaction realized at the single molecular level. Furthermore, the mechanistic studies revealed a proton relay-assisted tautomerization showing the importance of external factors such as solvent in such electric field-driven reactions. Finally, single-molecule charge transport and energetics calculations of different molecular species at various applied electric fields using a polarizable continuum solvent model confirm and support our experimental findings. Thus, this study demonstrates that mimicking an enzymatic pocket using a single molecular junction's interfacial electric field as a trigger for chemical reactions can open new avenues to the field of synthetic chemistry.

Organophosphate Hydrolysis by a Designed Metalloenzyme: Impact of Mutations Explained

The efficient design of novel enzymes has been attainable only by a combination of theoretical approaches and experimental refinement, suggesting inadequate performance of de novo design protocols. Based on the analysis of the evolutionary trajectory of a designed organophosphate hydrolase, this work aimed at developing and validating the improved theoretical models describing the catalytic activity of five enzyme variants (including wild-type as well as theoretically derived and experimentally refined enzymes) performing the hydrolysis of diethyl 7-hydroxycoumarinyl phosphate. The following aspects possibly important for enzyme design were addressed: the level of theory sufficient for a reliable description of enzyme-reactant interactions, the issue of ground state (GS) destabilization versus transition state (TS) stabilization, and the derivation of the proper side chain rotamers of amino acid residues. For enzyme variants analyzed herein, differential transition state stabilization (DTSS, i.e., preferential TS binding by an enzyme over the GS binding) calculated with a non-empirical model of the interaction energy (i.e., multipole electrostatic plus approximate dispersion terms, MED) displayed a superior performance in ranking the enzyme catalytic activity. The MED DTSS-based systematic rotamer refinement performed with an efficient scanning procedure and accounting for long-range interaction energy terms is an important step capable of unlocking the full potential impact of the given residue that could be otherwise overlooked with a conventional static approach featuring optimization to the nearby minimum. While TS stabilization is the main factor contributing to the increased catalytic activity of the de novo-designed variant studied in this work, directed evolution refinement appears to impact the catalytic activity of another enzyme variant analyzed herein via GS destabilization.

Unraveling proton-coupled electron transfer in cofactor-free oxidase- and oxygenase-catalyzed oxygen activation: a theoretical view

Oxygen plays a crucial role in the metabolic processes of non-anaerobic organisms. However, a detailed understanding of how triplet oxygen participates in the enzymatic oxidation of organic compounds involved in life processes is still lacking. It is noteworthy that recent studies have found that cofactor-free oxidase- and oxygenase-catalyzed oxygen activation occurs through proton-coupled electron transfer (PCET), which is significantly different from the previously proposed single electron transfer (SET) mechanism. Herein, we summarize the recent advances in the general mechanism of catalytic activation reactions of triplet oxygen by these enzymes. We believe that this review not only helps in providing a deep understanding of the processes involved in oxygen metabolism in organisms but also provides valuable theoretical reference data for designing more efficient enzyme mutants for treating diseases and handling environmental pollution in the future.

Toward the Electrostatic Catalysis of Nucleophilic Substitutions: A Surface Chemistry Study of the Menshutkin Reaction

The catalysis of nonredox reactions by external electric fields is one of the most rapidly expanding areas of chemistry. The Menshutkin reaction, a classic example of bimolecular nucleophilic substitution (SN2), involves the conversion of a tertiary amine to a quaternary ammonium salt by coupling it with an alkyl halide. The reaction barrier of the Menshutkin reaction is theoretically predicted to be highly sensitive to the magnitude and direction of an external electric field experienced by the transition state. In this study, we investigate how near-surface electric fields can drive this prototypical nucleophilic substitution by examining the coupling of a diffusive redox-tagged tertiary amine with an electrode-tethered alkyl bromide under a variable external bias. Our findings reveal a competition between electrostatically assisted reactions, solvent effects, and electrochemically triggered side reactions involving radical intermediates. We estimate that only about 5% of the coupling events are attributable to the external field, while the majority of the reaction products originate from electrochemically generated radical intermediates.

Understanding the Directed Evolution of a Natural-like Efficient Artificial Metalloenzyme

The artificial metalloenzyme containing iridium in place of iron along with four directed evolution mutations C317G, T213G, L69V, and V254L in a natural cytochrome P450 presents an important milestone in merging the extraordinary efficiency of biocatalysts with the versatility of small molecule chemical catalysts in catalyzing a new-to-nature carbene insertion reaction. This is a show-stopper enzyme, as it exhibits a catalytic efficiency similar to that of natural enzymes. Despite this remarkable discovery, there is no mechanistic and structural understanding as to why it displays extraordinary efficiency after the incorporation of the four active site mutations by directed evolution methods, which so far has been intractable to any experimental methods. In this study, we have deciphered how directed evolution mutations gradually alter the protein conformational ensemble to populate a catalytically active conformation to boost a multistep catalysis in a natural-like artificial metalloenzyme using large-scale molecular dynamics simulations, rigorous quantum chemical (QM), and multiscale quantum chemical/molecular mechanics (QM/MM) calculations. It reveals how evolution precisely positions the cofactor-substrate in an unusual but effective orientation within a reshaped active site in the catalytically active conformation stabilized by C-H···π interactions from more ordered mutated L69V and V254L residues to achieve preferential transition state stabilization compared to the ground state. This work essentially tracks down in atomistic detail the shift in the conformational ensemble of the highly active conformation from the less efficient single mutant to the most efficient quadruple mutant and offers valuable insights for designing better enzymes. The active conformation correctly reproduces the experimental barrier height and also accounts for the catalytic effect, which is in good agreement with experimental observations. Moreover, this conformation features an unusual bonding interaction in a metal-carbene species that preferentially stabilizes the rate-determining formation of an iridium porphyrin carbene intermediate to render the observed high catalytic rate acceleration. Our study provides crucial insights into the underlying rationale for directed evolution, reports the major catalytic role of nonelectrostatic interactions in enzyme catalysis different from the electrostatic model, and suggests a crucial principle toward designing enzymes with natural efficiency.

Electric Fields in Polymeric Systems

Polymer-based electronic devices are limited by slow transport and recombination of newly separated charges. Built-in electric fields, which arise from compositional gradients, are known to improve charge separation, directional charge transport, and to reduce recombination. Yet, the optimization of these fields through the rational design of polymeric materials is not prevalent. Indeed, polymers are disordered and generate nonuniform electric fields that are hard to measure, and therefore, hard to optimize. Here, we review work focusing on the intentional optimization of electric fields in polymeric systems with applications to catalysis, energy conversion, and storage. This includes chemical tuning of constituent monomers, linkers, morphology, etc. that result in stronger molecular dipoles, polarizability or crystallinity. We also review techniques to characterize electric fields in polymers and emerging processing strategies based on electric fields. These studies demonstrate the benefits of optimizing electric fields in polymers. However, rational design is often restricted to the molecular scale, deriving new pendants on, or linkers between, monomers. This does not always translate in strong electric fields at the polymer level, because they strongly depend on the monomer orientation. A better control of the morphology and monomer-to-polymer scaling relationship is therefore crucial to enhance electric fields in polymeric materials.

Computational Library Enables Pattern Recognition of Noncovalent Interactions and Application as a Modern Linear Free Energy Relationship

A quantitative and predictive understanding of how attractive noncovalent interactions (NCIs) influence functional outcomes is a long-standing goal in mechanistic chemistry. In that context, better comprehension of how substituent effects influence NCI strengths, and the origin of those effects, is still needed. We sought to build a resource capable of elucidating fundamental origins of substituent effects in NCIs and diagnosing NCIs in chemical systems. To accomplish this, a library of 893 NCI energies was calculated encompassing cation-π, anion-π, CH-π, and π-π interactions across 60 different arenes and heteroarenes. The interaction energies (IEs) were calculated using symmetry-adapted perturbation theory (SAPT), which identifies electrostatic, inductive, exchange-repulsive, and dispersive contributions to total IE. This descriptor library provides a comprehensive platform for evaluating substituent effect trends beyond traditional molecular descriptors such as Hammett values, frontier molecular orbital energies, and electrostatic potential, thereby expanding the tools available to analyze modern chemical processes that involve NCIs. To demonstrate the application of this library, three case studies in asymmetric catalysis and supramolecular chemistry are presented. These case studies informed the development of an automated NCI analysis tool, which employs statistical analyses to diagnose a particular NCI in a chemical system of interest.

Reactivity Inside Molecular Flasks: Acceleration Modes and Types of Selectivity Obtainable

There is increasing interest in the discovery and application of molecular flasks-supramolecular host structures capable of catalyzing organic reactions. Reminiscent of enzymes due to possessing a host cavity akin to an active site, molecular flasks can exhibit complex catalytic mechanisms and in many cases provide selectivity not achievable in bulk solvent. In this Review, we aim to organize the increasingly diverse examples through a two-part structure. In part one, we provide an overview of the different acceleration modes that operate within molecular flasks, while in part two we showcase, through selected examples, the different types of selectivity that are obtainable through the use of molecular flasks. Particular attention is given to examples that are relevant to current challenges in synthetic organic chemistry. We believe that this structure makes the field more approachable and thus will stimulate the development of novel applications of molecular flasks.

Catalytic mechanism, computational design, and crystal structure of a highly specific and efficient benzoylecgonine hydrolase

Enzyme therapy for cocaine detoxification should break down both cocaine and its primary toxic metabolite, benzoylecgonine (BZE), which is also the main form of cocaine contaminant in the environment. An ideal BZE-metabolizing enzyme (BZEase) is expected to be highly efficient and selective in BZE hydrolysis. Here, BZEase4 was engineered from bacterial cocaine esterase (CocE) by our reactant state-based enzyme design theories (RED), which has a 34,977-fold improved substrate discrimination between BZE and the neurotransmitter acetylcholine (ACh), compared with wild-type CocE. Under the physiological concentrations of BZE and ACh, the reaction velocity of BZEase4 against BZE is 2.25 × 106-fold higher than it against ACh, suggesting BZEase4 has extremely high substrate selectivity for BZE over ACh to minimize the potential cholinergic side-effects. This study provides additional evidence supporting the further development of BZEase4 toward a promising therapeutic for cocaine overdose, a potentially effective and eco-friendly enzymatic method for BZE degradation in the environment.

Hydrogen Bonding and Noncovalent Electric Field Effects in the Photoconversion of a Phytochrome

A profound understanding of protein structure and mechanism requires dedicated experimental and theoretical tools to elucidate electrostatic and hydrogen bonding interactions in proteins. In this work, we employed an approach to disentangle noncovalent and hydrogen-bonding electric field changes during the reaction cascade of a multidomain protein, i.e., the phytochrome Agp2. The approach exploits the spectroscopic properties of nitrile probes commonly used as reporter groups of the vibrational Stark effect. These probes were introduced into the protein through site-specific incorporation of noncanonical amino acids resulting in four variants with different positions and orientations of the nitrile groups. All substitutions left structures and the reaction mechanism unchanged. Structural models of the dark states (Pfr) were used to evaluate the total electric field at the nitrile label and its transition dipole moment. These quantities served as an internal standard to calculate the respective properties of the photoinduced products (Lumi-F, Meta-F, and Pr) based on the relative intensities of the nitrile stretching bands. In most cases, the spectral analysis revealed two substates with a nitrile in a hydrogen-bonded or hydrophobic environment. Using frequencies and intensities, we managed to extract the noncovalent contribution of the electric field from the individual substates. This analysis resulted in profiles of the noncovalent and hydrogen-bond-related electric fields during the photoinduced reaction cascade of Agp2. These profiles, which vary significantly among the four variants due to the different positions and orientations of the nitrile probes, were discussed in the context of the molecular events along the Pfr → Pr reaction cascade.

Long-Range Charge Transport in Molecular Wires

Long-range charge transport (LRCT) in molecular wires is crucial for the advancement of molecular electronics but remains insufficiently understood due to complex transport mechanisms and their dependencies on molecular structure. While short-range charge transport is typically dominated by off-resonant tunneling, which decays exponentially with molecular length, recent studies have highlighted certain molecular structures that facilitate LRCT with minimal attenuation over several nanometers. This Perspective reviews the latest progress in understanding LRCT, focusing on chemical designs and mechanisms that enable this phenomenon. Key strategies include π-conjugation, redox-active centers, and stabilization of radical intermediates, which support LRCT through mechanisms such as coherent resonant tunneling or incoherent hopping. We discuss how the effects of molecular structure, length, and temperature influence charge transport, and highlight emerging techniques like the Seebeck effect for distinguishing between transport mechanisms. By clarifying the principles behind LRCT and outlining future challenges, this work aims to guide the design of molecular systems capable of sustaining efficient long-distance charge transport, thereby paving the way for practical applications in molecular electronics and beyond.

Statistics of protein electrostatics

Molecular dynamics simulations of a small redox-active protein plastocyanin address two questions. (i) Do protein electrostatics equilibrate to the Gibbsian ensemble? (ii) Do the electrostatic potential and electric field inside proteins follow the Gaussian distribution? The statistics of electrostatic potential and electric field are probed by applying small charge and dipole perturbations to different sites within the protein. Nonergodic (non-Gibbsian) sampling is detectable through violations of exact statistical rules constraining the first and second statistical moments (fluctuation-dissipation relations) and the linear relation between free-energy surfaces of the collective coordinate representing the Hamiltonian electrostatic perturbation. We find weakly nonergodic statistics of the electrostatic potential (simulation time of 0.4-1.0 μs) and non-Gibbsian and non-Gaussian statistics of the electric field. A small dipolar perturbation of the protein results in structural instabilities of the protein-water interface and multi-modal distributions of the Hamiltonian energy gap. The variance of the electrostatic potential passes through a crossover at the glass transition temperature Ttr ≃ 170 K. The dipolar susceptibility, reflecting the variance of the electric field inside the protein, strongly increases, with lowering temperature, followed by a sharp drop at Ttr. The linear relation between free-energy surfaces can be directly tested by combining absorption and emission spectra of optical dyes. It was found that the statistics of the electrostatic potential perturbation are nearly Gibbsian/Gaussian, with little deviations from the prescribed statistical rules. On the contrary, the (nonergodic) statistics of dipolar perturbations are strongly non-Gibbsian/non-Gaussian due to structural instabilities of the protein hydration shell.

Unlocking the electrochemical functions of biomolecular condensates

Biomolecular condensation is a key mechanism for organizing cellular processes in a spatiotemporal manner. The phase-transition nature of this process defines a density transition of the whole solution system. However, the physicochemical features and the electrochemical functions brought about by condensate formation are largely unexplored. We here illustrate the fundamental principles of how the formation of condensates generates distinct electrochemical features in the dilute phase, the dense phase and the interfacial region. We discuss the principles by which these distinct chemical and electrochemical environments can modulate biomolecular functions through the effects brought about by water, ions and electric fields. We delineate the potential impacts on cellular behaviors due to the modulation of chemical and electrochemical environments through condensate formation. This Perspective is intended to serve as a general road map to conceptualize condensates as electrochemically active entities and to assess their functions from a physical chemistry aspect.

Molecular mechanism of thiocyanate dehydrogenase at atomic resolution

Some sulfur-oxidizing bacteria playing an important role in global geochemical cycles utilize thiocyanate as the sole source of energy and nitrogen. In these bacteria the process of thiocyanate into cyanate conversion is mediated by thiocyanate dehydrogenases - a recently discovered family of copper-containing enzymes with the three‑copper active site unique among the other copper proteins. To get a deeper insight into the structure and molecular mechanism of action of thiocyanate dehydrogenases we isolated, purified, and comprehensively characterized an enzyme from the bacterium Pelomicrobium methylotrophicum. High-resolution crystal structures of the thiocyanate dehydrogenase in the free state and in the complexes with the transition state analog, thiourea, and the closest substrate analog, selenocyanate, unveiled the fine details of molecular events occurring at the enzyme active site. During the reaction thiocyanate dehydrogenase undergoes profound conformational change that affects the position of the constituent copper ions and results in the activation of the attacking water molecule. The structure of the enzyme complex with the selenium atom bridged in-between two copper ions was obtained representing an important transient intermediate. Structures of the complexes with inhibitors supplemented with quantum chemical calculations clarify the role of copper ions and refine molecular mechanism of catalysis by thiocyanate dehydrogenase.

Electric fields imbue enzyme reactivity by aligning active site fragment orbitals

It is broadly recognized that intramolecular electric fields, produced by the protein scaffold and acting on the active site, facilitate enzymatic catalysis. This field effect can be described by several theoretical models, each of which is intuitive to varying degrees. In this contribution, we show that a fundamental effect of electric fields is to generate electrostatic potentials that facilitate the energetic alignment of reactant frontier orbitals. We apply this model to demystify the impact of electric fields on high-valent iron-oxo heme proteins: catalases, peroxidases, and peroxygenases/monooxygenases. Specifically, we show that this model easily accounts for the observed field-induced changes to the spin distribution within peroxidase active sites and explains the transition between epoxidation and hydroxylation pathways seen in Cytochrome P450 active site models. Thus, for the intuitive interpretation of the chemical effect of the field, the strategy involves analyzing the response of the orbitals of active site fragments, and their energetic alignment. We note that the energy difference between fragment orbitals involved in charge redistribution acts as a measure for the chemical hardness/softness of the reactive complex. This measure, and its sensitivity to electric fields, offers a single parameter model from which to quantitatively assess the effects of electric fields on reactivity and selectivity. Thus, the model provides an additional perspective to describe electrostatic preorganization and offers ways for its manipulation.

Chitosan-Based Charge-Controllable Supramolecular Carrier for Universal Immobilization of Enzymes with Different Isoelectric Points

Electrostatic adsorption is an enzyme immobilization method that effectively maintains enzyme activity and exhibits considerable binding efficiency. However, enzymes carry different charges at their respective reaction pH levels, which prevents the use of the same carrier to immobilize enzymes with different charges. In this study, we employed a template-mediated polysaccharide-enzyme coupling self-assembly strategy to develop a charge-controllable supramolecular immobilization carrier by regulating the charge properties of carboxymethyl chitosan, enabling the universal immobilization of enzymes with different charge levels across a range of reaction pH values. By using silica nanoparticles of certain sizes as templates, the size of the carrier can be precisely controlled and the hollow network structure formed after removing the template can effectively reduce mass transfer resistance. Trypsin and papain are used as model enzymes, and the experimental results show that the supramolecular self-assembly immobilization strategy does not disrupt the secondary structure of the enzyme molecules. After 2 h of reaction, the enzyme activities of immobilized papain and immobilized trypsin are 13.2% and 7.7% higher than those of the free enzymes, respectively. After 10 consecutive reactions, the enzyme activities of immobilized papain and immobilized trypsin retained 56.3% and 64.3% of their initial values, respectively.

Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits

The origin of the enzyme's powerful role in accelerating chemical reactions is one of the most critical and still widely discussed questions. It is already accepted that enzymes impose an electrostatic field onto their substrates by adopting complex three-dimensional structures; therefore, the preorganization of electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanisms and rate constant enhancement. In this work, we focus on three catalytically active β-subunits of 20S proteasomes with low sequence identity (∼30%) whose active sites, although situated in an electrostatically miscellaneous environment, catalyze the same chemical reaction with similar catalytic efficiency. Our in silico experiments reproduce the experimentally observed equivalent reactivity of the three sites and show that obliteration of the electrostatic potential in all active sites would deprive the enzymes of their catalytic power by slowing down the chemical process by a factor of 1035. To regain enzymatic efficiency, besides catalytic Thr1 and Lys33 residues, the presence of aspartic acid in position 17 and an aqueous solvent is required, proving that the electrostatic potential generated by the remaining residues is insignificant for catalysis. Moreover, it was found that the gradual decay of atomic charges on Asp17 strongly correlates with the enzyme's catalytic rate deterioration as well as with a change in the charge distributions due to introduced mutations. The computational procedure used and described here may help identify key residues for catalysis in other biomolecular systems and consequently may contribute to the process of designing enzyme-like synthetic catalysts.

Protein Medium Facilitates Electron Transfer in Photosynthetic Heliobacterial Reaction Center

This computational study addresses the question of how large membrane-bound proteins of electron transport chains facilitate fast vector-based charge transport. We study electron transfer reactions following ultrafast initial charge separation induced by absorption of light by P800 primary pair and leading to the electron localization at the A0 cofactor. Two subsequent, much slower reactions, electron transfer to the iron-sulfur cluster Fx and reduction of the menaquinone (MQ) cofactor, are studied by combining molecular dynamics simulations, electronic structure calculations, and theoretical modeling. The low value of the electronic coupling between A0 and Fx brings this reaction to the microsecond time scale even at the zero activation barrier. In contrast, A0-MQ electron transfer occurs on a subnanosecond time scale and might become the preferred route for charge transport. We elucidate mechanistic properties of the protein medium allowing fast, vectorial charge transfer. The electric field is high and inhomogeneous inside the protein and is coupled to high polarizabilities of cofactors to significantly lower the reaction barrier. The A0-MQ separation puts this reaction at the edge between the plateau characterizing the reaction dynamical control and exponential falloff due to electronic tunneling. A strong separation in relaxation times of the medium dynamics for the forward and backward reactions promotes vectorial charge transfer.

Noncanonical Amino Acids: Bringing New-to-Nature Functionalities to Biocatalysis

Biocatalysis has become an important component of modern organic chemistry, presenting an efficient and environmentally friendly approach to synthetic transformations. Advances in molecular biology, computational modeling, and protein engineering have unlocked the full potential of enzymes in various industrial applications. However, the inherent limitations of the natural building blocks have sparked a revolutionary shift. In vivo genetic incorporation of noncanonical amino acids exceeds the conventional 20 amino acids, opening new avenues for innovation. This review provides a comprehensive overview of applications of noncanonical amino acids in biocatalysis. We aim to examine the field from multiple perspectives, ranging from their impact on enzymatic reactions to the creation of novel active sites, and subsequent catalysis of new-to-nature reactions. Finally, we discuss the challenges, limitations, and promising opportunities within this dynamic research domain.

Catalysis in Extreme Field Environments: A Case Study of Strongly Ionized SiO2 Nanoparticle Surfaces

High electric fields can significantly alter catalytic environments and the resultant chemical processes. Such fields arise naturally in biological systems but can also be artificially induced through localized nanoscale excitations. Recently, strong field excitation of dielectric nanoparticles has emerged as an avenue for studying catalysis in highly ionized environments, producing extreme electric fields. While the dynamics of laser-driven surface ion emission has been extensively explored, understanding the molecular dynamics leading to fragmentation has remained elusive. Here, we employ a multiscale approach performing nonadiabatic quantum molecular dynamics (NAQMD) simulations on hydrogenated silica surfaces in both bare and wetted environments under field conditions mimicking those of an ionized nanoparticle. Our findings indicate that hole localization drives fragmentation dynamics, leading to surface silanol dissociation within 50 fs and charge transfer-induced water splitting in wetted environments within 150 fs. Further insight into such ultrafast mechanisms is critical for the advancement of catalysis on the surface of charged nanosystems.

Theoretical Insight into the Fluorescence Spectral Tuning Mechanism: A Case Study of Flavin-Dependent Bacterial Luciferase

Bioluminescence of bacteria is widely applied in biological imaging, environmental toxicant detection, and many other situations. Understanding the spectral tuning mechanism not only helps explain the diversity of colors observed in nature but also provides principles for bioengineering new color variants for practical applications. In this study, time-dependent density functional theory (TD-DFT) and quantum mechanics and molecular mechanics (QM/MM) calculations have been employed to understand the fluorescence spectral tuning mechanism of bacterial luciferase with a focus on the electrostatic effect. The spectrum can be tuned by both a homogeneous dielectric environment and oriented external electric fields (OEEFs). Increasing the solvent polarity leads to a redshift of the fluorescence emission maximum, λF, accompanied by a substantial increase in density. In contrast, applying an OEEF along the long axis of the isoalloxazine ring (X-axis) leads to a significant red- or blue-shift in λF, depending on the direction of the OEEF, yet with much smaller changes in intensity. The effect of polar solvents is directionless, and the red-shifts can be attributed to the larger dipole moment of the S1 state compared with that of the S0 state. However, the effect of OEEFs directly correlates with the difference dipole moment between the S1 and S0 states, which is directional and is determined by the charge redistribution upon deexcitation. Moreover, the electrostatic effect of bacterial luciferase is in line with the presence of an internal electric field (IEF) pointing in the negative X direction. Finally, the key residues that contribute to this IEF and strategies for modulating the spectrum through site-directed point mutations are discussed.

Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases

Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N-acyl L-homoserine lactones (AHLs). They play a role in a microbial communication system known as quorum sensing, which contributes to pathogenicity and biofilm formation. Designing quorum quenching (QQ) enzymes that can interfere with this communication allows them to be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific communication signals requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of GcL, which is a highly proficient and thermostable MLL with broad substrate specificity. We show that GcL not only accepts a broad range of substrates but also hydrolyzes these substrates through at least two different mechanisms. Further, the preferred mechanism appears to depend on both the substrate structure and/or the nature of the residues lining the active site. We demonstrate that other lactonases, such as AiiA and AaL, show similar mechanistic promiscuity, suggesting that this is a shared feature among MLLs. Mechanistic promiscuity has been seen previously in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and protein engineering perspective: in addition to optimizing for specific substrates, it may be possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes but also of other mechanistically promiscuous enzymes.

The Evolution of the Acylation Mechanism in β-Lactamase and Rapid Protein Dynamics

β-Lactamases are a class of well-studied enzymes that are known to have existed since billions of years ago, starting as a defense mechanism to stave off competitors and are now enzymes responsible for antibiotic resistance. Using ancestral sequence reconstruction, it is possible to study the crystal structure of a laboratory resurrected 2-3 billion year-old β-lactamase. Comparing the ancestral enzyme to its modern counterpart, a TEM-1 β-lactamase, the structural changes are minor, and it is probable that dynamic effects play an important role in the evolution of function. We used molecular dynamics simulations and employed transition path sampling methods to identify the presence of rate-enhancing dynamics at the femtosecond level in both systems, found that these fast motions are more efficiently coordinated in the modern enzyme, and examined how specific dynamics can pinpoint evolutionary effects that are essential for improving enzymatic catalysis.

Electrostatic ethanol fermentation: Experimental study and kinetic-based metabolic modeling

Due to the electrical nature of the cell, it is possible to modulate its behavior through the application of non-lethal external electric fields to improve fermentation processes. In this work, a microbial cell system with a chamber and two electrodes inside and connected to a voltage source was used. One of the electrodes was kept isolated to create an electric field without the flow of current. Cultures with two ethanol-producing microbial strains (Saccharomyces cerevisiae and Zymomonas mobilis) were conducted in this device. The application of voltages between 0 and 18 V was evaluated to determine the impact of the generated electric field on ethanol production. To analyze the possible effect of the field on the central carbon metabolism in each strain, biochemical-based kinetic models were formulated to describe the experimental fermentation kinetics obtained. It was found that low applied voltages did not have significant effects on growth rate in either strain, but all voltages evaluated increased substrate consumption and ethanol production rate in Z. mobilis, while only 18 V affected these rates in S. cerevisiae, indicating that Z. mobilis was the most sensitive to the electric field. At the end of the fermentation, significant increases in ethanol yields of 10.7% and 19.5% were detected for S. cerevisiae and Z. mobilis, respectively. The proposed mathematical models showed that substrate transport through the membrane catalyzed by the phosphotransferase system (PTS) for Z. mobilis and hexose transport proteins mechanism and hexokinase (HK) activity for S. cerevisiae and the transformation of pyruvate to ethanol, catalyzed by the decarboxylase (PDC) and alcohol dehydrogenase (ADH) enzymes, were the reactions most affected by the application of the external field.